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Wang Y, Wang T, Qi S, Zhao J, Kong J, Xue Z, Sun W, Zeng W. Genome-wide identification, expression profiling, and protein interaction analysis of the CCoAOMT gene family in the tea plant (Camellia sinensis). BMC Genomics 2024; 25:238. [PMID: 38438984 PMCID: PMC10913456 DOI: 10.1186/s12864-024-09972-y] [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: 09/15/2023] [Accepted: 01/04/2024] [Indexed: 03/06/2024] Open
Abstract
BACKGROUND The caffeoyl-CoA-O methyltransferase (CCoAOMT) family plays a crucial role in the oxidative methylation of phenolic substances and is involved in various plant processes, including growth, development, and stress response. However, there is a limited understanding of the interactions among CCoAOMT protein members in tea plants. RESULTS In this study, we identified 10 members of the CsCCoAOMT family in the genome of Camellia sinensis (cultivar 'HuangDan'), characterized by conserved gene structures and motifs. These CsCCoAOMT members were located on six different chromosomes (1, 2, 3, 4, 6, and 14). Based on phylogenetic analysis, CsCCoAOMT can be divided into two groups: I and II. Notably, the CsCCoAOMT members of group Ia are likely to be candidate genes involved in lignin biosynthesis. Moreover, through the yeast two-hybrid (Y2H) assay, we established protein interaction networks for the CsCCoAOMT family, revealing 9 pairs of members with interaction relationships. CONCLUSIONS We identified the CCoAOMT gene family in Camellia sinensis and conducted a comprehensive analysis of their classifications, phylogenetic and synteny relationships, gene structures, protein interactions, tissue-specific expression patterns, and responses to various stresses. Our findings shed light on the evolution and composition of CsCCoAOMT. Notably, the observed interaction among CCoAOMT proteins suggests the potential formation of the O-methyltransferase (OMT) complex during the methylation modification process, expanding our understanding of the functional roles of this gene family in diverse biological processes.
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Affiliation(s)
- Yiqing Wang
- College of Horticulture, Fujian Agriculture and Forestry University, 350002, Fuzhou, China
| | - Tao Wang
- College of Horticulture, Fujian Agriculture and Forestry University, 350002, Fuzhou, China
| | - Siyu Qi
- College of Horticulture, Fujian Agriculture and Forestry University, 350002, Fuzhou, China
| | - Jiamin Zhao
- College of Horticulture, Fujian Agriculture and Forestry University, 350002, Fuzhou, China
| | - Jiumei Kong
- College of Horticulture, Fujian Agriculture and Forestry University, 350002, Fuzhou, China
| | - Zhihui Xue
- Anxi College of Tea Science, Fujian Agriculture and Forestry University, 350028, Quanzhou, China
| | - Weijiang Sun
- College of Horticulture, Fujian Agriculture and Forestry University, 350002, Fuzhou, China.
| | - Wen Zeng
- College of Horticulture, Fujian Agriculture and Forestry University, 350002, Fuzhou, China.
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Lai Z, Wang J, Fu Y, Wang M, Ma H, Peng S, Chang F. Revealing the role of CCoAOMT1: fine-tuning bHLH transcription factors for optimal anther development. SCIENCE CHINA. LIFE SCIENCES 2024; 67:565-578. [PMID: 38097889 DOI: 10.1007/s11427-023-2461-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 10/12/2023] [Indexed: 03/05/2024]
Abstract
The tapetum, a crucial innermost layer encompassing male reproductive cells within the anther wall, plays a pivotal role in normal pollen development. The transcription factors (TFs) bHLH010/089/091 redundantly facilitate the rapid nuclear accumulation of DYSFUNCTIONAL TAPETUM 1, a gatekeeper TF in the tapetum. Nevertheless, the regulatory mechanisms governing the activity of bHLH010/089/091 remain unknown. In this study, we reveal that caffeoyl coenzyme A O-methyltransferase 1 (CCoAOMT1) is a negative regulator affecting the nuclear localization and function of bHLH010 and bHLH089, probably through their K259 site. Our findings underscore that CCoAOMT1 promotes the nuclear export and degradation of bHLH010 and bHLH089. Intriguingly, elevated CCoAOMT1 expression resulted in defective pollen development, mirroring the phenotype observed in bhlh010 bhlh089 mutants. Moreover, our investigation revealed that the K259A mutation in the bHLH089 protein disrupted its translocation from the nucleus to the cytosol and impeded its degradation induced by CCoAOMT1. Importantly, transgenic plants with the probHLH089::bHLH089K259A construct failed to rescue proper pollen development or gene expression in bhlh010 bhlh089 mutants. Collectively, these findings emphasize the need to maintain balanced TF homeostasis for male fertility. They firmly establish CCoAOMT1 as a pivotal regulator that is instrumental in achieving equilibrium between the induction of the tapetum transcriptional network and ensuring appropriate anther development.
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Affiliation(s)
- Zesen Lai
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and Institute of Biodiversity Sciences, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- School of Tropical Agriculture and Forestry, Agriculture-Rural Affairs and Rural Revitalization, Hainan University, Haikou, 570228, China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Jianzheng Wang
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and Institute of Biodiversity Sciences, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Ying Fu
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and Institute of Biodiversity Sciences, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Menghan Wang
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and Institute of Biodiversity Sciences, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Hong Ma
- Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802, USA
| | - Shiqing Peng
- School of Tropical Agriculture and Forestry, Agriculture-Rural Affairs and Rural Revitalization, Hainan University, Haikou, 570228, China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Fang Chang
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and Institute of Biodiversity Sciences, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China.
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Utomo JC, Barrell HB, Kumar R, Smith J, Brant MS, De la Hoz Siegler H, Ro DK. Reconstructing curcumin biosynthesis in yeast reveals the implication of caffeoyl-shikimate esterase in phenylpropanoid metabolic flux. Metab Eng 2024; 82:286-296. [PMID: 38387678 DOI: 10.1016/j.ymben.2024.02.011] [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: 10/04/2023] [Revised: 01/31/2024] [Accepted: 02/19/2024] [Indexed: 02/24/2024]
Abstract
Curcumin is a polyphenolic natural product from the roots of turmeric (Curcuma longa). It has been a popular coloring and flavoring agent in food industries with known health benefits. The conventional phenylpropanoid pathway is known to proceed from phenylalanine via p-coumaroyl-CoA intermediate. Although hydroxycinnamoyl-CoA: shikimate hydroxycinnamoyl transferase (HCT) plays a key catalysis in the biosynthesis of phenylpropanoid products at the downstream of p-coumaric acid, a recent discovery of caffeoyl-shikimate esterase (CSE) showed that an alternative pathway exists. Here, the biosynthetic efficiency of the conventional and the alternative pathway in producing feruloyl-CoA was examined using curcumin production in yeast. A novel modular multiplex genome-edit (MMG)-CRISPR platform was developed to facilitate rapid integrations of up to eight genes into the yeast genome in two steps. Using this MMG-CRISPR platform and metabolic engineering strategies, the alternative CSE phenylpropanoid pathway consistently showed higher titers (2-19 folds) of curcumin production than the conventional pathway in engineered yeast strains. In shake flask cultures using a synthetic minimal medium without phenylalanine, the curcumin production titer reached up to 1.5 mg/L, which is three orders of magnitude (∼4800-fold) improvement over non-engineered base strain. This is the first demonstration of de novo curcumin biosynthesis in yeast. Our work shows the critical role of CSE in improving the metabolic flux in yeast towards the phenylpropanoid biosynthetic pathway. In addition, we showcased the convenience and reliability of modular multiplex CRISPR/Cas9 genome editing in constructing complex synthetic pathways in yeast.
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Affiliation(s)
- Joseph Christian Utomo
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
| | - Hailey Brynn Barrell
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
| | - Rahul Kumar
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
| | - Jessica Smith
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
| | - Maximilian Simon Brant
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
| | - Hector De la Hoz Siegler
- Department of Chemical and Petroleum Engineering, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
| | - Dae-Kyun Ro
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada.
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McInnes KJ, van der Hooft JJJ, Sharma A, Herzyk P, Hundleby PAC, Schoonbeek HJ, Amtmann A, Ridout C, Jenkins GI. Overexpression of Brassica napus COMT1 in Arabidopsis heightens UV-B-mediated resistance to Plutella xylostella herbivory. Photochem Photobiol Sci 2023; 22:2341-2356. [PMID: 37505444 PMCID: PMC10509076 DOI: 10.1007/s43630-023-00455-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 07/04/2023] [Indexed: 07/29/2023]
Abstract
UV-B radiation regulates numerous morphogenic, biochemical and physiological responses in plants, and can stimulate some responses typically associated with other abiotic and biotic stimuli, including invertebrate herbivory. Removal of UV-B from the growing environment of various plant species has been found to increase their susceptibility to consumption by invertebrate pests, however, to date, little research has been conducted to investigate the effects of UV-B on crop susceptibility to field pests. Here, we report findings from a multi-omic and genetic-based study investigating the mechanisms of UV-B-stimulated resistance of the crop, Brassica napus (oilseed rape), to herbivory from an economically important lepidopteran specialist of the Brassicaceae, Plutella xylostella (diamondback moth). The UV-B photoreceptor, UV RESISTANCE LOCUS 8 (UVR8), was not found to mediate resistance to this pest. RNA-Seq and untargeted metabolomics identified components of the sinapate/lignin biosynthetic pathway that were similarly regulated by UV-B and herbivory. Arabidopsis mutants in genes encoding two enzymes in the sinapate/lignin biosynthetic pathway, CAFFEATE O-METHYLTRANSFERASE 1 (COMT1) and ELICITOR-ACTIVATED GENE 3-2 (ELI3-2), retained UV-B-mediated resistance to P. xylostella herbivory. However, the overexpression of B. napus COMT1 in Arabidopsis further reduced plant susceptibility to P. xylostella herbivory in a UV-B-dependent manner. These findings demonstrate that overexpression of a component of the sinapate/lignin biosynthetic pathway in a member of the Brassicaceae can enhance UV-B-stimulated resistance to herbivory from P. xylostella.
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Affiliation(s)
- Kirsty J McInnes
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
- School of Natural and Environmental Sciences, Newcastle University, King's Road, Newcastle, NE1 7RU, UK
| | - Justin J J van der Hooft
- Glasgow Polyomics, University of Glasgow, Garscube Campus, Glasgow, G61 1QH, UK
- Bioinformatics Group, Plant Sciences Group, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - Ashutosh Sharma
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
- School of Biological Sciences, University of Bristol, Bristol, BS8 1TQ, UK
| | - Pawel Herzyk
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
- Glasgow Polyomics, University of Glasgow, Garscube Campus, Glasgow, G61 1QH, UK
| | | | | | - Anna Amtmann
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | | | - Gareth I Jenkins
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK.
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Li H, Wang W, Liu R, Tong B, Dai X, Lu Y, Yu Y, Dai S, Ruan L. Long non-coding RNA-mediated competing endogenous RNA regulatory network during flower development and color formation in Melastoma candidum. FRONTIERS IN PLANT SCIENCE 2023; 14:1215044. [PMID: 37575929 PMCID: PMC10415103 DOI: 10.3389/fpls.2023.1215044] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 07/06/2023] [Indexed: 08/15/2023]
Abstract
M. candidum, an evergreen shrubby flower known for its superior adaptation ability in South China, has gained increased attention in garden applications. However, scant attention has been paid to its flower development and color formation process at the non-coding RNA level. To fill this gap, we conducted a comprehensive analysis based on long non-coding RNA sequencing (lncRNA-seq), RNA-seq, small RNA sequencing (sRNA-seq), and widely targeted metabolome detection of three different flower developmental stages of M. candidum. After differentially expressed lncRNAs (DElncRNAs), differentially expressed mRNAs (DEmRNAs), differentially expressed microRNAs (DEmiRNAs), and differentially synthesized metabolites (DSmets) analyses between the different flower developmental stages, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were conducted to identify some key genes and metabolites in flavonoid, flavone, anthocyanin, carotenoid, and alkaloid-related GO terms and biosynthetic pathways. Three direct-acting models, including antisense-acting, cis-acting, and trans-acting between lncRNAs and mRNAs, were detected to illustrate the direct function of lncRNAs on target genes during flower development and color formation. Based on the competitive endogenous RNA (ceRNA) regulatory theory, we constructed a lncRNA-mediated regulatory network composed of DElncRNAs, DEmiRNAs, DEmRNAs, and DSmets to elucidate the indirect role of lncRNAs in the flower development and color formation of M. candidum. By utilizing correlation analyses between DERNAs and DSmets within the ceRNA regulatory network, alongside verification trials of the ceRNA regulatory mechanism, the study successfully illustrated the significance of lncRNAs in flower development and color formation process. This research provides a foundation for improving and regulating flower color at the lncRNA level in M. candidum, and sheds light on the potential applications of non-coding RNA in studies of flower development.
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Affiliation(s)
- Hui Li
- Department of Botany, Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou, China
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Wei Wang
- Department of Botany, Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou, China
| | - Rui Liu
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
| | - Botong Tong
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Xinren Dai
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
| | - Yan Lu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Nanjing, Jiangsu, China
| | - Yixun Yu
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Seping Dai
- Department of Botany, Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou, China
| | - Lin Ruan
- Department of Botany, Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou, China
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Jia D, Jin C, Gong S, Wang X, Wu T. RNA-Seq and Iso-Seq Reveal the Important Role of COMT and CCoAOMT Genes in Accumulation of Scopoletin in Noni ( Morinda citrifolia). Genes (Basel) 2022; 13:1993. [PMID: 36360230 PMCID: PMC9689816 DOI: 10.3390/genes13111993] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 10/27/2022] [Indexed: 11/24/2023] Open
Abstract
Scopoletin, the main component of clinical drugs and the functional component of health products, is highly abundant in noni fruit (Morinda citrifolia). Multiple enzyme genes regulate scopoletin accumulation. In the present study, differentially expressed genes of noni were analyzed by RNA sequencing (RNA-Seq) and the full-length genes by isoform-sequencing (Iso-Seq) to find the critical genes in the scopoletin accumulation mechanism pathway. A total of 32,682 full-length nonchimeric reads (FLNC) were obtained, out of which 16,620 non-redundant transcripts were validated. Based on KEGG (Kyoto Encyclopedia of Genes and Genomes) annotation and differential expression analysis, two differentially expressed genes, caffeic acid 3-O-methyltransferase (COMT) and caffeoyl-CoA O-methyltransferase (CCoAOMT), were found in the scopoletin accumulation pathway of noni. Real-time quantitative polymerase chain reaction (q-PCR), phylogenetic tree analysis, gene expression analysis, and the change in scopoletin content confirmed that these two proteins are important in this pathway. Based on these results, the current study supposed that COMT and CCoAOMT play a significant role in the accumulation of scopoletin in noni fruit, and COMT (gene number: gene 7446, gene 8422, and gene 6794) and CCoAOMT (gene number: gene 12,084) were more significant. These results provide the importance of COMT and CCoAOMT and a basis for further understanding the accumulation mechanism of scopoletin in noni.
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Affiliation(s)
| | | | | | | | - Tian Wu
- Southwest Landscape Architecture Engineering Research Center of State Forestry Administration, Landscape Architecture and Horticulture Science School, Southwest Forestry University, Kunming 650000, China
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WGCNA Identifies a Comprehensive and Dynamic Gene Co-Expression Network That Associates with Smut Resistance in Sugarcane. Int J Mol Sci 2022; 23:ijms231810770. [PMID: 36142681 PMCID: PMC9506403 DOI: 10.3390/ijms231810770] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/02/2022] [Accepted: 09/13/2022] [Indexed: 11/29/2022] Open
Abstract
Sugarcane smut is a major fungal disease caused by Sporisorium scitamineum, which seriously reduces the yield and quality of sugarcane. In this study, 36 transcriptome data were collected from two sugarcane genotypes, YT93-159 (resistant) and ROC22 (susceptible) upon S. scitamineum infection. Data analysis revealed 20,273 (12,659 up-regulated and 7614 down-regulated) and 11,897 (7806 up-regulated and 4091 down-regulated) differentially expressed genes (DEGs) in YT93-159 and ROC22, respectively. A co-expression network was then constructed by weighted gene co-expression network analysis (WGCNA), which identified 5010 DEGs in 15 co-expressed gene modules. Four of the 15 modules, namely, Skyblue, Salmon, Darkorange, and Grey60, were significantly associated with smut resistance. The GO and KEGG enrichment analyses indicated that the DEGs involving in these four modules could be enriched in stress-related metabolic pathways, such as MAPK and hormone signal transduction, plant-pathogen interaction, amino acid metabolism, glutathione metabolism, and flavonoid, and phenylpropanoid biosynthesis. In total, 38 hub genes, including six from the Skyblue module, four from the Salmon module, 12 from the Darkorange module, and 16 from the Grey60 module, were screened as candidate hub genes by calculating gene connectivity in the corresponding network. Only 30 hub genes were amplifiable with RT-qPCR, of which 27 were up-regulated upon S. scitamineum infection. The results were consistent with the trend of gene expression in RNA-Seq, suggesting their positive roles in smut resistance. Interestingly, the expression levels of AOX, Cyb5, and LAC were higher in ROC22 than in YT93-159, indicating these three genes may act as negative regulators in response to S. scitamineum infection. This study revealed the transcriptome dynamics in sugarcane challenged by S. scitamineum infection and provided gene targets for smut resistance breeding in sugarcane.
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Khodavirdipour A, Safaralizadeh R, Haghi M, Hosseinpourfeizi MA. Comparative de novo transcriptome analysis of flower and root of Oliveria decumbens Vent. to identify putative genes in terpenes biosynthesis pathway. Front Genet 2022; 13:916183. [PMID: 35991569 PMCID: PMC9386285 DOI: 10.3389/fgene.2022.916183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 06/29/2022] [Indexed: 11/13/2022] Open
Abstract
The Oliveria decumbens Vent. is a wild, rare, annual medicinal plant and endemic plant of Iran that has metabolites (mostly terpenes) which make it a precious plant in Persian Traditional Medicine and also a potential chemotherapeutic agent. The lack of genetic resources has slowed the discovery of genes involved in the terpenes biosynthesis pathway. It is a wild relative of Daucus carota. In this research, we performed the transcriptomic differences between two samples, flower and root of Oliveria decumbens, and also analyze the expression value of the genes involved in terpenoid biosynthesis by RNA-seq and its essential oil’s phytochemicals analyzed by GC/MS. In total, 136,031,188 reads from two samples of flower and root have been produced. The result shows that the MEP pathway is mostly active in the flower and the MVA in the root. Three genes of GPP, FPPS, and GGPP that are the precursors in the synthesis of mono, di, and triterpenes are upregulated in root and 23 key genes were identified that are involved in the biosynthesis of terpenes. Three genes had the highest upregulation in the root including, and on the other hand, another three genes had the expression only in the flower. Meanwhile, 191 and 185 upregulated genes in the flower and root of the plant, respectively, were selected for the gene ontology analysis and reconstruction of co-expression networks. The current research is the first of its kind on Oliveria decumbens transcriptome and discussed 67 genes that have been deposited into the NCBI database. Collectively, the information obtained in this study unveils the new insights into characterizing the genetic blueprint of Oliveria decumbens Vent. which paved the way for medical/plant biotechnology and the pharmaceutical industry in the future.
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Yang G, Pan W, Zhang R, Pan Y, Guo Q, Song W, Zheng W, Nie X. Genome-wide identification and characterization of caffeoyl-coenzyme A O-methyltransferase genes related to the Fusarium head blight response in wheat. BMC Genomics 2021; 22:504. [PMID: 34218810 PMCID: PMC8254967 DOI: 10.1186/s12864-021-07849-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 06/21/2021] [Indexed: 02/01/2023] Open
Abstract
Background Lignin is one of the main components of the cell wall and is directly associated with plant development and defence mechanisms in plants, especially in response to Fusarium graminearum (Fg) infection. Caffeoyl-coenzyme A O-methyltransferase (CCoAOMT) is the main regulator determining the efficiency of lignin synthesis and composition. Although it has been characterized in many plants, to date, the importance of the CCoAOMT family in wheat is not well understood. Results Here, a total of 21 wheat CCoAOMT genes (TaCCoAOMT) were identified through an in silico genome search method and they were classified into four groups based on phylogenetic analysis, with the members of the same group sharing similar gene structures and conserved motif compositions. Furthermore, the expression patterns and co-expression network in which TaCCoAOMT is involved were comprehensively investigated using 48 RNA-seq samples from Fg infected and mock samples of 4 wheat genotypes. Combined with qRT-PCR validation of 11 Fg-responsive TaCCoAOMT genes, potential candidates involved in the FHB response and their regulation modules were preliminarily suggested. Additionally, we investigated the genetic diversity and main haplotypes of these CCoAOMT genes in bread wheat and its relative populations based on resequencing data. Conclusions This study identified and characterized the CCoAOMT family in wheat, which not only provided potential targets for further functional analysis, but also contributed to uncovering the mechanism of lignin biosynthesis and its role in FHB tolerance in wheat and beyond. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07849-y.
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Affiliation(s)
- Guang Yang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, 712100, Yangling, Shaanxi, China
| | - Wenqiu Pan
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, 712100, Yangling, Shaanxi, China
| | - Ruoyu Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, 712100, Yangling, Shaanxi, China
| | - Yan Pan
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, 712100, Yangling, Shaanxi, China
| | - Qifan Guo
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, 712100, Yangling, Shaanxi, China
| | - Weining Song
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, 712100, Yangling, Shaanxi, China.,ICARDA-NWSUAF Joint Research Centre, Northwest A&F University, 712100, Yangling, Shaanxi, China
| | - Weijun Zheng
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, 712100, Yangling, Shaanxi, China.
| | - Xiaojun Nie
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, 712100, Yangling, Shaanxi, China. .,ICARDA-NWSUAF Joint Research Centre, Northwest A&F University, 712100, Yangling, Shaanxi, China.
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Chun HJ, Lim LH, Cheong MS, Baek D, Park MS, Cho HM, Lee SH, Jin BJ, No DH, Cha YJ, Lee YB, Hong JC, Yun DJ, Kim MC. Arabidopsis CCoAOMT1 Plays a Role in Drought Stress Response via ROS- and ABA-Dependent Manners. PLANTS 2021; 10:plants10050831. [PMID: 33919418 PMCID: PMC8143326 DOI: 10.3390/plants10050831] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 04/19/2021] [Accepted: 04/20/2021] [Indexed: 12/31/2022]
Abstract
Plants possess adaptive reprogramed modules to prolonged environmental stresses, including adjustment of metabolism and gene expression for physiological and morphological adaptation. CCoAOMT1 encodes a caffeoyl CoA O-methyltransferase and is known to play an important role in adaptation of Arabidopsis plants to prolonged saline stress. In this study, we showed that the CCoAOMT1 gene plays a role in drought stress response. Transcript of CCoAOMT1 was induced by salt, dehydration (drought), and methyl viologen (MV), and loss of function mutants of CCoAOMT1, ccoaomt1-1, and ccoaomt1-2 exhibit hypersensitive phenotypes to drought and MV stresses. The ccoaomt1 mutants accumulated higher level of H2O2 in the leaves and expressed lower levels of drought-responsive genes including RD29B, RD20, RD29A, and ERD1, as well as ABA3 3 and NCED3 encoding ABA biosynthesis enzymes during drought stress compared to wild-type plants. A seed germination assay of ccoaomt1 mutants in the presence of ABA also revealed that CCoAOMT1 functions in ABA response. Our data suggests that CCoAOMT1 plays a positive role in response to drought stress response by regulating H2O2 accumulation and ABA signaling.
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Affiliation(s)
- Hyun Jin Chun
- Institute of Agriculture and Life Science, Gyeongsang National University, Jinju 52828, Korea; (H.J.C.); (M.S.C.); (Y.B.L.)
| | - Lack Hyeon Lim
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju 52828, Korea; (L.H.L.); (H.M.C.); (S.H.L.); (B.J.J.); (D.H.N.); (Y.J.C.)
| | - Mi Sun Cheong
- Institute of Agriculture and Life Science, Gyeongsang National University, Jinju 52828, Korea; (H.J.C.); (M.S.C.); (Y.B.L.)
| | - Dongwon Baek
- Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea; (D.B.); (M.S.P.); (J.C.H.)
| | - Mi Suk Park
- Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea; (D.B.); (M.S.P.); (J.C.H.)
| | - Hyun Min Cho
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju 52828, Korea; (L.H.L.); (H.M.C.); (S.H.L.); (B.J.J.); (D.H.N.); (Y.J.C.)
| | - Su Hyeon Lee
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju 52828, Korea; (L.H.L.); (H.M.C.); (S.H.L.); (B.J.J.); (D.H.N.); (Y.J.C.)
| | - Byung Jun Jin
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju 52828, Korea; (L.H.L.); (H.M.C.); (S.H.L.); (B.J.J.); (D.H.N.); (Y.J.C.)
| | - Dong Hyeon No
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju 52828, Korea; (L.H.L.); (H.M.C.); (S.H.L.); (B.J.J.); (D.H.N.); (Y.J.C.)
| | - Ye Jin Cha
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju 52828, Korea; (L.H.L.); (H.M.C.); (S.H.L.); (B.J.J.); (D.H.N.); (Y.J.C.)
| | - Yong Bok Lee
- Institute of Agriculture and Life Science, Gyeongsang National University, Jinju 52828, Korea; (H.J.C.); (M.S.C.); (Y.B.L.)
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju 52828, Korea; (L.H.L.); (H.M.C.); (S.H.L.); (B.J.J.); (D.H.N.); (Y.J.C.)
| | - Jong Chan Hong
- Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea; (D.B.); (M.S.P.); (J.C.H.)
| | - Dae-Jin Yun
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Korea;
| | - Min Chul Kim
- Institute of Agriculture and Life Science, Gyeongsang National University, Jinju 52828, Korea; (H.J.C.); (M.S.C.); (Y.B.L.)
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju 52828, Korea; (L.H.L.); (H.M.C.); (S.H.L.); (B.J.J.); (D.H.N.); (Y.J.C.)
- Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea; (D.B.); (M.S.P.); (J.C.H.)
- Correspondence: ; Tel.: +82-55-772-1874
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Madritsch S, Bomers S, Posekany A, Burg A, Birke R, Emerstorfer F, Turetschek R, Otte S, Eigner H, Sehr EM. Integrative transcriptomics reveals genotypic impact on sugar beet storability. PLANT MOLECULAR BIOLOGY 2020; 104:359-378. [PMID: 32754876 PMCID: PMC7593311 DOI: 10.1007/s11103-020-01041-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 07/25/2020] [Indexed: 06/11/2023]
Abstract
An integrative comparative transcriptomic approach on six sugar beet varieties showing different amount of sucrose loss during storage revealed genotype-specific main driver genes and pathways characterizing storability. Sugar beet is next to sugar cane one of the most important sugar crops accounting for about 15% of the sucrose produced worldwide. Since its processing is increasingly centralized, storage of beet roots over an extended time has become necessary. Sucrose loss during storage is a major concern for the sugar industry because the accumulation of invert sugar and byproducts severely affect sucrose manufacturing. This loss is mainly due to ongoing respiration, but changes in cell wall composition and pathogen infestation also contribute. While some varieties can cope better during storage, the underlying molecular mechanisms are currently undiscovered. We applied integrative transcriptomics on six varieties exhibiting different levels of sucrose loss during storage. Already prior to storage, well storable varieties were characterized by a higher number of parenchyma cells, a smaller cell area, and a thinner periderm. Supporting these findings, transcriptomics identified changes in genes involved in cell wall modifications. After 13 weeks of storage, over 900 differentially expressed genes were detected between well and badly storable varieties, mainly in the category of defense response but also in carbohydrate metabolism and the phenylpropanoid pathway. These findings were confirmed by gene co-expression network analysis where hub genes were identified as main drivers of invert sugar accumulation and sucrose loss. Our data provide insight into transcriptional changes in sugar beet roots during storage resulting in the characterization of key pathways and hub genes that might be further used as markers to improve pathogen resistance and storage properties.
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Affiliation(s)
- Silvia Madritsch
- AIT Austrian Institute of Technology, Center for Health & Bioresources, Tulln, Austria
- Center for Integrative Bioinformatics Vienna, Max Perutz Labs, University of Vienna, Medical University of Vienna, Vienna, Austria
| | - Svenja Bomers
- AIT Austrian Institute of Technology, Center for Health & Bioresources, Tulln, Austria
| | - Alexandra Posekany
- University of Technology Vienna, Research Unit of Computational Statistics, Vienna, Austria
| | - Agnes Burg
- AIT Austrian Institute of Technology, Center for Health & Bioresources, Tulln, Austria
| | - Rebekka Birke
- AGRANA Research & Innovation Center GmbH, Tulln, Austria
| | | | | | - Sandra Otte
- Strube Research GmbH & Co. KG, Söllingen, Germany
| | - Herbert Eigner
- AGRANA Research & Innovation Center GmbH, Tulln, Austria
| | - Eva M Sehr
- AIT Austrian Institute of Technology, Center for Health & Bioresources, Tulln, Austria.
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Sun X, Ma Y, Yang C, Li J. Rice OVATE family protein 6 regulates leaf angle by modulating secondary cell wall biosynthesis. PLANT MOLECULAR BIOLOGY 2020; 104:249-261. [PMID: 32715397 DOI: 10.1007/s11103-020-01039-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 07/20/2020] [Indexed: 06/11/2023]
Abstract
Secondary cell wall not only provides rigidity and mechanical resistance to plants, but also has a large impact on plant growth and adaptation to environments. Biosynthesis of secondary cell wall is regulated by a complicated signaling transduction network; however, it is still unclear how the transcriptional regulation of secondary cell wall biosynthesis works at the molecular level. Here, we report in rice that OVATE family proteins 6 (OsOFP6) is a positive regulator in modulating expression of the genes related to biosynthesis of the secondary cell wall. Transgenic plants with knock-down of OsOFP6 by RNA interference showed increased leaf angle, which resulted from the thinner secondary cell wall with reduced amounts of cellulose and lignin, whilst overexpression of OsOFP6 in rice led to the thinker secondary cell wall with increased lignin content. Protein-protein interaction analysis revealed that OsOFP6 interacts with Oryza sativa homeobox 15 (OSH15), a class I KNOX protein. The interaction of OsOFP6 and OSH15 enhanced the transcriptional activity of OSH15 which binds to the promoter of OsIRX9 (Oryza sativa IRREGULAR XYLEM 9). Taken together, our study provides insights into the function of OsOFP6 in regulating leaf angle and the control of biosynthesis of secondary cell wall.
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Affiliation(s)
- Xiaoxuan Sun
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, Botanical Garden, Chinese Academy of Sciences, Guangzhou, South China, 510650, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yamei Ma
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, Botanical Garden, Chinese Academy of Sciences, Guangzhou, South China, 510650, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chao Yang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, Botanical Garden, Chinese Academy of Sciences, Guangzhou, South China, 510650, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jianxiong Li
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, Botanical Garden, Chinese Academy of Sciences, Guangzhou, South China, 510650, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650, China.
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Zhang C, Yu D, Ke F, Zhu M, Xu J, Zhang M. Seedless mutant 'Wuzi Ougan' (Citrus suavissima Hort. ex Tanaka 'seedless') and the wild type were compared by iTRAQ-based quantitative proteomics and integratedly analyzed with transcriptome to improve understanding of male sterility. BMC Genet 2018; 19:106. [PMID: 30458706 PMCID: PMC6245639 DOI: 10.1186/s12863-018-0693-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 11/08/2018] [Indexed: 12/13/2022] Open
Abstract
Background Bud mutation is a vital method of citrus. ‘Wuzi Ougan’ (mutant type, MT) as a bud variant of ‘Ougan’ (wild type, WT) was first found in 1996 and has become popular because of its male sterility and seedless character. Previous analysis of its cytological sections and transcriptome revealed that the abnormal microsporogenesis that occurs before the tetrad stage of anther development might be the result of down-regulated oxidation-reduction biological processes in MT. To reveal the mechanism behind the male sterility in MT at the post-transcriptional stage, proteome profiling and integrative analysis on previously obtained transcriptome and proteome data were performed in two strains. Results The proteome profiling was performed by iTRAQ (isobaric Tags for relative and absolute quantitation) analysis and 6201 high-confidence proteins were identified, among which there were 487 differentially expressed proteins (DEPs) in one or more developmental stages of anthers between MT and WT. The main functional subcategories associated with the main category biological process into which the DEPs were classified were sporopollenin biosynthesis process and pollen exine formation. The enriched pathways were phenylpropanoid biosynthesis, flavonoid biosynthesis, and phenylalanine metabolism. Moreover, there were eight pathways linked in terms of being related to phenylpropanoid metabolism. Eighteen important genes related to phenylpropanoid metabolism were also analysized by qRT-PCR (quantitative real time PCR). An integrative analysis of the fold change at the transcript (log2 FPKM ratios) and protein (log1.2 iTRAQ ratios) levels was performed to reveal the consistency of gene expression at transcriptional and proteomic level. In general, the expression of genes and proteins tended to be positively correlated, in which the correlation coefficients were 0.3414 (all genes and all proteins) and 0.5686 (DEPs and according genes). Conclusion This study is the first to offer a comprehensive understanding of the gene regulation in ‘Wuzi Ougan’ and its wild type, especially during the microsporocyte to meiosis stage. Specifically, the involved genes include those in phenylpropanoid biosynthesis, flavonoid biosynthesis, and phenylalanine metabolism, as determined by integrative transcriptome and proteome analysis. Electronic supplementary material The online version of this article (10.1186/s12863-018-0693-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chi Zhang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, No.666, WuSu Street, Hangzhou, Zhejiang province, People's Republic of China, 311300.,The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, Zhejiang A & F University, Hangzhou, 311300, China
| | - Dihu Yu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, No.666, WuSu Street, Hangzhou, Zhejiang province, People's Republic of China, 311300
| | - Fuzhi Ke
- Zhejiang Citrus Research Institute, Huangyan, 318020, China
| | - Mimi Zhu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, No.666, WuSu Street, Hangzhou, Zhejiang province, People's Republic of China, 311300
| | - Jianguo Xu
- Zhejiang Citrus Research Institute, Huangyan, 318020, China
| | - Min Zhang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, No.666, WuSu Street, Hangzhou, Zhejiang province, People's Republic of China, 311300. .,The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, Zhejiang A & F University, Hangzhou, 311300, China.
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Increased experimental conditions and marker densities identified more genetic loci associated with southern and northern leaf blight resistance in maize. Sci Rep 2018; 8:6848. [PMID: 29717181 PMCID: PMC5931595 DOI: 10.1038/s41598-018-25304-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 04/19/2018] [Indexed: 01/01/2023] Open
Abstract
Southern leaf blight (SLB) and northern leaf blight (NLB) are the two major foliar diseases limiting maize production worldwide. Upon previous study with the nested association mapping (NAM) population, which consist of 5,000 recombinant inbred lines from 25 parents crossed with B73, we expanded the phenotyping environments from the United States (US) to China, and increased the marker densities from 1106 to 7386 SNPs for linkage mapping, and from 1.6 to 28.5 million markers for association mapping. We identified 49 SLB and 48 NLB resistance-related unique QTLs in linkage mapping, and multiple loci in association mapping with candidate genes involved in known plant disease-resistance pathways. Furthermore, an independent natural population with 282 diversified inbred lines were sequenced for four candidate genes selected based on their biological functions. Three of them demonstrated significant associations with disease resistance. These findings provided valuable resources for further implementations to develop varieties with superior resistance for NLB and SLB.
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Function Analysis of Caffeoyl-CoA O-Methyltransferase for Biosynthesis of Lignin and Phenolic Acid in Salvia miltiorrhiza. Appl Biochem Biotechnol 2016; 181:562-572. [PMID: 27613617 DOI: 10.1007/s12010-016-2231-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 08/29/2016] [Indexed: 10/21/2022]
Abstract
In this study, we cloned a full-length cDNA and the genomic DNA sequence of SmCCoAOMT (GenBank ID JQ007585) from Salvia miltiorrhiza. The 744-bp open-reading frame encodes a protein of 247 amino acids that shares 95 % similarity with one in Vitis vinifera. Real-time quantitative PCR analysis revealed that SmCCoAOMT is most highly expressed in the stems and can be induced by methyl jasmonate (MeJA) and XC-1 treatment. To evaluate its function in vivo, we generated RNA interference transgenic plants through Agrobacterium tumefaciens-mediated gene transfer. Compared with untransformed control plants, the transgenics had significantly less lignin and the expression of lignin-biosynthetic genes SmCCR and SmCOMT was depressed. In 90-day-old roots from plants of transgenic line M5, accumulations of rosmarinic acid and salvianolic acid B (Sal B) were greatly reduced by 0.89- and 0.69-fold, respectively. This low-Sal B phenotype was stable in the roots, with the level of accumulation being approximately 43.58 mg g-1 dry weight, which was 52 % of the amount measured in the untransformed control. Our results suggest that SmCCoAOMT is involved in lignin biosynthesis and affects the accumulation of phenolic acids. This study also provides potential guidance for using lignin-related genes to genetically engineer Salvia miltiorrhiza.
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He F, Karve AA, Maslov S, Babst BA. Large-Scale Public Transcriptomic Data Mining Reveals a Tight Connection between the Transport of Nitrogen and Other Transport Processes in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2016; 7:1207. [PMID: 27563305 PMCID: PMC4981021 DOI: 10.3389/fpls.2016.01207] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 07/29/2016] [Indexed: 05/29/2023]
Abstract
Movement of nitrogen to the plant tissues where it is needed for growth is an important contribution to nitrogen use efficiency. However, we have very limited knowledge about the mechanisms of nitrogen transport. Loading of nitrogen into the xylem and/or phloem by transporter proteins is likely important, but there are several families of genes that encode transporters of nitrogenous molecules (collectively referred to as N transporters here), each comprised of many gene members. In this study, we leveraged publicly available microarray data of Arabidopsis to investigate the gene networks of N transporters to elucidate their possible biological roles. First, we showed that tissue-specificity of nitrogen (N) transporters was well reflected among the public microarray data. Then, we built coexpression networks of N transporters, which showed relationships between N transporters and particular aspects of plant metabolism, such as phenylpropanoid biosynthesis and carbohydrate metabolism. Furthermore, genes associated with several biological pathways were found to be tightly coexpressed with N transporters in different tissues. Our coexpression networks provide information at the systems-level that will serve as a resource for future investigation of nitrogen transport systems in plants, including candidate gene clusters that may work together in related biological roles.
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Affiliation(s)
- Fei He
- Biological, Environmental and Climate Sciences Department, Brookhaven National LaboratoryUpton, NY, USA
| | - Abhijit A. Karve
- Biological, Environmental and Climate Sciences Department, Brookhaven National LaboratoryUpton, NY, USA
- Purdue Research FoundationWest Lafayette, IN, USA
| | - Sergei Maslov
- Biological, Environmental and Climate Sciences Department, Brookhaven National LaboratoryUpton, NY, USA
- Department of Bioengineering, Carl R. Woese Institute for Genomic Biology, National Center for Supercomputing Applications, University of Illinois at Urbana-ChampaignUrbana, IL, USA
| | - Benjamin A. Babst
- Biological, Environmental and Climate Sciences Department, Brookhaven National LaboratoryUpton, NY, USA
- Arkansas Forest Resources Center, The University of Arkansas at MonticelloMonticello, AR, USA
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17
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Meyer RS, Whitaker BD, Little DP, Wu SB, Kennelly EJ, Long CL, Litt A. Parallel reductions in phenolic constituents resulting from the domestication of eggplant. PHYTOCHEMISTRY 2015; 115:194-206. [PMID: 25813879 DOI: 10.1016/j.phytochem.2015.02.006] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 12/21/2014] [Accepted: 02/04/2015] [Indexed: 05/19/2023]
Abstract
Crop domestication is often accompanied by changes in metabolite compositions that alter traits such as flavor, color, or other beneficial properties. Fruits of eggplants (Solanum melongena L.) and related species are abundant and diverse in pharmacologically interesting phenolic compounds, particularly hydroxycinnamic acid (HCA) conjugates such as the antioxidant caffeoylquinic acids (CQA) and HCA-polyamine amides (HCAA). To understand metabolite variability through the lens of natural and artificial selection, HPLC-DAD was used to generate phenolic profiles for 32 compounds in fruits from 93 accessions representing 9 Solanum species. Profiles were used for identification of species-level and infraspecific chemical patterns across both genetic distance and landscape. Sampling of plant lines included the undomesticated progenitor of eggplant and Asian landraces with a genetic background associated with three Asian regions near proposed separate centers of domestication to test whether chemical changes were convergent despite different origins. Results showed ten compounds were unique to species, and ten other compounds varied significantly in abundance among species. Five CQAs and three HCA-polyamine conjugates were more abundant in wild (undomesticated) versus domesticated eggplant, indicating that artificial selection may have led to reduced phenolic levels. No chemical abundance patterns were associated with site-origin. However, one genetically distinct lineage of geographically-restricted SE Asian eggplants (S. melongena subsp. ovigerum) had a higher HCAA content and diversity than other lineages, which is suggested to be related to artificial selection for small, firm fruit. Overall, patterns show that fruit size, palatability and texture were preferentially selected over health-beneficial phytochemical content during domestication of several nightshade crops.
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Affiliation(s)
- Rachel S Meyer
- The New York Botanical Garden, 2900 Southern Blvd, Bronx, NY 10458, United States; The Graduate Center, The City University of New York, 365 Fifth Avenue, New York, NY 10016, United States; New York University, Center for Genomics and Systems Biology, 12 Waverly Place, New York, NY 10003, United States.
| | - Bruce D Whitaker
- Food Quality Laboratory, Building 002, Room 117, Beltsville Agricultural Research Center-West, Agricultural Research Service, USDA, 10300 Baltimore Avenue, Beltsville, MD 20705, United States
| | - Damon P Little
- The New York Botanical Garden, 2900 Southern Blvd, Bronx, NY 10458, United States
| | - Shi-Biao Wu
- Department of Biological Sciences, Lehman College, The City University of New York, 250 Bedford Park Boulevard West, Bronx, NY 10468, United States
| | - Edward J Kennelly
- The Graduate Center, The City University of New York, 365 Fifth Avenue, New York, NY 10016, United States; Department of Biological Sciences, Lehman College, The City University of New York, 250 Bedford Park Boulevard West, Bronx, NY 10468, United States
| | - Chun-Lin Long
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, PR China
| | - Amy Litt
- The New York Botanical Garden, 2900 Southern Blvd, Bronx, NY 10458, United States
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Brandt W, Manke K, Vogt T. A catalytic triad--Lys-Asn-Asp--Is essential for the catalysis of the methyl transfer in plant cation-dependent O-methyltransferases. PHYTOCHEMISTRY 2015; 113:130-139. [PMID: 25596806 DOI: 10.1016/j.phytochem.2014.12.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Revised: 12/10/2014] [Accepted: 12/16/2014] [Indexed: 06/04/2023]
Abstract
Crystal structure data of cation-dependent catechol O-methyltransferases (COMTs) from mammals and related caffeoyl coenzyme A OMTs (CCoAOMTs) from plants have suggested operative molecular mechanisms. These include bivalent cations that facilitate deprotonation of vicinal aromatic dihydroxy systems and illustrate a conserved arrangement of hydroxyl and carboxyl ligands consistent with the requirements of a metal-activated catalytic mechanism. The general concept of metal-dependent deprotonation via a complexed aspartate is only one part of a more pronounced proton relay, as shown by semiempirical and DFT quantum mechanical calculations and experimental validations. A previously undetected catalytic triad, consisting of Lys157-Asn181-Asp228 residues is required for complete methyl transfer in case of a cation-dependent phenylpropanoid and flavonoid OMT, as described in this report. This triad appears essential for efficient methyl transfer to catechol-like hydroxyl group in phenolics. The observation is consistent with a catalytic lysine in the case of mammalian COMTs, but jettisons existing assumptions on the initial abstraction of the meta-hydroxyl proton to the metal stabilizing Asp154 (PFOMT) or comparable Asp-carboxyl groups in type of cation-dependent enzymes in plants. The triad is conserved among all characterized plant CCoAOMT-like enzymes, which are required not only for methylation of soluble phenylpropanoids like coumarins or monolignol monomers, but is also present in the similar microbial and mammalian cation-dependent enzymes which methylate a comparable set of substrates.
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Affiliation(s)
- Wolfgang Brandt
- Leibniz Institute of Plant Biochemistry, Dept. Bioorganic Chemistry, Weinberg 3, D-06120 Halle(Saale), Germany.
| | - Kerstin Manke
- Leibniz Institute of Plant Biochemistry, Dept. Cell and Metabolic Biology, Weinberg 3, D-06120 Halle(Saale), Germany
| | - Thomas Vogt
- Leibniz Institute of Plant Biochemistry, Dept. Cell and Metabolic Biology, Weinberg 3, D-06120 Halle(Saale), Germany
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Yonekura-Sakakibara K, Nakabayashi R, Sugawara S, Tohge T, Ito T, Koyanagi M, Kitajima M, Takayama H, Saito K. A flavonoid 3-O-glucoside:2"-O-glucosyltransferase responsible for terminal modification of pollen-specific flavonols in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 79:769-82. [PMID: 24916675 PMCID: PMC4282749 DOI: 10.1111/tpj.12580] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Revised: 05/25/2014] [Accepted: 06/03/2014] [Indexed: 05/17/2023]
Abstract
Flavonol 3-O-diglucosides with a 1→2 inter-glycosidic linkage are representative pollen-specific flavonols that are widely distributed in plants, but their biosynthetic genes and physiological roles are not well understood. Flavonoid analysis of four Arabidopsis floral organs (pistils, stamens, petals and calyxes) and flowers of wild-type and male sterility 1 (ms1) mutants, which are defective in normal development of pollen and tapetum, showed that kaempferol/quercetin 3-O-β-d-glucopyranosyl-(1→2)-β-d-glucopyranosides accumulated in Arabidopsis pollen. Microarray data using wild-type and ms1 mutants, gene expression patterns in various organs, and phylogenetic analysis of UDP-glycosyltransferases (UGTs) suggest that UGT79B6 (At5g54010) is a key modification enzyme for determining pollen-specific flavonol structure. Kaempferol and quercetin 3-O-glucosyl-(1→2)-glucosides were absent from two independent ugt79b6 knockout mutants. Transgenic ugt79b6 mutant lines transformed with the genomic UGT79B6 gene had the same flavonoid profile as wild-type plants. Recombinant UGT79B6 protein converted kaempferol 3-O-glucoside to kaempferol 3-O-glucosyl-(1→2)-glucoside. UGT79B6 recognized 3-O-glucosylated/galactosylated anthocyanins/flavonols but not 3,5- or 3,7-diglycosylated flavonoids, and prefers UDP-glucose, indicating that UGT79B6 encodes flavonoid 3-O-glucoside:2″-O-glucosyltransferase. A UGT79B6-GUS fusion showed that UGT79B6 was localized in tapetum cells and microspores of developing anthers.
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Affiliation(s)
- Keiko Yonekura-Sakakibara
- RIKEN Center for Sustainable Resource Science1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Ryo Nakabayashi
- RIKEN Center for Sustainable Resource Science1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Satoko Sugawara
- RIKEN Center for Sustainable Resource Science1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Takayuki Tohge
- RIKEN Center for Sustainable Resource Science1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Takuya Ito
- RIKEN Center for Sustainable Resource Science2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Misuzu Koyanagi
- Graduate School of Pharmaceutical Sciences, Chiba University1-8-1 Inohana, Chuo-ku, Chiba, 260-8675, Japan
| | - Mariko Kitajima
- Graduate School of Pharmaceutical Sciences, Chiba University1-8-1 Inohana, Chuo-ku, Chiba, 260-8675, Japan
| | - Hiromitsu Takayama
- Graduate School of Pharmaceutical Sciences, Chiba University1-8-1 Inohana, Chuo-ku, Chiba, 260-8675, Japan
| | - Kazuki Saito
- RIKEN Center for Sustainable Resource Science1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
- Graduate School of Pharmaceutical Sciences, Chiba University1-8-1 Inohana, Chuo-ku, Chiba, 260-8675, Japan
- *For correspondence (e-mail )
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Gaquerel E, Gulati J, Baldwin IT. Revealing insect herbivory-induced phenolamide metabolism: from single genes to metabolic network plasticity analysis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 79:679-92. [PMID: 24617849 PMCID: PMC5140026 DOI: 10.1111/tpj.12503] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 02/20/2014] [Accepted: 03/03/2014] [Indexed: 05/18/2023]
Abstract
The phenylpropanoid metabolic space comprises a network of interconnected metabolic branches that contribute to the biosynthesis of a large array of compounds with functions in plant development and stress adaptation. During biotic challenges, such as insect attack, a major rewiring of gene networks associated with phenylpropanoid metabolism is observed. This rapid reconfiguration of gene expression allows prioritized production of metabolites that help the plant solve ecological problems. Phenolamides are a group of phenolic derivatives that originate from diversion of hydroxycinnamoyl acids from the main phenylpropanoid pathway after N-acyltransferase-dependent conjugation to polyamines or aryl monoamines. These structurally diverse metabolites are abundant in the reproductive organs of many plants, and have recently been shown to play roles as induced defenses in vegetative tissues. In the wild tobacco, Nicotiana attenuata, in which herbivory-induced regulation of these metabolites has been studied, rapid elevations of the levels of phenolamides that function as induced defenses result from a multi-hormonal signaling network that re-shapes connected metabolic pathways. In this review, we summarize recent findings in the regulation of phenolamides obtained by mass spectrometry-based metabolomics profiling, and outline a conceptual framework for gene discovery in this pathway. We also introduce a multifactorial approach that is useful in deciphering metabolic pathway reorganizations among tissues in response to stress.
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Affiliation(s)
- Emmanuel Gaquerel
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knoell-Str. 8, 07745 Jena, Germany
- Center for Organismal Studies, University of Heidelberg, Im Neuenheimer Feld 360,69120 Heidelberg, Germany
| | - Jyotasana Gulati
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knoell-Str. 8, 07745 Jena, Germany
| | - Ian T. Baldwin
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knoell-Str. 8, 07745 Jena, Germany
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Ahou A, Martignago D, Alabdallah O, Tavazza R, Stano P, Macone A, Pivato M, Masi A, Rambla JL, Vera-Sirera F, Angelini R, Federico R, Tavladoraki P. A plant spermine oxidase/dehydrogenase regulated by the proteasome and polyamines. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:1585-603. [PMID: 24550437 DOI: 10.1093/jxb/eru016] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Polyamine oxidases (PAOs) are flavin-dependent enzymes involved in polyamine catabolism. In Arabidopsis five PAO genes (AtPAO1-AtPAO5) have been identified which present some common characteristics, but also important differences in primary structure, substrate specificity, subcellular localization, and tissue-specific expression pattern, differences which may suggest distinct physiological roles. In the present work, AtPAO5, the only so far uncharacterized AtPAO which is specifically expressed in the vascular system, was partially purified from 35S::AtPAO5-6His Arabidopsis transgenic plants and biochemically characterized. Data presented here allow AtPAO5 to be classified as a spermine dehydrogenase. It is also shown that AtPAO5 oxidizes the polyamines spermine, thermospermine, and N(1)-acetylspermine, the latter being the best in vitro substrate of the recombinant enzyme. AtPAO5 also oxidizes these polyamines in vivo, as was evidenced by analysis of polyamine levels in the 35S::AtPAO5-6His Arabidopsis transgenic plants, as well as in a loss-of-function atpao5 mutant. Furthermore, subcellular localization studies indicate that AtPAO5 is a cytosolic protein undergoing proteasomal control. Positive regulation of AtPAO5 expression by polyamines at the transcriptional and post-transcriptional level is also shown. These data provide new insights into the catalytic properties of the PAO gene family and the complex regulatory network controlling polyamine metabolism.
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Affiliation(s)
- Abdellah Ahou
- Department of Science, University 'ROMA TRE', Rome, Italy
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Wils CR, Brandt W, Manke K, Vogt T. A single amino acid determines position specificity of anArabidopsis thalianaCCoAOMT-likeO-methyltransferase. FEBS Lett 2013; 587:683-9. [DOI: 10.1016/j.febslet.2013.01.040] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Revised: 01/21/2013] [Accepted: 01/22/2013] [Indexed: 11/25/2022]
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