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Wu ZZ, Gan ZW, Zhang YX, Chen SB, Gan CD, Yang K, Yang JY. Transcriptomic and metabolomic perspectives for the growth of alfalfa (Medicago sativa L.) seedlings with the effect of vanadium exposure. CHEMOSPHERE 2023:139222. [PMID: 37343642 DOI: 10.1016/j.chemosphere.2023.139222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 06/12/2023] [Accepted: 06/13/2023] [Indexed: 06/23/2023]
Abstract
Hitherto, the effect of vanadium on higher plant growth remains an open topic. Therefore, nontargeted metabolomic and RNA-Seq profiling were implemented to unravel the possible alteration in alfalfa seedlings subjected to 0.1 mg L-1 (B group) and 0.5 mg L-1 (C group) pentavalent vanadium [(V(V)] versus control (A group) in this study. Results revealed that vanadium exposure significantly altered some pivotal transcripts and metabolites. The number of differentially expressed genes (DEGs) markedly up- and down-regulated was 21 and 23 in B_vs_A, 27 and 33 in C_vs_A, and 24 and 43 in C_vs_B, respectively. The number for significantly up- and down-regulated differential metabolites was 17 and 15 in B_vs_A, 43 and 20 in C_vs_A, and 24 and 16 in C_vs_B, respectively. Metabolomics and transcriptomics co-analysis characterized three significantly enriched metabolic pathways in C_vs_A comparing group, viz., α-linolenic acid metabolism, flavonoid biosynthesis, and phenylpropanoid biosynthesis, from which some differentially expressed genes and differential metabolites participated. The metabolite of traumatic acid in α-linolenic acid metabolism and apigenin in flavonoid biosynthesis were markedly upregulated, while phenylalanine in phenylpropanoid biosynthesis was remarkably downregulated. The genes of allene oxide cyclase (AOC) and acetyl-CoA acyltransferase (fadA) in α-linolenic acid metabolism, and chalcone synthase (CHS), flavonoid 3'-monooxygenase (CYP75B1), and flavonol synthase (FLS) in flavonoid biosynthesis, and caffeoyl-CoA O-methyltransferase (CCoAOMT) in phenylpropanoid biosynthesis were significantly downregulated. While shikimate O-hydroxycinnamoyltransferase (HCT) in flavanoid and phenylpropanoid biosynthesis were conspicuously upregulated. Briefly, vanadium exposure induces a readjustment yielding in metabolite and the correlative synthetic precursors (transcripts/unigenes) in some branched metabolic pathways. This study provides a practical and in-depth perspective from transcriptomics and metabolomics in investigating the effects conferred by vanadium on plant growth and development.
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Affiliation(s)
- Zhen-Zhong Wu
- College of Architecture and Environment, Sichuan University, Chengdu, 610065, Sichuan, China; College of Earth and Environmental Sciences, Lanzhou University, Lanzhou, 730000, Gansu, China
| | - Zhi-Wei Gan
- College of Architecture and Environment, Sichuan University, Chengdu, 610065, Sichuan, China
| | - You-Xian Zhang
- College of Earth and Environmental Sciences, Lanzhou University, Lanzhou, 730000, Gansu, China
| | - Si-Bei Chen
- College of Architecture and Environment, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Chun-Dan Gan
- College of Architecture and Environment, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Kai Yang
- College of Architecture and Environment, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Jin-Yan Yang
- College of Architecture and Environment, Sichuan University, Chengdu, 610065, Sichuan, China.
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Li Y, Zhang T, Kang Y, Wang P, Yu W, Wang J, Li W, Jiang X, Zhou Y. Integrated metabolome, transcriptome analysis, and multi-flux full-length sequencing offer novel insights into the function of lignin biosynthesis as a Sesuvium portulacastrum response to salt stress. Int J Biol Macromol 2023; 237:124222. [PMID: 36990407 DOI: 10.1016/j.ijbiomac.2023.124222] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/21/2023] [Accepted: 03/24/2023] [Indexed: 03/30/2023]
Abstract
Sesuvium portulacastrum is a typical halophyte. However, few studies have investigated its salt-tolerant molecular mechanism. In this study, metabolome, transcriptome, and multi-flux full-length sequencing analysis were conducted to investigate the significantly different metabolites (SDMs) and differentially expressed genes (DEGs) of S. portulacastrum samples under salinity. The complete-length transcriptome of S. portulacastrum was developed, which contained 39,659 non-redundant unigenes. RNA-seq results showed that 52 DEGs involved in lignin biosynthesis may be responsible for S. portulacastrum salt tolerance. Furthermore, 130 SDMs were identified, and the salt response could be attributed to the p-coumaryl alcohol-rich in lignin biosynthesis. The co-expression network that was constructed after comparing the different salt treatment processes showed that the p-Coumaryl alcohol was linked to 30 DEGs. Herein, 8 structures genes, i.e., Sp4CL, SpCAD, SpCCR, SpCOMT, SpF5H, SpCYP73A, SpCCoAOMT, and SpC3'H were identified as significant factors in regulating lignin biosynthesis. Further investigation revealed that 64 putative transcription factors (TFs) may interact with the promoters of the above-mentioned genes. Together, the data revealed a potential regulatory network comprising important genes, putative TFs, and metabolites involved in the lignin biosynthesis of S. portulacastrum roots under salt stress, which could serve as a rich useful genetic resource for breeding excellent salt-tolerant plants.
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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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Li R, Luo C, Qiu J, Li Y, Zhang H, Tan H. Metabolomic and transcriptomic investigation of the mechanism involved in enantioselective toxicity of imazamox in Lemna minor. JOURNAL OF HAZARDOUS MATERIALS 2022; 425:127818. [PMID: 34875416 DOI: 10.1016/j.jhazmat.2021.127818] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 11/03/2021] [Accepted: 11/14/2021] [Indexed: 05/27/2023]
Abstract
Imazamox (IM) is a chiral pesticide that has been widely used in agriculture. Currently, few studies have investigated the toxicity mechanisms of imazamox to aquatic macrophyte from the enantiomer level. In this study, the enantioselective effects of IM on the toxicity and physiological and biochemical system of aquatic macrophyte Lemna minor were systematically investigated. Metabolomic and transcriptomic for Lemna minor were used to identify potential mechanisms of toxicity. 7 d EC50s for racemic-, R-, and S-IM were 0.036, 0.035, and 0.203 mg/L, respectively, showing enantioselective toxicity. In addition, IM caused Lemna minor lipid peroxidation and antioxidant damage, and inhibited the activities of the target enzymes. Metabolomic and transcriptomic data indicated that R-IM interferenced differentially expressed genes and metabolites of Lemna minor which were enriched in carbon fixation during photosynthesis, glutathione metabolic pathway, pentose phosphate pathway, zeatin biosynthesis, and porphyrin and chlorophyll metabolism. S-IM affected phenylalanine metabolism, phenylpropanoid biosynthesis, zeatin biosynthesis and secondary metabolite biosynthesis. Racemic-IM influenced carbon fixation during operation, glutathione metabolic pathway, zeatin biosynthesis and pentose phosphate pathway. The results provide new insights into the enantioselective toxicity mechanisms of IM to Lemna minor, and lay the foundation for conducting environmental risk assessments.
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Affiliation(s)
- Rui Li
- Guangxi key laboratory of Agric-Environment and Agric-products Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi 530004, People's Republic of China
| | - Chenxi Luo
- Guangxi key laboratory of Agric-Environment and Agric-products Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi 530004, People's Republic of China
| | - Jingsi Qiu
- Guangxi key laboratory of Agric-Environment and Agric-products Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi 530004, People's Republic of China
| | - Yuanfu Li
- Guangxi key laboratory of Agric-Environment and Agric-products Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi 530004, People's Republic of China
| | - Hui Zhang
- Guangxi key laboratory of Agric-Environment and Agric-products Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi 530004, People's Republic of China
| | - Huihua Tan
- Guangxi key laboratory of Agric-Environment and Agric-products Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi 530004, People's Republic of China.
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Cheng L, Zhao C, Zhao M, Han Y, Li S. Lignin Synthesis, Affected by Sucrose in Lotus ( Nelumbo nucifera) Seedlings, Was Involved in Regulation of Root Formation in the Arabidopsis thanliana. Int J Mol Sci 2022; 23:ijms23042250. [PMID: 35216366 PMCID: PMC8875098 DOI: 10.3390/ijms23042250] [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: 01/19/2022] [Revised: 02/04/2022] [Accepted: 02/15/2022] [Indexed: 11/16/2022] Open
Abstract
Adventitious roots (ARs) have an unmatched status in plant growth and metabolism due to the degeneration of primary roots in lotuses. In the present study, we sought to assess the effect of sucrose on ARs formation and observed that lignin synthesis was involved in ARs development. We found that the lignification degree of the ARs primordium was weaker in plants treated with 20 g/L sucrose than in 50 g/L sucrose treatment and control plants. The contents of lignin were lower in plants treated with 20 g/L sucrose and higher in plants treated with 50 g/L sucrose. The precursors of monomer lignin, including p-coumaric acid, caffeate, sinapinal aldehyde, and ferulic acid, were lower in the GL50 library than in the GL20 library. Further analysis revealed that the gene expression of these four metabolites had no novel difference in the GL50/GL20 libraries. However, a laccase17 gene (NnLAC17), involved in polymer lignin synthesis, had a higher expression in the GL50 library than in the GL20 library. Therefore, NnLAC17 was cloned and the overexpression of NnLAC17 was found to directly result in a decrease in the root number in transgenic Arabidopsis plants. These findings suggest that lignin synthesis is probably involved in ARs formation in lotus seedlings.
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Affiliation(s)
- Libao Cheng
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China; (C.Z.); (M.Z.); (Y.H.)
- Correspondence:
| | - Chen Zhao
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China; (C.Z.); (M.Z.); (Y.H.)
| | - Minrong Zhao
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China; (C.Z.); (M.Z.); (Y.H.)
| | - Yuyan Han
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China; (C.Z.); (M.Z.); (Y.H.)
| | - Shuyan Li
- College of Guangling, Yangzhou University, Yangzhou 225009, China;
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Complexity of gene paralogues resolved in biosynthetic pathway of hepatoprotective iridoid glycosides in a medicinal herb, Picrorhiza kurroa through differential NGS transcriptomes. Mol Genet Genomics 2021; 296:863-876. [PMID: 33899140 DOI: 10.1007/s00438-021-01787-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 04/13/2021] [Indexed: 10/21/2022]
Abstract
Picrorhiza kurroa is a medicinal herb with diverse pharmacological applications due to the presence of iridoid glycosides, picroside-I (P-I), and picroside-II (P-II), among others. Any genetic improvement in this medicinal herb can only be undertaken if the biosynthetic pathway genes are correctly identified. Our previous studies have deciphered biosynthetic pathways for P-I and P-II, however, the occurrence of multiple copies of genes has been a stumbling block in their usage. Therefore, a methodological strategy was designed to identify and prioritize paralogues of pathway genes associated with contents of P-I and P-II. We used differential transcriptomes varying for P-I and P-II contents in different tissues of P. kurroa. All transcripts for a particular pathway gene were identified, clustered based on multiple sequence alignment to notify as a representative of the same gene (≥ 99% sequence identity) or a paralogue of the same gene. Further, individual paralogues were tested for their expression level via qRT-PCR in tissue-specific manner. In total 44 paralogues in 14 key genes have been identified out of which 19 gene paralogues showed the highest expression pattern via qRT-PCR. Overall analysis shortlisted 6 gene paralogues, PKHMGR3, PKPAL2, PKDXPS1, PK4CL2, PKG10H2 and PKIS2 that might be playing role in the biosynthesis of P-I and P-II, however, their functional analysis need to be further validated either through gene silencing or over-expression. The usefulness of this approach can be expanded to other non-model plant species for which transcriptome resources have been generated.
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Han MH, Yang N, Wan QW, Teng RM, Duan AQ, Wang YH, Zhuang J. Exogenous melatonin positively regulates lignin biosynthesis in Camellia sinensis. Int J Biol Macromol 2021; 179:485-499. [PMID: 33684430 DOI: 10.1016/j.ijbiomac.2021.03.025] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 02/07/2021] [Accepted: 03/04/2021] [Indexed: 01/23/2023]
Abstract
Melatonin (MT) is a bioactive molecule that can regulate various developmental processes. Changes in lignin content play important roles in plant growth and development. Herein, quantitative analysis and histochemical staining showed that lignin content significantly increased over time, and melatonin treatment triggered the lignification at 8 and 16 d in tea leaves. The POD activity participated in lignin formation had also been significantly improved. The effect of melatonin on the increase of lignin content was attenuation over time. Sequencing results based on transcriptome at 8 and 16 d showed that 5273 and 3019 differentially expressed genes (DEGs) were identified in CK1 vs. MT1 and CK2 vs. MT2, respectively. A total of 67 DEGs were annotated to lignin biosynthesis, and 38 and 9 genes were significantly up-regulated under melatonin treatment, respectively. Some transcription factor genes such as MYB were also identified among the two pairwise comparisons, which might relate to lignin metabolism. Melatonin increased the degree of lignification in tea leaves by modifying the enzyme genes expression involved in lignin synthesis pathway. These results provide a reference for further study on the molecular mechanism of the dynamic changes of lignin content induced by melatonin treatment in tea plants.
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Affiliation(s)
- Miao-Hua Han
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Ni Yang
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Qi-Wen Wan
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Rui-Min Teng
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Ao-Qi Duan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Ya-Hui Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Jing Zhuang
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China.
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Wu X, Yan Z, Dong X, Cao F, Peng J, Li M. Cloning and characterization of a CCoAOMT gene involved in rapid lignification of endocarp in dove tree (Davidia involucrata Baill.). BIOTECHNOL BIOTEC EQ 2019. [DOI: 10.1080/13102818.2018.1525324] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Xiaobo Wu
- Department of Bioengineering, College of Life Science and Technology, Central South University of Forestry and Technology, Changsha, PR China
| | - Ziwei Yan
- Department of Bioengineering, College of Life Science and Technology, Central South University of Forestry and Technology, Changsha, PR China
| | - Xujie Dong
- Department of Bioengineering, College of Life Science and Technology, Central South University of Forestry and Technology, Changsha, PR China
| | - Fuxiang Cao
- Department of Horticulture, College of Horticulture and Landscape, Hunan Agricultural University, Changsha, PR China
| | - Jiqing Peng
- Department of Bioengineering, College of Life Science and Technology, Central South University of Forestry and Technology, Changsha, PR China
| | - Meng Li
- Department of Bioengineering, College of Life Science and Technology, Central South University of Forestry and Technology, Changsha, PR China
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Gill US, Uppalapati SR, Gallego-Giraldo L, Ishiga Y, Dixon RA, Mysore KS. Metabolic flux towards the (iso)flavonoid pathway in lignin modified alfalfa lines induces resistance against Fusarium oxysporum f. sp. medicaginis. PLANT, CELL & ENVIRONMENT 2018; 41:1997-2007. [PMID: 29047109 DOI: 10.1111/pce.13093] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 10/05/2017] [Accepted: 10/06/2017] [Indexed: 05/07/2023]
Abstract
Downregulation of lignin in alfalfa (Medicago sativa L.) is associated with increased availability of cell wall polysaccharides in plant cells. We tested transgenic alfalfa plants downregulated for Caffeoyl-CoA O-methyltransferase (CCoAOMT) against an economically important fungal disease of alfalfa, Fusarium wilt caused by Fusarium oxysporum f. sp. medicaginis, and found it more resistant to this disease. Transcriptomic and metabolomic analyses indicated that the improved disease resistance against Fusarium wilt is due to increased accumulation and/or spillover of flux towards the (iso)flavonoid pathway. Some (iso)flavonoids and their pathway intermediate compounds showed strong accumulation in CCoAOMT downregulated plants after F. oxysporum f. sp. medicaginis inoculation. The identified (iso)flavonoids, including medicarpin and 7,4'-dihydroxyflavone, inhibited the in vitro growth of F. oxysporum f. sp. medicaginis. These results suggested that the increased accumulation and/or shift/spillover of flux towards the (iso)flavonoid pathway in CCoAOMT downregulated plants is associated with induced disease resistance.
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Rakoczy M, Femiak I, Alejska M, Figlerowicz M, Podkowinski J. Sorghum CCoAOMT and CCoAOMT-like gene evolution, structure, expression and the role of conserved amino acids in protein activity. Mol Genet Genomics 2018; 293:1077-1089. [PMID: 29721721 PMCID: PMC6153501 DOI: 10.1007/s00438-018-1441-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 04/24/2018] [Indexed: 11/28/2022]
Abstract
Sorghum is a crop plant that is grown for seeds, sucrose, forage and biofuel production. In all these applications, lignin is a superfluous component that decreases the efficiency of technological processes. Caffeoyl-coenzyme A O-methyltransferase (CCoAOMT) is an enzyme involved in monolignol synthesis that affects the efficiency of lignification and lignin composition. The sorghum genome harbors one CCoAOMT gene and six closely related CCoAOMT-like genes. The structures of four sorghum CCoAOMT-like enzymes suggest that these proteins might methylate caffeoyl coenzyme A and contribute to monolignol synthesis. In this study, two sorghum genes, CCoAOMT and one CCoAOMT-like, were found to be highly expressed in leaves, stems and immature seeds. The promoters of these genes possess clusters of transcription factor-binding sites specific for lignification, and this suggests that they are important for lignification. Phylogenetic analysis revealed that one sorghum CCoAOMT-like enzyme is closely related to ancestral cyanobacterial CCoAOMT-like proteins. The remaining CCoAOMT-like enzymes, including the one highly expressed in the leaves and stem, are closely related to CCoAOMT. Genes from these two groups possess different, evolutionarily conserved gene structures. The structure of the sorghum CCoAOMT-like protein from the ancestral clade was modeled and differences between enzymes from the two clades were analyzed. These results facilitate a better understanding of the evolution of genes involved in lignification, and provide valuable data for sorghum improvement through traditional breeding or molecular genetic techniques. The findings suggest that CCoAOMT-like genes might be recruited in lignification and raise questions of the frequency of such functional shifts.
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Affiliation(s)
- M Rakoczy
- Institute of Bioorganic Chemistry PAS, ul. Noskowskiego 12/14, 61-704, Poznan, Poland
| | - I Femiak
- Institute of Bioorganic Chemistry PAS, ul. Noskowskiego 12/14, 61-704, Poznan, Poland
| | - M Alejska
- Institute of Bioorganic Chemistry PAS, ul. Noskowskiego 12/14, 61-704, Poznan, Poland
| | - M Figlerowicz
- Institute of Bioorganic Chemistry PAS, ul. Noskowskiego 12/14, 61-704, Poznan, Poland
| | - J Podkowinski
- Institute of Bioorganic Chemistry PAS, ul. Noskowskiego 12/14, 61-704, Poznan, Poland.
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Jin Y, Ye N, Zhu F, Li H, Wang J, Jiang L, Zhang J. Calcium-dependent protein kinase CPK28 targets the methionine adenosyltransferases for degradation by the 26S proteasome and affects ethylene biosynthesis and lignin deposition in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:304-318. [PMID: 28112445 DOI: 10.1111/tpj.13493] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 12/30/2016] [Accepted: 01/11/2017] [Indexed: 05/26/2023]
Abstract
S-adenosylmethionine (AdoMet) is synthesized by methionine adenosyltransferase (MAT), and plays an essential role in ethylene biosynthesis and other methylation reactions. Despite increasing knowledge of MAT regulation at transcriptional levels, how MAT is post-translationally regulated remains unknown in plant cells. Phosphorylation is an important post-translational modification for regulating the activity of enzymes, protein function and signaling transduction. Using molecular and biochemical approaches, we have identified the phosphorylation of MAT proteins by calcium-dependent protein kinase (CPK28). Phenotypically, both MAT2-overexpressing transgenic plants and cpk28 mutants display short hypocotyls and ectopic lignifications. Their shortened hypocotyl phenotypes are caused by ethylene overproduction and rescued by ethylene biosynthesis inhibitor aminoethoxyvinylglycine treatment. Genetic evidence reveals that MAT2 mutation restores the phenotype of ectopic lignification in CPK28-deficient plants. We find that total MAT proteins and AdoMet are increased in cpk28 mutants, but decreased in CPK28-overexpressing seedlings. We also find that MATs in OE::CPK28 are degraded through the 26S proteasome pathway. Our work suggests that CPK28 targets MATs (MAT1, MAT2 and MAT3) for degradation by the 26S proteasome pathway, and thus affects ethylene biosynthesis and lignin deposition in Arabidopsis.
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Affiliation(s)
- Yu Jin
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Nenghui Ye
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Fuyuan Zhu
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Haoxuan Li
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Juan Wang
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Liwen Jiang
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Jianhua Zhang
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
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12
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Zhang X, Liu Y, Fang Z, Li Z, Yang L, Zhuang M, Zhang Y, Lv H. Comparative Transcriptome Analysis between Broccoli ( Brassica oleracea var. italica) and Wild Cabbage ( Brassica macrocarpa Guss.) in Response to Plasmodiophora brassicae during Different Infection Stages. FRONTIERS IN PLANT SCIENCE 2016; 7:1929. [PMID: 28066482 DOI: 10.1007/s11104-019-04196-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 12/05/2016] [Indexed: 05/27/2023]
Abstract
Clubroot, one of the most devastating diseases to the Brassicaceae family, is caused by the obligate biotrophic pathogen Plasmodiophora brassicae. However, studies of the molecular basis of disease resistance are still poor especially in quantitative resistance. In the present paper, two previously identified genotypes, a clubroot-resistant genotype (wild cabbage, B2013) and a clubroot-susceptible genotype (broccoli, 90196) were inoculated by P. brassicae for 0 (T0), 7 (T7), and 14 (T14) day after inoculation (DAI). Gene expression pattern analysis suggested that response changes in transcript level of two genotypes under P. brassicae infection were mainly activated at the primary stage (T7). Based on the results of DEGs functional enrichments from two infection stages, genes associated with cell wall biosynthesis, glucosinolate biosynthesis, and plant hormone signal transduction showed down-regulated at T14 compared to T7, indicating that defense responses to P. brassicae were induced earlier, and related pathways were repressed at T14. In addition, the genes related to NBS-LRR proteins, SA signal transduction, cell wall and phytoalexins biosynthesis, chitinase, Ca2+ signals and RBOH proteins were mainly up-regulated in B2013 by comparing those of 90196, indicating the pathways of response defense to clubroot were activated in the resistant genotype. This is the first report about comparative transcriptome analysis for broccoli and its wild relative during the different stages of P. brassicae infection and the results should be useful for molecular assisted screening and breeding of clubroot-resistant genotypes.
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Affiliation(s)
- Xiaoli Zhang
- Group of Cabbage and Broccoli Breeding, Institute of Vegetables and Flowers - Chinese Academy of Agricultural Sciences Beijing, China
| | - Yumei Liu
- Group of Cabbage and Broccoli Breeding, Institute of Vegetables and Flowers - Chinese Academy of Agricultural Sciences Beijing, China
| | - Zhiyuan Fang
- Group of Cabbage and Broccoli Breeding, Institute of Vegetables and Flowers - Chinese Academy of Agricultural Sciences Beijing, China
| | - Zhansheng Li
- Group of Cabbage and Broccoli Breeding, Institute of Vegetables and Flowers - Chinese Academy of Agricultural Sciences Beijing, China
| | - Limei Yang
- Group of Cabbage and Broccoli Breeding, Institute of Vegetables and Flowers - Chinese Academy of Agricultural Sciences Beijing, China
| | - Mu Zhuang
- Group of Cabbage and Broccoli Breeding, Institute of Vegetables and Flowers - Chinese Academy of Agricultural Sciences Beijing, China
| | - Yangyong Zhang
- Group of Cabbage and Broccoli Breeding, Institute of Vegetables and Flowers - Chinese Academy of Agricultural Sciences Beijing, China
| | - Honghao Lv
- Group of Cabbage and Broccoli Breeding, Institute of Vegetables and Flowers - Chinese Academy of Agricultural Sciences Beijing, China
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Jiang MX, Zhai LJ, Yang H, Zhai SM, Zhai CK. Analysis of Active Components and Proteomics of Chinese Wild Rice (Zizania latifolia (Griseb) Turcz) and Indica Rice (Nagina22). J Med Food 2016; 19:798-804. [DOI: 10.1089/jmf.2015.3612] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Ming-xia Jiang
- School of Public Health, Southeast University, Nanjing, China
| | - Li-jie Zhai
- Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Hua Yang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, China
| | - Shu-menghui Zhai
- Department of Public Health, Center for Asian Health, Temple University, Philadelphia, Pennsylvania, USA
| | - Cheng-kai Zhai
- School of Public Health, Southeast University, Nanjing, China
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14
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Wang GL, Huang Y, Zhang XY, Xu ZS, Wang F, Xiong AS. Transcriptome-based identification of genes revealed differential expression profiles and lignin accumulation during root development in cultivated and wild carrots. PLANT CELL REPORTS 2016; 35:1743-55. [PMID: 27160835 DOI: 10.1007/s00299-016-1992-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 04/28/2016] [Indexed: 05/09/2023]
Abstract
Carrot root development associates lignin deposition and regulation. Carrot is consumed worldwide and is a good source of nutrients. However, excess lignin deposition may reduce the taste and quality of carrot root. Molecular mechanisms underlying lignin accumulation in carrot are still lacking. To address this problem, we collected taproots of wild and cultivated carrots at five developmental stages and analyzed the lignin content and characterized the lignin distribution using histochemical staining and autofluorescence microscopy. Genes involved in lignin biosynthesis were identified, and their expression profiles were determined. Results showed that lignin was mostly deposited in xylem vessels of carrot root. In addition, lignin content continuously decreased during root development, which was achieved possibly by reducing the expression of the genes involved in lignin biosynthesis. Carrot root may also prevent cell lignification to meet the demands of taproot growth. Our results will serve as reference for lignin biosynthesis in carrot and may also assist biologists to improve carrot quality.
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Affiliation(s)
- Guang-Long Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ying Huang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xin-Yue Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhi-Sheng Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Feng Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ai-Sheng Xiong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
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Wan L, Li B, Pandey MK, Wu Y, Lei Y, Yan L, Dai X, Jiang H, Zhang J, Wei G, Varshney RK, Liao B. Transcriptome Analysis of a New Peanut Seed Coat Mutant for the Physiological Regulatory Mechanism Involved in Seed Coat Cracking and Pigmentation. FRONTIERS IN PLANT SCIENCE 2016; 7:1491. [PMID: 27790222 PMCID: PMC5063860 DOI: 10.3389/fpls.2016.01491] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 09/20/2016] [Indexed: 05/21/2023]
Abstract
Seed-coat cracking and undesirable color of seed coat highly affects external appearance and commercial value of peanuts (Arachis hypogaea L.). With an objective to find genetic solution to the above problems, a peanut mutant with cracking and brown colored seed coat (testa) was identified from an EMS treated mutant population and designated as "peanut seed coat crack and brown color mutant line (pscb)." The seed coat weight of the mutant was almost twice of the wild type, and the germination time was significantly shorter than wild type. Further, the mutant had lower level of lignin, anthocyanin, proanthocyanidin content, and highly increased level of melanin content as compared to wild type. Using RNA-Seq, we examined the seed coat transcriptome in three stages of seed development in the wild type and the pscb mutant. The RNA-Seq analysis revealed presence of highly differentially expressed phenylpropanoid and flavonoid pathway genes in all the three seed development stages, especially at 40 days after flowering (DAF40). Also, the expression of polyphenol oxidases and peroxidase were found to be activated significantly especially in the late seed developmental stage. The genome-wide comparative study of the expression profiles revealed 62 differentially expressed genes common across all the three stages. By analyzing the expression patterns and the sequences of the common differentially expressed genes of the three stages, three candidate genes namely c36498_g1 (CCoAOMT1), c40902_g2 (kinesin), and c33560_g1 (MYB3) were identified responsible for seed-coat cracking and brown color phenotype. Therefore, this study not only provided candidate genes but also provided greater insights and molecular genetic control of peanut seed-coat cracking and color variation. The information generated in this study will facilitate further identification of causal gene and diagnostic markers for breeding improved peanut varieties with smooth and desirable seed coat color.
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Affiliation(s)
- Liyun Wan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural SciencesWuhan, China
| | - Bei Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural SciencesWuhan, China
| | - Manish K. Pandey
- Center of Excellence in Genomics, International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
| | - Yanshan Wu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural SciencesWuhan, China
| | - Yong Lei
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural SciencesWuhan, China
| | - Liying Yan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural SciencesWuhan, China
| | - Xiaofeng Dai
- Institute of Food Science and Technology of Chinese Academy of Agricultural SciencesBeijing, China
| | - Huifang Jiang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural SciencesWuhan, China
| | - Juncheng Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural SciencesWuhan, China
| | - Guo Wei
- Institute of Food Science and Technology of Chinese Academy of Agricultural SciencesBeijing, China
| | - Rajeev K. Varshney
- Center of Excellence in Genomics, International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
- School of Plant Biology and Institute of Agriculture, The University of Western AustraliaCrawley, WA, Australia
| | - Boshou Liao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural SciencesWuhan, China
- *Correspondence: Boshou Liao
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Abdollah Hosseini S, Gharechahi J, Heidari M, Koobaz P, Abdollahi S, Mirzaei M, Nakhoda B, Hosseini Salekdeh G. Comparative proteomic and physiological characterisation of two closely related rice genotypes with contrasting responses to salt stress. FUNCTIONAL PLANT BIOLOGY : FPB 2015; 42:527-542. [PMID: 32480698 DOI: 10.1071/fp14274] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 02/07/2015] [Indexed: 06/11/2023]
Abstract
Salinity is a limiting factor affecting crop growth. We evaluated the responses of a salt-tolerant recombinant inbred rice (Oryza sativa L.) line, FL478, and the salt-sensitive IR29. Seedlings were exposed to salt stress and the growth rate was monitored to decipher the effect of long-term stress. At Day 16, IR29 produced lower shoot biomass than FL478. Significant differences for Na+ and K+ concentrations and Na+ : K+ ratios in roots and shoots were observed between genotypes. Changes in the proteomes of control and salt-stressed plants were analysed, identifying 59 and 39 salt-responsive proteins in roots and leaves, respectively. Proteomic analysis showed greater downregulation of proteins in IR29. In IR29, proteins related to pathways involved in salt tolerance (e.g. oxidative stress response, amino acid biosynthesis, polyamine biosynthesis, the actin cytoskeleton and ion compartmentalisation) changed to combat salinity. We found significant downregulation of proteins related to photosynthetic electron transport in IR29, indicating that photosynthesis was influenced, probably increasing the risk of reactive oxygen species formation. The sensitivity of IR29 might be related to its inability to exclude salt from its transpiration stream, to compartmentalise excess ions and to maintain a healthy photosynthetic apparatus during salt stress, or might be because of the leakiness of its roots, allowing excess salt to enter apoplastically. In FL478, superoxide dismutase, ferredoxin thioredoxin reductase, fibre protein and inorganic pyrophosphatase, which may participate in salt tolerance, increased in abundance. Our analyses provide novel insights into the mechanisms behind salt tolerance and sensitivity in genotypes with close genetic backgrounds.
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Affiliation(s)
- Seyed Abdollah Hosseini
- Department of Molecular Physiology, Agricultural Biotechnology Research Institute of Iran, PO Box 31535-1897, Karaj 3135933151, Iran
| | - Javad Gharechahi
- Chemical Injuries Research Center, Baqiyatallah University of Medical Sciences, PO Box 19395-5478, Tehran 1435916471, Iran
| | - Manzar Heidari
- Department of Molecular Physiology, Agricultural Biotechnology Research Institute of Iran, PO Box 31535-1897, Karaj 3135933151, Iran
| | - Parisa Koobaz
- Department of Molecular Physiology, Agricultural Biotechnology Research Institute of Iran, PO Box 31535-1897, Karaj 3135933151, Iran
| | - Shapour Abdollahi
- Department of Molecular Physiology, Agricultural Biotechnology Research Institute of Iran, PO Box 31535-1897, Karaj 3135933151, Iran
| | - Mehdi Mirzaei
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Babak Nakhoda
- Department of Molecular Physiology, Agricultural Biotechnology Research Institute of Iran, PO Box 31535-1897, Karaj 3135933151, Iran
| | - Ghasem Hosseini Salekdeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, PO Box 31535-1897, Karaj 3135933151, Iran
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Srivastava AC, Chen F, Ray T, Pattathil S, Peña MJ, Avci U, Li H, Huhman DV, Backe J, Urbanowicz B, Miller JS, Bedair M, Wyman CE, Sumner LW, York WS, Hahn MG, Dixon RA, Blancaflor EB, Tang Y. Loss of function of folylpolyglutamate synthetase 1 reduces lignin content and improves cell wall digestibility in Arabidopsis. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:224. [PMID: 26697113 PMCID: PMC4687376 DOI: 10.1186/s13068-015-0403-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 11/30/2015] [Indexed: 05/02/2023]
Abstract
BACKGROUND One-carbon (C1) metabolism is important for synthesizing a range of biologically important compounds that are essential for life. In plants, the C1 pathway is crucial for the synthesis of a large number of secondary metabolites, including lignin. Tetrahydrofolate and its derivatives, collectively referred to as folates, are crucial co-factors for C1 metabolic pathway enzymes. Given the link between the C1 and phenylpropanoid pathways, we evaluated whether folylpolyglutamate synthetase (FPGS), an enzyme that catalyzes the addition of a glutamate tail to folates to form folylpolyglutamates, can be a viable target for reducing cell wall recalcitrance in plants. RESULTS Consistent with its role in lignocellulosic formation, FPGS1 was preferentially expressed in vascular tissues. Total lignin was low in fpgs1 plants leading to higher saccharification efficiency of the mutant. The decrease in total lignin in fpgs1 was mainly due to lower guaiacyl (G) lignin levels. Glycome profiling revealed subtle alterations in the cell walls of fpgs1. Further analyses of hemicellulosic polysaccharides by NMR showed that the degree of methylation of 4-O-methyl glucuronoxylan was reduced in the fpgs1 mutant. Microarray analysis and real-time qRT-PCR revealed that transcripts of a number of genes in the C1 and lignin pathways had altered expression in fpgs1 mutants. Consistent with the transcript changes of C1-related genes, a significant reduction in S-adenosyl-l-methionine content was detected in the fpgs1 mutant. The modified expression of the various methyltransferases and lignin-related genes indicate possible feedback regulation of C1 pathway-mediated lignin biosynthesis. CONCLUSIONS Our observations provide genetic and biochemical support for the importance of folylpolyglutamates in the lignocellulosic pathway and reinforces previous observations that targeting a single FPGS isoform for down-regulation leads to reduced lignin in plants. Because fpgs1 mutants had no dramatic defects in above ground biomass, selective down-regulation of individual components of C1 metabolism is an approach that should be explored further for the improvement of lignocellulosic feedstocks.
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Affiliation(s)
- Avinash C. Srivastava
- />Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK 73401 USA
- />BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN 37831 USA
| | - Fang Chen
- />BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN 37831 USA
- />Department of Biological Sciences, University of North Texas, Denton, TX 76203 USA
| | - Tui Ray
- />Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK 73401 USA
| | - Sivakumar Pattathil
- />BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN 37831 USA
- />Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602 USA
- />Department of Plant Biology, University of Georgia, Athens, GA 30602 USA
| | - Maria J. Peña
- />BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN 37831 USA
- />Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602 USA
| | - Utku Avci
- />BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN 37831 USA
- />Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602 USA
- />Department of Plant Biology, University of Georgia, Athens, GA 30602 USA
| | - Hongjia Li
- />BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN 37831 USA
- />Center for Environmental Research and Technology (CE-CERT), Bourns College of Engineering, University of California, Riverside, CA 92507 USA
| | - David V. Huhman
- />Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK 73401 USA
| | - Jason Backe
- />BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN 37831 USA
- />Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602 USA
| | - Breeanna Urbanowicz
- />BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN 37831 USA
- />Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602 USA
| | - Jeffrey S. Miller
- />Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602 USA
| | - Mohamed Bedair
- />Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK 73401 USA
| | - Charles E. Wyman
- />BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN 37831 USA
- />Center for Environmental Research and Technology (CE-CERT), Bourns College of Engineering, University of California, Riverside, CA 92507 USA
| | - Lloyd W. Sumner
- />Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK 73401 USA
| | - William S. York
- />BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN 37831 USA
- />Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602 USA
- />Department of Plant Biology, University of Georgia, Athens, GA 30602 USA
| | - Michael G. Hahn
- />BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN 37831 USA
- />Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602 USA
- />Department of Plant Biology, University of Georgia, Athens, GA 30602 USA
| | - Richard A. Dixon
- />BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN 37831 USA
- />Department of Biological Sciences, University of North Texas, Denton, TX 76203 USA
| | - Elison B. Blancaflor
- />Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK 73401 USA
- />BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN 37831 USA
| | - Yuhong Tang
- />Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK 73401 USA
- />BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN 37831 USA
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18
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Identification of proteins of altered abundance in oil palm infected with Ganoderma boninense. Int J Mol Sci 2014; 15:5175-92. [PMID: 24663087 PMCID: PMC3975447 DOI: 10.3390/ijms15035175] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 03/05/2014] [Accepted: 03/05/2014] [Indexed: 01/19/2023] Open
Abstract
Basal stem rot is a common disease that affects oil palm, causing loss of yield and finally killing the trees. The disease, caused by fungus Ganoderma boninense, devastates thousands of hectares of oil palm plantings in Southeast Asia every year. In the present study, root proteins of healthy oil palm seedlings, and those infected with G. boninense, were analyzed by 2-dimensional gel electrophoresis (2-DE). When the 2-DE profiles were analyzed for proteins, which exhibit consistent significant change of abundance upon infection with G. boninense, 21 passed our screening criteria. Subsequent analyses by mass spectrometry and database search identified caffeoyl-CoA O-methyltransferase, caffeic acid O-methyltransferase, enolase, fructokinase, cysteine synthase, malate dehydrogenase, and ATP synthase as among proteins of which abundances were markedly altered.
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19
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Proteomics study reveals the molecular mechanisms underlying water stress tolerance induced by Piriformospora indica in barley. J Proteomics 2013; 94:289-301. [DOI: 10.1016/j.jprot.2013.09.017] [Citation(s) in RCA: 113] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 09/26/2013] [Accepted: 09/30/2013] [Indexed: 11/24/2022]
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20
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Naaz H, Pandey VP, Singh S, Dwivedi UN. Structure-function analyses and molecular modeling of caffeic acid-O-methyltransferase and caffeoyl-CoA-O-methyltransferase: revisiting the basis of alternate methylation pathways during monolignol biosynthesis. Biotechnol Appl Biochem 2013; 60:170-89. [PMID: 23600572 DOI: 10.1002/bab.1075] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Accepted: 12/04/2012] [Indexed: 11/11/2022]
Abstract
Ten protein sequences, each of caffeic acid-O-methyltransferase (COMT) and caffeoyl-coenzyme A-O-methyltransferase (CCoAOMT), catalyzing methylation of precursors of monolignol from selected dicots and monocots have been analyzed and compared on the basis of their amino acid sequence, motifs/domains, three-dimensional (3D) structure, and substrate binding. The isoelectric points of all the COMT and CCoAOMT sequences analyzed were found to vary in the pH range of 5 to 6. Molecular weight analyses suggested CCoAOMT to be smaller monomeric proteins (27-29 kDa) as compared with those of COMTs (39-40 kDa), which were dimeric. On the basis of phylogenetic analysis, COMT and CCoAOMT were clustered into two major groups, each of which could be further divided into two subgroups of monocots and dicots. Modeling and superimposition of COMT and CCoAOMT sequences of alfalfa (Medicago sativa) revealed that both were quite different at the 3D levels, although they had similarity in the core region. Molecular docking of 16 putative substrates (intermediates of monolignol biosynthesis pathway) revealed that both enzymes interact with all 16 substrates in a similar manner, with thiol esters being the most potent and binding of these putative substrates to CCoAOMT being more efficient.
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Affiliation(s)
- Huma Naaz
- Department of Biochemistry, Bioinformatics Infrastructure Facility, Centre of Excellence in Bioinformatics, University of Lucknow, Lucknow, U.P., India
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21
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Gharechahi J, Khalili M, Hasanloo T, Salekdeh GH. An integrated proteomic approach to decipher the effect of methyl jasmonate elicitation on the proteome of Silybum marianum L. hairy roots. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2013; 70:115-22. [PMID: 23771036 DOI: 10.1016/j.plaphy.2013.05.031] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 05/21/2013] [Indexed: 06/02/2023]
Abstract
Jasmonate and its methyl derivative, methyl jasmonate (MeJA), are naturally occurring compounds that mediate several plant physiological processes in response to pathogen attack, wounding, and ozone. Exogenous application of jasmonates triggers defense responses that resemble those initiated by pathogen infection and also modulates the production of certain secondary metabolites in a variety of plant species. In this study, we treated the hairy root cultures of Silybum marianum L. with 100 μM MeJA and then measured the content of Silymarin (SLM). We observed that the SLM content increased significantly after 48 h of MeJA treatment and remained constant for 120 h. However, MeJA treatment caused a significant growth reduction after 96 h incubation. The activity of lipoxygenase as a key enzyme in the jasmonate biosynthesis pathway and anti-oxidative enzymes; peroxidase and ascorbate peroxidase was also significantly increased after MeJA treatment. To elucidate the global effect of jasmonate on gene expression of S. marianum, we employed high resolution two-dimensional gel electrophoresis coupled with tandem mass spectrometry. Out of 670 reproducibly detected protein spots which were analyzed on each given gel, 32 spots were up- or down regulated upon MeJA treatment. Of them, ten proteins such as ER binding protein, glutamine synthetase, pathogenesis-related protein, caffeoyl CoA O-methyltransferase, and profilin-1 could be identified by mass spectrometry analysis. The possible implications of the identified proteins on physiological outcome of MeJA application in S. marianum hairy root culture will be discussed.
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Affiliation(s)
- Javad Gharechahi
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Karaj, Iran.
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22
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Sharifi G, Ebrahimzadeh H, Ghareyazie B, Gharechahi J, Vatankhah E. Identification of differentially accumulated proteins associated with embryogenic and non-embryogenic calli in saffron (Crocus sativus L.). Proteome Sci 2012; 10:3. [PMID: 22243837 PMCID: PMC3349542 DOI: 10.1186/1477-5956-10-3] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2011] [Accepted: 01/13/2012] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Somatic embryogenesis (SE) is a complex biological process that occurs under inductive conditions and causes fully differentiated cells to be reprogrammed to an embryo like state. In order to get a better insight about molecular basis of the SE in Crocus sativus L. and to characterize differentially accumulated proteins during the process, a proteomic study based on two-dimensional gel electrophoresis and matrix-assisted laser desorption/ionization time of flight mass spectrometry has been carried out. RESULTS We have compared proteome profiles of non-embryogenic and embryogenic calli with native corm explants. Total soluble proteins were phenol-extracted and loaded on 18 cm IPG strips for the first dimension and 11.5% sodium dodecyl sulfate-polyacrylamide gels for the second dimension. Fifty spots with more than 1.5-fold change in abundance were subjected to mass spectrometry analysis for further characterization. Among them 36 proteins could be identified, which are classified into defense and stress response, protein synthesis and processing, carbohydrate and energy metabolism, secondary metabolism, and nitrogen metabolism. CONCLUSION Our results showed that diverse cellular and molecular processes were affected during somatic to embryogenic transition. Differential proteomic analysis suggests a key role for ascorbate metabolism during early stage of SE, and points to the possible role of ascorbate-glutathione cycle in establishing somatic embryos.
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Affiliation(s)
- Golandam Sharifi
- Department of Basic Sciences, Iranian Encyclopedia Compiling Foundation, Tehran, Iran
- Department of Botany, Faculty of Science, University of Tehran, Tehran, Iran
| | - Hassan Ebrahimzadeh
- Department of Botany, Faculty of Science, University of Tehran, Tehran, Iran
| | - Behzad Ghareyazie
- Department of Genomics, Agricultural Biotechnology Research Institute of Iran, Karaj, Iran
| | - Javad Gharechahi
- Department of Molecular Genetics, National Institute for Genetic Engineering and Biotechnology, Tehran, Iran
| | - Elaheh Vatankhah
- Department of Botany, Faculty of Science, University of Tehran, Tehran, Iran
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Cloning and functional characterization of a caffeic acid O-methyltransferase from Trigonella foenum-graecum L. Mol Biol Rep 2011; 39:1601-8. [PMID: 21604170 DOI: 10.1007/s11033-011-0899-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Accepted: 05/17/2011] [Indexed: 10/18/2022]
Abstract
A cDNA encoding an O-methyltransferase (namely FGCOMT1) was identified from the medicinal plant Trigonella foenum-graecum L. The FGCOMT1 enzyme is a functional caffeic acid O-methyltransferase (COMT) and is localized in the cytosol. Kinetic analysis indicated that FGCOMT1 protein exhibited the highest catalyzing efficiency towards 5-hydroxy ferulic acid and caffeic acid as substrates, but did not possess the abilities to methylate either quercetin or tricetin in vitro. Furthermore, transformation of Arabidopsis loss-of-function Atomt1 mutant with a FGCOMT1 cDNA partially complements accumulation of sinapoyl derivatives but did not function to produce the major methylated flavonol isorhamnetin in seeds. The results from this study indicated that FGCOMT1 is a COMT with substrate preference to monomeric lignin precursors but is not involved in the flavonoid methylation in T. foenum-graecum L.
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24
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Shi R, Sun YH, Li Q, Heber S, Sederoff R, Chiang VL. Towards a Systems Approach for Lignin Biosynthesis in Populus trichocarpa: Transcript Abundance and Specificity of the Monolignol Biosynthetic Genes. ACTA ACUST UNITED AC 2009; 51:144-63. [DOI: 10.1093/pcp/pcp175] [Citation(s) in RCA: 221] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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25
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Abstract
Grapevine ( Vitis vinifera) products, grape and grape juice, represent a valuable source of bioactive phytochemicals, synthesized by three secondary metabolic pathways (phenylpropanoid, isoprenoid and alkaloid biosynthetic routes) and stored in different plant tissues. In the last decades, compelling evidence suggested that regular consumption of these products may contribute to reducing the incidence of chronic illnesses, such as cancer, cardiovascular diseases, ischemic stroke, neurodegenerative disorders and aging, in a context of the Mediterranean dietary tradition. The health benefits arising from grape product intake can be ascribed to the potpourri of biologically active chemicals occurring in grapes. Among them, the recently discovered presence of melatonin adds a new element to the already complex grape chemistry. Melatonin, and its possible synergistic action with the great variety of polyphenols, contributes to further explaining the observed health benefits associated with regular grape product consumption.
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Affiliation(s)
- Marcello Iriti
- Dipartimento di Produzione Vegetale, Università di Milano and Istituto di Virologia Vegetale, CNR, Dipartimento Agroalimentare, Via Celoria 2, 20133 Milano, Italy
| | - Franco Faoro
- Dipartimento di Produzione Vegetale, Università di Milano and Istituto di Virologia Vegetale, CNR, Dipartimento Agroalimentare, Via Celoria 2, 20133 Milano, Italy
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Fellenberg C, Milkowski C, Hause B, Lange PR, Böttcher C, Schmidt J, Vogt T. Tapetum-specific location of a cation-dependent O-methyltransferase in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2008; 56:132-145. [PMID: 18557837 DOI: 10.1111/j.1365-313x.2008.03576.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Cation- and S-adenosyl-L-methionine (AdoMet)-dependent plant natural product methyltransferases are referred to as CCoAOMTs because of their preferred substrate, caffeoyl coenzyme A (CCoA). The enzymes are encoded by a small family of genes, some of which with a proven role in lignin monomer biosynthesis. In Arabidopsis thaliana individual members of this gene family are temporally and spatially regulated. The gene At1g67990 is specifically expressed in flower buds, and is not detected in any other organ, such as roots, leaves or stems. Several lines of evidence indicate that the At1g67990 transcript is located in the flower buds, whereas the corresponding CCoAOMT-like protein, termed AtTSM1, is located exclusively in the tapetum of developing stamen. Flowers of At1g67990 RNAi-suppressed plants are characterized by a distinct flower chemotype with severely reduced levels of the N ',N ''-bis-(5-hydroxyferuloyl)-N '''-sinapoylspermidine compensated for by N(1),N(5),N(10)-tris-(5-hydroxyferuloyl)spermidine derivative, which is characterized by the lack of a single methyl group in the sinapoyl moiety. This severe change is consistent with the observed product profile of AtTSM1 for aromatic phenylpropanoids. Heterologous expression of the recombinant protein shows the highest activity towards a series of caffeic acid esters, but 5-hydroxyferuloyl spermidine conjugates are also accepted substrates. The in vitro substrate specificity and the in vivo RNAi-mediated suppression data of the corresponding gene suggest a role of this cation-dependent CCoAOMT-like protein in the stamen/pollen development of A. thaliana.
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Affiliation(s)
- Christin Fellenberg
- Department of Secondary Metabolism, Leibniz Institute of Plant Biochemistry, Weinberg 3, D-06120 Halle (Saale), Germany
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Targeted modulation of sinapine biosynthesis pathway for seed quality improvement in Brassica napus. Transgenic Res 2008; 18:31-44. [DOI: 10.1007/s11248-008-9194-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2008] [Accepted: 05/29/2008] [Indexed: 11/27/2022]
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28
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Ma QH, Xu Y. Characterization of a caffeic acid 3-O-methyltransferase from wheat and its function in lignin biosynthesis. Biochimie 2008; 90:515-24. [PMID: 17976886 DOI: 10.1016/j.biochi.2007.09.016] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2007] [Accepted: 09/21/2007] [Indexed: 10/22/2022]
Abstract
Caffeic acid 3-O-methyltransferase (COMT) catalyzes the multi-step methylation reactions of hydroxylated monomeric lignin precursors, and is believed to occupy a pivotal position in the lignin biosynthetic pathway. A cDNA (TaCM) was identified from wheat and it was found to be expressed constitutively in stem, leaf and root tissues. The deduced amino acid sequence of TaCM showed a high degree of identity with COMT from other plants, particularly in SAM binding motif and the residues responsible for catalytic and substrate specificity. The predicted TaCM three-dimensional structure is very similar with a COMT from alfalfa (MsCOMT), and TaCM protein had high immunoreactive activity with MsCOMT antibody. Kinetic analysis indicated that the recombinant TaCM protein exhibited the highest catalyzing efficiency towards caffeoyl aldehyde and 5-hydroxyconiferaldehyde as substrates, suggesting a pathway leads to S lignin via aldehyde precursors. Authority of TaCM encoding a COMT was confirmed by the expression of antisense TaCM gene in transgenic tobacco which specifically down-regulated the COMT enzyme activity. Lignin analysis showed that the reduction in COMT activity resulted in a marginal decrease in lignin content but sharp reduction in the syringl lignin. Furthermore, the TaCM protein exhibited a strong activity towards ester precursors including caffeoyl-CoA and 5-hydroxyferuloyl-CoA. Our results demonstrate that TaCM is a typical COMT involved in lignin biosynthesis. It also supports the notion, in agreement with a structural analysis, that COMT has a broad substrate preference.
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Affiliation(s)
- Qing-Hu Ma
- Key Laboratory of Photosynthesis and Environmental Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Xiangshan, Beijing, China.
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29
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Do CT, Pollet B, Thévenin J, Sibout R, Denoue D, Barrière Y, Lapierre C, Jouanin L. Both caffeoyl Coenzyme A 3-O-methyltransferase 1 and caffeic acid O-methyltransferase 1 are involved in redundant functions for lignin, flavonoids and sinapoyl malate biosynthesis in Arabidopsis. PLANTA 2007; 226:1117-29. [PMID: 17594112 DOI: 10.1007/s00425-007-0558-3] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2007] [Accepted: 05/16/2007] [Indexed: 05/16/2023]
Abstract
Two methylation steps are necessary for the biosynthesis of monolignols, the lignin precursors. Caffeic acid O-methyltransferase (COMT) O-methylates at the C5 position of the phenolic ring. COMT is responsible for the biosynthesis of sinapyl alcohol, the precursor of syringyl lignin units. The O-methylation at the C3 position of the phenolic ring involves the Caffeoyl CoA 3-O-methyltransferase (CCoAOMT). The CCoAOMT 1 gene (At4g34050) is believed to encode the enzyme responsible for the first O-methylation in Arabidopsis thaliana. A CCoAOMT1 promoter-GUS fusion and immunolocalization experiments revealed that this gene is strongly and exclusively expressed in the vascular tissues of stems and roots. An Arabidopsis T-DNA null mutant named ccomt 1 was identified and characterised. The mutant stems are slightly smaller than wild-type stems in short-day growth conditions and has collapsed xylem elements. The lignin content of the stem is low and the S/G ratio is high mainly due to fewer G units. These results suggest that this O-methyltransferase is involved in G-unit biosynthesis but does not act alone to perform this step in monolignol biosynthesis. To determine which O-methyltransferase assists CCoAOMT 1, a comt 1 ccomt1 double mutant was generated and studied. The development of comt 1 ccomt1 is arrested at the plantlet stage in our growth conditions. Lignins of these plantlets are mainly composed of p-hydroxyphenyl units. Moreover, the double mutant does not synthesize sinapoyl malate, a soluble phenolic. These results suggest that CCoAOMT 1 and COMT 1 act together to methylate the C3 position of the phenolic ring of monolignols in Arabidopsis. In addition, they are both involved in the formation of sinapoyl malate and isorhamnetin.
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Affiliation(s)
- Cao-Trung Do
- Biologie Cellulaire, INRA, 78026, Versailles cedex, France
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30
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Sakakibara N, Nakatsubo T, Suzuki S, Shibata D, Shimada M, Umezawa T. Metabolic analysis of the cinnamate/monolignol pathway in Carthamus tinctorius seeds by a stable-isotope-dilution method. Org Biomol Chem 2007. [PMID: 17315067 DOI: 10.1007/s11101-009-9155-3] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/27/2023]
Abstract
The present study established a system for comprehensive metabolic analysis of the cinnamate/monolignol and lignan pathways by the use of a stable-isotope-dilution method. The system was successfully applied to characterization of the pathways in Carthamus tinctorius cv. Round-leaved White maturing seeds in combination with administration of stable-isotope-labelled precursors. Experimental results obtained using this technique strongly suggested the intermediacy of ferulic acid in lignan biosynthesis in the plant.
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Affiliation(s)
- Norikazu Sakakibara
- Research Institute for Sustainable Humanosphare, Kyoto University, Uji, Kyoto 611-0011, Japan
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Cristofani-Yaly M, Berger IJ, Targon MLP, Takita MA, Dorta SDO, Freitas-Astúa J, Souza AAD, Boscariol-Camargo RL, Reis MS, Machado MA. Differential expression of genes identified from Poncirus trifoliata tissue inoculated with CTV through EST analysis and in silico hybridization. Genet Mol Biol 2007. [DOI: 10.1590/s1415-47572007000500025] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Chapter two Structural, functional, and evolutionary basis for methylation of plant small molecules. RECENT ADVANCES IN PHYTOCHEMISTRY 2003. [DOI: 10.1016/s0079-9920(03)80017-5] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
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Bolwell GP, Patten AM, Lewis NG. The Holy Grail of wood evolution - from wood anatomy to tissue-specific gene expression: to what extent do molecular studies of biosynthesis of cell wall biopolymers help the understanding of the evolution of woody species? PHYTOCHEMISTRY 2001; 57:805-810. [PMID: 11423132 DOI: 10.1016/s0031-9422(01)00149-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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