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Rao X, Barros J. Modeling lignin biosynthesis: a pathway to renewable chemicals. TRENDS IN PLANT SCIENCE 2024; 29:546-559. [PMID: 37802691 DOI: 10.1016/j.tplants.2023.09.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 09/01/2023] [Accepted: 09/18/2023] [Indexed: 10/08/2023]
Abstract
Plant biomass contains lignin that can be converted into high-value-added chemicals, fuels, and materials. The precise genetic manipulation of lignin content and composition in plant cells offers substantial environmental and economic benefits. However, the intricate regulatory mechanisms governing lignin formation challenge the development of crops with specific lignin profiles. Mathematical models and computational simulations have recently been employed to gain fundamental understanding of the metabolism of lignin and related phenolic compounds. This review article discusses the strategies used for modeling plant metabolic networks, focusing on the application of mathematical modeling for flux network analysis in monolignol biosynthesis. Furthermore, we highlight how current challenges might be overcome to optimize the use of metabolic modeling approaches for developing lignin-engineered plants.
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Affiliation(s)
- Xiaolan Rao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China.
| | - Jaime Barros
- Division of Plant Sciences and Interdisciplinary Plant Group, University of Missouri, Columbia, MO 65211, USA.
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2
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Sharma S, Malhotra PK, Goyal M, Sharma V, Mittal A, Yadav IS, Sanghera GS, Chhuneja P. Characterization of sugarcane mutants developed through gamma irradiations for their lignin content and caffeic acid-O-methyl transferase ( COMT) gene mutations. Int J Radiat Biol 2024; 100:619-626. [PMID: 38166242 DOI: 10.1080/09553002.2023.2295962] [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: 08/18/2023] [Accepted: 12/05/2023] [Indexed: 01/04/2024]
Abstract
PURPOSE Bagasse, the residue left after extracting juice from sugarcane stalks, is rich in lignocellulosic biomass. The lignin present in this plant biomass is the key factor that hinders the efficient extraction of ethanol from the bagasse. In the current study, γ-irradiated sugarcane mutants were evaluated for variation in lignin content and its corresponding caffeic acid-O-methyl transferase (COMT) gene. MATERIALS AND METHODS The acetyl bromide method was used to estimate lignin content in sugarcane mutants. PCR-based cloning of the COMT gene was performed in low lignin mutants as well as control plants in E. coli (strain DH5α) to understand the mechanism of variation at the molecular level. The Sanger sequencing for cloned gene was performed to check variation in gene sequence. RESULTS In comparison to the control (21.5%), the mutant plants' lignin content ranged from 13 to 28%. The Sanger sequencing revealed approximately the same length of the gene from mutants as well as a control plant. In comparison to the reference gene, the mutated gene showed SNPs and indels in different regions, which may have an impact on lignin content. CONCLUSIONS Therefore, γ-irradiated mutagenesis is an acceptable approach to develop novel mutants of sugarcane with low lignin content to enhance bioethanol production from waste material using bioprocess technology.
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Affiliation(s)
- Shaweta Sharma
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Pawan Kumar Malhotra
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Meenakshi Goyal
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Vishal Sharma
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
- Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Solan, India
| | - Amandeep Mittal
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Inderjit Singh Yadav
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | | | - Parveen Chhuneja
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
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3
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Wang Y, Shang B, Génard M, Hilbert-Masson G, Delrot S, Gomès E, Poni S, Keller M, Renaud C, Kong J, Chen J, Liang Z, Dai Z. Model-assisted analysis for tuning anthocyanin composition in grape berries. ANNALS OF BOTANY 2023; 132:1033-1050. [PMID: 37850481 PMCID: PMC10808033 DOI: 10.1093/aob/mcad165] [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: 09/06/2023] [Accepted: 10/17/2023] [Indexed: 10/19/2023]
Abstract
Anthocyanin composition is responsible for the red colour of grape berries and wines, and contributes to their organoleptic quality. However, anthocyanin biosynthesis is under genetic, developmental and environmental regulation, making its targeted fine-tuning challenging. We constructed a mechanistic model to simulate the dynamics of anthocyanin composition throughout grape ripening in Vitis vinifera, employing a consensus anthocyanin biosynthesis pathway. The model was calibrated and validated using six datasets from eight cultivars and 37 growth conditions. Tuning the transformation and degradation parameters allowed us to accurately simulate the accumulation process of each individual anthocyanin under different environmental conditions. The model parameters were robust across environments for each genotype. The coefficients of determination (R2) for the simulated versus observed values for the six datasets ranged from 0.92 to 0.99, while the relative root mean square errors (RRMSEs) were between 16.8 and 42.1 %. The leave-one-out cross-validation for three datasets showed R2 values of 0.99, 0.96 and 0.91, and RRMSE values of 28.8, 32.9 and 26.4 %, respectively, suggesting a high prediction quality of the model. Model analysis showed that the anthocyanin profiles of diverse genotypes are relatively stable in response to parameter perturbations. Virtual experiments further suggested that targeted anthocyanin profiles may be reached by manipulating a minimum of three parameters, in a genotype-dependent manner. This model presents a promising methodology for characterizing the temporal progression of anthocyanin composition, while also offering a logical foundation for bioengineering endeavours focused on precisely adjusting the anthocyanin composition of grapes.
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Affiliation(s)
- Yongjian Wang
- State Key Laboratory of Plant Diversity and Specialty Crops and Beijing Key Laboratory of Grape Science and Enology, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Boxing Shang
- State Key Laboratory of Plant Diversity and Specialty Crops and Beijing Key Laboratory of Grape Science and Enology, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Michel Génard
- INRAE, UR1115, Unité Plantes et Systèmes de Culture Horticoles, Avignon, France
| | | | - Serge Delrot
- EGFV, University of Bordeaux, Bordeaux-Sciences Agro, INRAE, ISVV, Villenave d’Ornon, France
| | - Eric Gomès
- EGFV, University of Bordeaux, Bordeaux-Sciences Agro, INRAE, ISVV, Villenave d’Ornon, France
| | - Stefano Poni
- Department of Sustainable Crop Production, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy
| | - Markus Keller
- Department of Viticulture and Enology, Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, WA, USA
| | - Christel Renaud
- EGFV, University of Bordeaux, Bordeaux-Sciences Agro, INRAE, ISVV, Villenave d’Ornon, France
| | - Junhua Kong
- State Key Laboratory of Plant Diversity and Specialty Crops and Beijing Key Laboratory of Grape Science and Enology, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Jinliang Chen
- Center for Agricultural Water Research in China, China Agricultural University, Beijing, 100083, China
| | - Zhenchang Liang
- State Key Laboratory of Plant Diversity and Specialty Crops and Beijing Key Laboratory of Grape Science and Enology, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhanwu Dai
- State Key Laboratory of Plant Diversity and Specialty Crops and Beijing Key Laboratory of Grape Science and Enology, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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4
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The combination treatment of chlorogenic acid and sodium alginate coating could accelerate the wound healing of pear fruit by promoting the metabolic pathway of phenylpropane. Food Chem 2023; 414:135689. [PMID: 36809727 DOI: 10.1016/j.foodchem.2023.135689] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 12/18/2022] [Accepted: 02/10/2023] [Indexed: 02/18/2023]
Abstract
Water loss and microbial infection induced by mechanical injury are the main sources of harvested loss of fruits and vegetables. Plenty studies have shown that regulating phenylpropane-related metabolic pathways can effectively accelerate wound healing. The combination treatment of chlorogenic acid and sodium alginate coating on postharvest wound healing of pear fruit were investigated in this work. The result shows combination treatment reduced weight loss and disease index of the pears, enhanced texture of healing tissues, maintained the integrity of cell membrane system. Moreover, chlorogenic acid increased the content of total phenols and flavonoids, and ultimately leads to the accumulation of suberin poly phenolic (SPP) and lignin around wound cell wall. Activities of phenylalanine metabolism-related enzymes (PAL, C4H, 4CL, CAD, POD and PPO) in wound-healing tissue were enhanced. The contents of major substrates such as trans-cinnamic, p-coumaric, caffeic, and ferulic acids also increased. The presented results suggested that the combination treatment of chlorogenic acid and sodium alginate coating stimulated wound healing in pears by elevating the phenylpropanoid metabolism pathway, so that maintain high postharvest fruit quality.
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Wang Z, Yao XM, Jia CH, Xu BY, Wang JY, Liu JH, Jin ZQ. Identification and analysis of lignin biosynthesis genes related to fruit ripening and stress response in banana ( Musa acuminata L. AAA group, cv. Cavendish). FRONTIERS IN PLANT SCIENCE 2023; 14:1072086. [PMID: 37035063 PMCID: PMC10074854 DOI: 10.3389/fpls.2023.1072086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 02/28/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND Lignin is a key component of the secondary cell wall of plants, providing mechanical support and facilitating water transport as well as having important impact effects in response to a variety of biological and abiotic stresses. RESULTS In this study, we identified 104 genes from ten enzyme gene families related to lignin biosynthesis in Musa acuminata genome and found the number of MaCOMT gene family was the largest, while MaC3Hs had only two members. MaPALs retained the original members, and the number of Ma4CLs in lignin biosynthesis was significantly less than that of flavonoids. Segmental duplication existed in most gene families, except for MaC3Hs, and tandem duplication was the main way to expand the number of MaCOMTs. Moreover, the expression profiles of lignin biosynthesis genes during fruit development, postharvest ripening stages and under various abiotic and biological stresses were investigated using available RNA-sequencing data to obtain fruit ripening and stress response candidate genes. Finally, a co-expression network of lignin biosynthesis genes was constructed by weighted gene co-expression network analysis to elucidate the lignin biosynthesis genes that might participate in lignin biosynthesis in banana during development and in response to stresses. CONCLUSION This study systematically identified the lignin biosynthesis genes in the Musa acuminata genome, providing important candidate genes for further functional analysis. The identification of the major genes involved in lignin biosynthesis in banana provides the basis for the development of strategies to improve new banana varieties tolerant to biological and abiotic stresses with high yield and high quality.
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Affiliation(s)
- Zhuo Wang
- Key Laboratory of Tropical Crop Biotechnology of Ministry of Agriculture and Rural Affairs, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
- Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
- Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
| | - Xiao-ming Yao
- Beijing Genomics Institute (BGI)-Sanya, Beijing Genomics Institute (BGI)-Shenzhen, Sanya, China
| | - Cai-hong Jia
- Key Laboratory of Tropical Crop Biotechnology of Ministry of Agriculture and Rural Affairs, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
- Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Bi-yu Xu
- Key Laboratory of Tropical Crop Biotechnology of Ministry of Agriculture and Rural Affairs, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
- Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Jing-yi Wang
- Key Laboratory of Tropical Crop Biotechnology of Ministry of Agriculture and Rural Affairs, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
- Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Ju-hua Liu
- Key Laboratory of Tropical Crop Biotechnology of Ministry of Agriculture and Rural Affairs, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
- Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
- Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
| | - Zhi-qiang Jin
- Key Laboratory of Tropical Crop Biotechnology of Ministry of Agriculture and Rural Affairs, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
- Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
- Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
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Mahmood U, Li X, Qian M, Fan Y, Yu M, Li S, Shahzad A, Qu C, Li J, Liu L, Lu K. Comparative transcriptome and co-expression network analysis revealed the genes associated with senescence and polygalacturonase activity involved in pod shattering of rapeseed. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:20. [PMID: 36750865 PMCID: PMC9906875 DOI: 10.1186/s13068-023-02275-6] [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: 05/27/2022] [Accepted: 02/01/2023] [Indexed: 02/09/2023]
Abstract
BACKGROUND The pod shattering (PS) trait negatively affects the crop yield in rapeseed especially under dry conditions. To better understand the trait and cultivate higher resistance varieties, it's necessary to identify key genes and unravel the PS mechanism thoroughly. RESULTS In this study, we conducted a comparative transcriptome analysis between two materials significantly different in silique shatter resistance lignin deposition and polygalacturonase (PG) activity. Here, we identified 10,973 differentially expressed genes at six pod developmental stages. We found that the late pod development stages might be crucial in preparing the pods for upcoming shattering events. GO enrichment results from K-means clustering and weighed gene correlation network analysis (WGCNA) both revealed senescence-associated genes play an important role in PS. Two hub genes Bna.A05ABI5 and Bna.C03ERF/AP2-3 were selected from the MEyellow module, which possibly regulate the PS through senescence-related mechanisms. Further investigation found that senescence-associated transcription factor Bna.A05ABI5 upregulated the expression of SAG2 and ERF/AP2 to control the shattering process. In addition, the upregulation of Bna.C03ERF/AP2-3 is possibly involved in the transcription of downstream SHP1/2 and LEA proteins to trigger the shattering mechanism. We also analyzed the PS marker genes and found Bna.C07SHP1/2 and Bna.PG1/2 were significantly upregulated in susceptible accession. Furthermore, the role of auxin transport by Bna.WAG2 was also observed, which could reduce the PG activity to enhance the PS resistance through the cell wall loosening process. CONCLUSION Based on comparative transcriptome evaluation, this study delivers insights into the regulatory mechanism primarily underlying the variation of PS in rapeseed. Taken together, these results provide a better understanding to increase the yield of rapeseed by reducing the PS through better engineered crops.
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Affiliation(s)
- Umer Mahmood
- grid.263906.80000 0001 0362 4044College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
| | - Xiaodong Li
- grid.263906.80000 0001 0362 4044College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
| | - Mingchao Qian
- grid.263906.80000 0001 0362 4044College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
| | - Yonghai Fan
- grid.263906.80000 0001 0362 4044College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
| | - Mengna Yu
- grid.263906.80000 0001 0362 4044College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
| | - Shengting Li
- grid.263906.80000 0001 0362 4044College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
| | - Ali Shahzad
- grid.263906.80000 0001 0362 4044College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
| | - Cunmin Qu
- grid.263906.80000 0001 0362 4044College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China ,grid.263906.80000 0001 0362 4044Academy of Agricultural Sciences, Southwest University, Chongqing, 400715 China ,grid.419897.a0000 0004 0369 313XEngineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, 400715 China
| | - Jiana Li
- grid.263906.80000 0001 0362 4044College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China ,grid.263906.80000 0001 0362 4044Academy of Agricultural Sciences, Southwest University, Chongqing, 400715 China ,grid.419897.a0000 0004 0369 313XEngineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, 400715 China
| | - Liezhao Liu
- grid.263906.80000 0001 0362 4044College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China ,grid.263906.80000 0001 0362 4044Academy of Agricultural Sciences, Southwest University, Chongqing, 400715 China ,grid.419897.a0000 0004 0369 313XEngineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, 400715 China
| | - Kun Lu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China. .,Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China. .,Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, 400715, China.
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Wu TY, Krishnamoorthi S, Boonyaves K, Al-Darabsah I, Leong R, Jones AM, Ishizaki K, Liao KL, Urano D. G protein controls stress readiness by modulating transcriptional and metabolic homeostasis in Arabidopsis thaliana and Marchantia polymorpha. MOLECULAR PLANT 2022; 15:1889-1907. [PMID: 36321200 DOI: 10.1016/j.molp.2022.10.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 10/03/2022] [Accepted: 10/28/2022] [Indexed: 06/16/2023]
Abstract
The core G protein signaling module, which consists of Gα and extra-large Gα (XLG) subunits coupled with the Gβγ dimer, is a master regulator of various stress responses. In this study, we compared the basal and salt stress-induced transcriptomic, metabolomic and phenotypic profiles in Gα, Gβ, and XLG-null mutants of two plant species, Arabidopsis thaliana and Marchantia polymorpha, and showed that G protein mediates the shift of transcriptional and metabolic homeostasis to stress readiness status. We demonstrated that such stress readiness serves as an intrinsic protection mechanism against further stressors through enhancing the phenylpropanoid pathway and abscisic acid responses. Furthermore, WRKY transcription factors were identified as key intermediates of G protein-mediated homeostatic shifts. Statistical and mathematical model comparisons between A. thaliana and M. polymorpha revealed evolutionary conservation of transcriptional and metabolic networks over land plant evolution, whereas divergence has occurred in the function of plant-specific atypical XLG subunit. Taken together, our results indicate that the shifts in transcriptional and metabolic homeostasis at least partially act as the mechanisms of G protein-coupled stress responses that are conserved between two distantly related plants.
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Affiliation(s)
- Ting-Ying Wu
- Temasek Life Sciences Laboratory, Singapore, Singapore.
| | | | - Kulaporn Boonyaves
- Temasek Life Sciences Laboratory, Singapore, Singapore; Singapore-MIT Alliance for Research and Technology, Singapore, Singapore
| | - Isam Al-Darabsah
- Department of Mathematics, University of Manitoba, Winnipeg, MB, Canada
| | - Richalynn Leong
- Temasek Life Sciences Laboratory, Singapore, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
| | - Alan M Jones
- Departments of Biology and Pharmacology, University of North Carolina, Chapel Hill, NC, USA
| | - Kimitsune Ishizaki
- Graduate School of Science, Kobe University, Kobe, Hyogo 657-8501, Japan
| | - Kang-Ling Liao
- Department of Mathematics, University of Manitoba, Winnipeg, MB, Canada.
| | - Daisuke Urano
- Temasek Life Sciences Laboratory, Singapore, Singapore; Singapore-MIT Alliance for Research and Technology, Singapore, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore.
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Zhuo C, Wang X, Docampo-Palacios M, Sanders BC, Engle NL, Tschaplinski TJ, Hendry JI, Maranas CD, Chen F, Dixon RA. Developmental changes in lignin composition are driven by both monolignol supply and laccase specificity. SCIENCE ADVANCES 2022; 8:eabm8145. [PMID: 35263134 PMCID: PMC8906750 DOI: 10.1126/sciadv.abm8145] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 01/17/2022] [Indexed: 05/25/2023]
Abstract
The factors controlling lignin composition remain unclear. Catechyl (C)-lignin is a homopolymer of caffeyl alcohol with unique properties as a biomaterial and precursor of industrial chemicals. The lignin synthesized in the seed coat of Cleome hassleriana switches from guaiacyl (G)- to C-lignin at around 12 to 14 days after pollination (DAP), associated with a rerouting of the monolignol pathway. Lack of synthesis of caffeyl alcohol limits C-lignin formation before around 12 DAP, but coniferyl alcohol is still synthesized and highly accumulated after 14 DAP. We propose a model in which, during C-lignin biosynthesis, caffeyl alcohol noncompetitively inhibits oxidation of coniferyl alcohol by cell wall laccases, a process that might limit movement of coniferyl alcohol to the apoplast. Developmental changes in both substrate availability and laccase specificity together account for the metabolic fates of G- and C-monolignols in the Cleome seed coat.
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Affiliation(s)
- Chunliu Zhuo
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, 1155 Union Circle #311428, Denton, TX 76203, USA
- Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Xin Wang
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, 1155 Union Circle #311428, Denton, TX 76203, USA
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Maite Docampo-Palacios
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, 1155 Union Circle #311428, Denton, TX 76203, USA
| | - Brian C. Sanders
- Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Nancy L. Engle
- Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Timothy J. Tschaplinski
- Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - John I. Hendry
- Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Costas D. Maranas
- Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Fang Chen
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, 1155 Union Circle #311428, Denton, TX 76203, USA
- Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Richard A. Dixon
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, 1155 Union Circle #311428, Denton, TX 76203, USA
- Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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Assessing the impact of substrate-level enzyme regulations limiting ethanol titer in Clostridium thermocellum using a core kinetic model. Metab Eng 2022; 69:286-301. [PMID: 34982997 DOI: 10.1016/j.ymben.2021.12.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 12/16/2021] [Accepted: 12/29/2021] [Indexed: 11/20/2022]
Abstract
Clostridium thermocellum is a promising candidate for consolidated bioprocessing because it can directly ferment cellulose to ethanol. Despite significant efforts, achieved yields and titers fall below industrially relevant targets. This implies that there still exist unknown enzymatic, regulatory, and/or possibly thermodynamic bottlenecks that can throttle back metabolic flow. By (i) elucidating internal metabolic fluxes in wild-type C. thermocellum grown on cellobiose via 13C-metabolic flux analysis (13C-MFA), (ii) parameterizing a core kinetic model, and (iii) subsequently deploying an ensemble-docking workflow for discovering substrate-level regulations, this paper aims to reveal some of these factors and expand our knowledgebase governing C. thermocellum metabolism. Generated 13C labeling data were used with 13C-MFA to generate a wild-type flux distribution for the metabolic network. Notably, flux elucidation through MFA alluded to serine generation via the mercaptopyruvate pathway. Using the elucidated flux distributions in conjunction with batch fermentation process yield data for various mutant strains, we constructed a kinetic model of C. thermocellum core metabolism (i.e. k-ctherm138). Subsequently, we used the parameterized kinetic model to explore the effect of removing substrate-level regulations on ethanol yield and titer. Upon exploring all possible simultaneous (up to four) regulation removals we identified combinations that lead to many-fold model predicted improvement in ethanol titer. In addition, by coupling a systematic method for identifying putative competitive inhibitory mechanisms using K-FIT kinetic parameterization with the ensemble-docking workflow, we flagged 67 putative substrate-level inhibition mechanisms across central carbon metabolism supported by both kinetic formalism and docking analysis.
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10
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Zhang X, Chen B, Wang L, Ali S, Guo Y, Liu J, Wang J, Xie L, Zhang Q. Genome-Wide Identification and Characterization of Caffeic Acid O-Methyltransferase Gene Family in Soybean. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10122816. [PMID: 34961287 PMCID: PMC8703356 DOI: 10.3390/plants10122816] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 12/17/2021] [Accepted: 12/17/2021] [Indexed: 05/17/2023]
Abstract
Soybean is one of the most important legumes, providing high-quality protein for humans. The caffeic acid O-methyltransferase (COMT) gene has previously been demonstrated to be a critical gene that regulates lignin production in plant cell walls and plays an important function in plant growth and development. However, the COMT gene family has not been studied in soybeans. In this study, 55 COMT family genes in soybean were identified by phylogenetic analysis and divided into two groups, I and II. The analysis of conserved domains showed that all GmCOMTs genes contained Methyltransferase-2 domains. Further prediction of cis-acting elements showed that GmCOMTs genes were associated with growth, light, stress, and hormonal responses. Eventually, based on the genomic data of soybean under different stresses, the results showed that the expression of GmCOMTs genes was different under different stresses, such as salt and drought stress. This study has identified and characterized the COMT gene family in soybean, which provides an important theoretical basis for further research on the biological functions of COMT genes and promotes revealing the role of GmCOMTs genes under stress resistance.
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Affiliation(s)
- Xu Zhang
- College of Life Science, Northeast Forestry University, Harbin 150040, China; (X.Z.); (B.C.); (L.W.); (S.A.); (Y.G.); (J.L.); (J.W.)
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Bowei Chen
- College of Life Science, Northeast Forestry University, Harbin 150040, China; (X.Z.); (B.C.); (L.W.); (S.A.); (Y.G.); (J.L.); (J.W.)
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Lishan Wang
- College of Life Science, Northeast Forestry University, Harbin 150040, China; (X.Z.); (B.C.); (L.W.); (S.A.); (Y.G.); (J.L.); (J.W.)
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Shahid Ali
- College of Life Science, Northeast Forestry University, Harbin 150040, China; (X.Z.); (B.C.); (L.W.); (S.A.); (Y.G.); (J.L.); (J.W.)
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Yile Guo
- College of Life Science, Northeast Forestry University, Harbin 150040, China; (X.Z.); (B.C.); (L.W.); (S.A.); (Y.G.); (J.L.); (J.W.)
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Jiaxi Liu
- College of Life Science, Northeast Forestry University, Harbin 150040, China; (X.Z.); (B.C.); (L.W.); (S.A.); (Y.G.); (J.L.); (J.W.)
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Jiang Wang
- College of Life Science, Northeast Forestry University, Harbin 150040, China; (X.Z.); (B.C.); (L.W.); (S.A.); (Y.G.); (J.L.); (J.W.)
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Linan Xie
- College of Life Science, Northeast Forestry University, Harbin 150040, China; (X.Z.); (B.C.); (L.W.); (S.A.); (Y.G.); (J.L.); (J.W.)
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin 150040, China
- Correspondence: (L.X.); (Q.Z.)
| | - Qingzhu Zhang
- College of Life Science, Northeast Forestry University, Harbin 150040, China; (X.Z.); (B.C.); (L.W.); (S.A.); (Y.G.); (J.L.); (J.W.)
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- Correspondence: (L.X.); (Q.Z.)
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11
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Wang X, Chao N, Zhang A, Kang J, Jiang X, Gai Y. Systematic Analysis and Biochemical Characterization of the Caffeoyl Shikimate Esterase Gene Family in Poplar. Int J Mol Sci 2021; 22:ijms222413366. [PMID: 34948162 PMCID: PMC8704367 DOI: 10.3390/ijms222413366] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/09/2021] [Accepted: 12/10/2021] [Indexed: 02/07/2023] Open
Abstract
Caffeoyl shikimate esterase (CSE) hydrolyzes caffeoyl shikimate into caffeate and shikimate in the phenylpropanoid pathway. In this study, we performed a systematic analysis of the CSE gene family and investigated the possible roles of CSE and CSE-like genes in Populus. We conducted a genome-wide analysis of the CSE gene family, including functional and phylogenetic analyses of CSE and CSE-like genes, using the poplar (Populus trichocarpa) genome. Eighteen CSE and CSE-like genes were identified in the Populus genome, and five phylogenetic groups were identified from phylogenetic analysis. CSEs in Group Ia, which were proposed as bona fide CSEs, have probably been lost in most monocots except Oryza sativa. Primary functional classification showed that PoptrCSE1 and PoptrCSE2 had putative function in lignin biosynthesis. In addition, PoptrCSE2, along with PoptrCSE12, might also respond to stress with a function in cell wall biosynthesis. Enzymatic assay of PoptoCSE1 (Populus tomentosa), -2 and -12 showed that PoptoCSE1 and -2 maintained CSE activity. PoptoCSE1 and 2 had similar biochemical properties, tissue expression patterns and subcellular localization. Most of the PoptrCSE-like genes are homologs of AtMAGL (monoacylglycerol lipase) genes in Arabidopsis and may function as MAG lipase in poplar. Our study provides a systematic understanding of this novel gene family and suggests the function of CSE in monolignol biosynthesis in Populus.
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Affiliation(s)
- Xuechun Wang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (X.W.); (N.C.); (A.Z.); (J.K.); (X.J.)
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory, National Forestry and Grassland Administration, Beijing 100083, China
- National Engineering Laboratory for Tree Breeding, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing 100083, China
| | - Nan Chao
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (X.W.); (N.C.); (A.Z.); (J.K.); (X.J.)
- Jiangsu Key Laboratory of Sericutural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212018, China
| | - Aijing Zhang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (X.W.); (N.C.); (A.Z.); (J.K.); (X.J.)
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory, National Forestry and Grassland Administration, Beijing 100083, China
- National Engineering Laboratory for Tree Breeding, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing 100083, China
| | - Jiaqi Kang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (X.W.); (N.C.); (A.Z.); (J.K.); (X.J.)
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory, National Forestry and Grassland Administration, Beijing 100083, China
- National Engineering Laboratory for Tree Breeding, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing 100083, China
| | - Xiangning Jiang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (X.W.); (N.C.); (A.Z.); (J.K.); (X.J.)
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory, National Forestry and Grassland Administration, Beijing 100083, China
- National Engineering Laboratory for Tree Breeding, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing 100083, China
| | - Ying Gai
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (X.W.); (N.C.); (A.Z.); (J.K.); (X.J.)
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory, National Forestry and Grassland Administration, Beijing 100083, China
- National Engineering Laboratory for Tree Breeding, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing 100083, China
- Correspondence: ; Tel.: +86-10-6233-8063
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12
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Lin CY, Sun Y, Song J, Chen HC, Shi R, Yang C, Liu J, Tunlaya-Anukit S, Liu B, Loziuk PL, Williams CM, Muddiman DC, Lin YCJ, Sederoff RR, Wang JP, Chiang VL. Enzyme Complexes of Ptr4CL and PtrHCT Modulate Co-enzyme A Ligation of Hydroxycinnamic Acids for Monolignol Biosynthesis in Populus trichocarpa. FRONTIERS IN PLANT SCIENCE 2021; 12:727932. [PMID: 34691108 PMCID: PMC8527181 DOI: 10.3389/fpls.2021.727932] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 09/13/2021] [Indexed: 06/13/2023]
Abstract
Co-enzyme A (CoA) ligation of hydroxycinnamic acids by 4-coumaric acid:CoA ligase (4CL) is a critical step in the biosynthesis of monolignols. Perturbation of 4CL activity significantly impacts the lignin content of diverse plant species. In Populus trichocarpa, two well-studied xylem-specific Ptr4CLs (Ptr4CL3 and Ptr4CL5) catalyze the CoA ligation of 4-coumaric acid to 4-coumaroyl-CoA and caffeic acid to caffeoyl-CoA. Subsequently, two 4-hydroxycinnamoyl-CoA:shikimic acid hydroxycinnamoyl transferases (PtrHCT1 and PtrHCT6) mediate the conversion of 4-coumaroyl-CoA to caffeoyl-CoA. Here, we show that the CoA ligation of 4-coumaric and caffeic acids is modulated by Ptr4CL/PtrHCT protein complexes. Downregulation of PtrHCTs reduced Ptr4CL activities in the stem-differentiating xylem (SDX) of transgenic P. trichocarpa. The Ptr4CL/PtrHCT interactions were then validated in vivo using biomolecular fluorescence complementation (BiFC) and protein pull-down assays in P. trichocarpa SDX extracts. Enzyme activity assays using recombinant proteins of Ptr4CL and PtrHCT showed elevated CoA ligation activity for Ptr4CL when supplemented with PtrHCT. Numerical analyses based on an evolutionary computation of the CoA ligation activity estimated the stoichiometry of the protein complex to consist of one Ptr4CL and two PtrHCTs, which was experimentally confirmed by chemical cross-linking using SDX plant protein extracts and recombinant proteins. Based on these results, we propose that Ptr4CL/PtrHCT complexes modulate the metabolic flux of CoA ligation for monolignol biosynthesis during wood formation in P. trichocarpa.
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Affiliation(s)
- Chien-Yuan Lin
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Yi Sun
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Jina Song
- Department of Electrical and Computer Engineering, North Carolina State University, Raleigh, NC, United States
| | - Hsi-Chuan Chen
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
| | - Rui Shi
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
| | - Chenmin Yang
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
| | - Jie Liu
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
| | - Sermsawat Tunlaya-Anukit
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
| | - Baoguang Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- Department of Forestry, Beihua University, Jilin, China
| | - Philip L. Loziuk
- W.M. Keck FTMS Laboratory, Department of Chemistry, North Carolina State University, Raleigh, NC, United States
| | - Cranos M. Williams
- Department of Electrical and Computer Engineering, North Carolina State University, Raleigh, NC, United States
| | - David C. Muddiman
- W.M. Keck FTMS Laboratory, Department of Chemistry, North Carolina State University, Raleigh, NC, United States
| | - Ying-Chung Jimmy Lin
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Ronald R. Sederoff
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
| | - Jack P. Wang
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Vincent L. Chiang
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
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13
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Feduraev P, Skrypnik L, Riabova A, Pungin A, Tokupova E, Maslennikov P, Chupakhina G. Phenylalanine and Tyrosine as Exogenous Precursors of Wheat ( Triticum aestivum L.) Secondary Metabolism through PAL-Associated Pathways. PLANTS 2020; 9:plants9040476. [PMID: 32283640 PMCID: PMC7238280 DOI: 10.3390/plants9040476] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 03/31/2020] [Accepted: 04/02/2020] [Indexed: 11/17/2022]
Abstract
Reacting to environmental exposure, most higher plants activate secondary metabolic pathways, such as the metabolism of phenylpropanoids. This pathway results in the formation of lignin, one of the most important polymers of the plant cell, as well as a wide range of phenolic secondary metabolites. Aromatic amino acids, such as phenylalanine and tyrosine, largely stimulate this process, determining two ways of lignification in plant tissues, varying in their efficiency. The current study analyzed the effect of phenylalanine and tyrosine, involved in plant metabolism through the phenylalanine ammonia-lyase (PAL) pathway, on the synthesis and accumulation of phenolic compounds, as well as lignin by means of the expression of a number of genes responsible for its biosynthesis, based on the example of common wheat (Triticum aestivum L.).
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14
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Dixon RA, Barros J. Lignin biosynthesis: old roads revisited and new roads explored. Open Biol 2019; 9:190215. [PMID: 31795915 PMCID: PMC6936255 DOI: 10.1098/rsob.190215] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Accepted: 10/30/2019] [Indexed: 12/31/2022] Open
Abstract
Lignin is a major component of secondarily thickened plant cell walls and is considered to be the second most abundant biopolymer on the planet. At one point believed to be the product of a highly controlled polymerization procedure involving just three potential monomeric components (monolignols), it is becoming increasingly clear that the composition of lignin is quite flexible. Furthermore, the biosynthetic pathways to the major monolignols also appear to exhibit flexibility, particularly as regards the early reactions leading to the formation of caffeic acid from coumaric acid. The operation of parallel pathways to caffeic acid occurring at the level of shikimate esters or free acids may help provide robustness to the pathway under different physiological conditions. Several features of the pathway also appear to link monolignol biosynthesis to both generation and detoxification of hydrogen peroxide, one of the oxidants responsible for creating monolignol radicals for polymerization in the apoplast. Monolignol transport to the apoplast is not well understood. It may involve passive diffusion, although this may be targeted to sites of lignin initiation/polymerization by ordered complexes of both biosynthetic enzymes on the cytosolic side of the plasma membrane and structural anchoring of proteins for monolignol oxidation and polymerization on the apoplastic side. We present several hypothetical models to illustrate these ideas and stimulate further research. These are based primarily on studies in model systems, which may or may not reflect the major lignification process in forest trees.
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Affiliation(s)
- Richard A. Dixon
- Hagler Institute for Advanced Studies and Department of Biological Sciences, Texas A&M University, College Station, TX, USA
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, 1155 Union Circle #311428, Denton, TX 76203-5017, USA
| | - Jaime Barros
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, 1155 Union Circle #311428, Denton, TX 76203-5017, USA
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15
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Zhuo C, Rao X, Azad R, Pandey R, Xiao X, Harkelroad A, Wang X, Chen F, Dixon RA. Enzymatic basis for C-lignin monomer biosynthesis in the seed coat of Cleome hassleriana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 99:506-520. [PMID: 31002459 DOI: 10.1111/tpj.14340] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 03/05/2019] [Accepted: 03/28/2019] [Indexed: 06/09/2023]
Abstract
C-lignin is a linear polymer of caffeyl alcohol, found in the seed coats of several exotic plant species, with promising properties for generation of carbon fibers and high value chemicals. In the ornamental plant Cleome hassleriana, guaiacyl (G) lignin is deposited in the seed coat for the first 6-12 days after pollination, after which G-lignin deposition ceases and C-lignin accumulates, providing an excellent model system to study C-lignin biosynthesis. We performed RNA sequencing of seed coats harvested at 2-day intervals throughout development. Bioinformatic analysis identified a complete set of lignin biosynthesis genes for Cleome. Transcript analysis coupled with kinetic analysis of recombinant enzymes in Escherichia coli revealed that the switch to C-lignin formation was accompanied by down-regulation of transcripts encoding functional caffeoyl CoA- and caffeic acid 3-O-methyltransferases (CCoAOMT and COMT) and a form of cinnamyl alcohol dehydrogenase (ChCAD4) with preference for coniferaldehyde as substrate, and up-regulation of a form of CAD (ChCAD5) with preference for caffealdehyde. Based on these analyses, blockage of lignin monomer methylation by down-regulation of both O-methyltransferases (OMTs) and methionine synthase (for provision of C1 units) appears to be the major factor in diversion of flux to C-lignin in the Cleome seed coat, although the change in CAD specificity also contributes based on the reduction of C-lignin levels in transgenic Cleome with down-regulation of ChCAD5. Structure modeling and mutational analysis identified amino acid residues important for the preference of ChCAD5 for caffealdehyde.
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Affiliation(s)
- Chunliu Zhuo
- BioDiscovery Institute, University of North Texas, Denton, TX, USA
- Department of Biological Science, University of North Texas, Denton, TX, USA
| | - Xiaolan Rao
- BioDiscovery Institute, University of North Texas, Denton, TX, USA
- Department of Biological Science, University of North Texas, Denton, TX, USA
| | - Rajeev Azad
- BioDiscovery Institute, University of North Texas, Denton, TX, USA
- Department of Biological Science, University of North Texas, Denton, TX, USA
- Department of Mathematics, University of North Texas, Denton, TX, USA
| | - Ravi Pandey
- BioDiscovery Institute, University of North Texas, Denton, TX, USA
- Department of Biological Science, University of North Texas, Denton, TX, USA
| | - Xirong Xiao
- BioDiscovery Institute, University of North Texas, Denton, TX, USA
- Department of Biological Science, University of North Texas, Denton, TX, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TX, USA
| | - Aaron Harkelroad
- BioDiscovery Institute, University of North Texas, Denton, TX, USA
- Department of Biological Science, University of North Texas, Denton, TX, USA
| | - Xiaoqiang Wang
- BioDiscovery Institute, University of North Texas, Denton, TX, USA
- Department of Biological Science, University of North Texas, Denton, TX, USA
| | - Fang Chen
- BioDiscovery Institute, University of North Texas, Denton, TX, USA
- Department of Biological Science, University of North Texas, Denton, TX, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TX, USA
| | - Richard A Dixon
- BioDiscovery Institute, University of North Texas, Denton, TX, USA
- Department of Biological Science, University of North Texas, Denton, TX, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TX, USA
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16
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Wang JP, Matthews ML, Naik PP, Williams CM, Ducoste JJ, Sederoff RR, Chiang VL. Flux modeling for monolignol biosynthesis. Curr Opin Biotechnol 2019; 56:187-192. [DOI: 10.1016/j.copbio.2018.12.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 10/30/2018] [Accepted: 12/02/2018] [Indexed: 10/27/2022]
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17
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Integration of Transcriptome, Proteome, and Metabolome Provides Insights into How Calcium Enhances the Mechanical Strength of Herbaceous Peony Inflorescence Stems. Cells 2019; 8:cells8020102. [PMID: 30704139 PMCID: PMC6406379 DOI: 10.3390/cells8020102] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 01/23/2019] [Accepted: 01/28/2019] [Indexed: 12/21/2022] Open
Abstract
Weak stem mechanical strength severely restrains cut flowers quality and stem weakness can be alleviated by calcium (Ca) treatment, but the mechanisms underlying Ca-mediated enhancement of stem mechanical strength remain largely unknown. In this study, we performed a comparative transcriptomic, proteomic, and metabolomic analysis of herbaceous peony (Paeonia lactiflora Pall.) inflorescence stems treated with nanometer Ca carbonate (Nano-CaCO₃). In total, 2643 differentially expressed genes (DEGs) and 892 differentially expressed proteins (DEPs) were detected between the Control and nano-CaCO₃ treatment. Among the 892 DEPs, 152 were coregulated at both the proteomic and transcriptomic levels, and 24 DEPs related to the secondary cell wall were involved in signal transduction, energy metabolism, carbohydrate metabolism and lignin biosynthesis, most of which were upregulated after nano-CaCO₃ treatment during the development of inflorescence stems. Among these four pathways, numerous differentially expressed metabolites (DEMs) related to lignin biosynthesis were identified. Furthermore, structural observations revealed the thickening of the sclerenchyma cell walls, and the main wall constitutive component lignin accumulated significantly in response to nano-CaCO₃ treatment, thereby indicating that Ca can enhance the mechanical strength of the inflorescence stems by increasing the lignin accumulation. These results provided insights into how Ca treatment enhances the mechanical strength of inflorescence stems in P. lactiflora.
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18
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Tang Y, Zhao D, Meng J, Tao J. EGTA reduces the inflorescence stem mechanical strength of herbaceous peony by modifying secondary wall biosynthesis. HORTICULTURE RESEARCH 2019; 6:36. [PMID: 30854212 PMCID: PMC6395589 DOI: 10.1038/s41438-019-0117-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Revised: 12/19/2018] [Accepted: 12/30/2018] [Indexed: 05/12/2023]
Abstract
The mechanical strength of inflorescence stems is an important trait in cut flowers. Calcium ions (Ca2+) play a pivotal role in maintaining stem strength, but little is known about the underlying molecular mechanisms. In this study, we treated herbaceous peony (Paeonia lactiflora Pall.) with ethyl glycol tetraacetic acid (EGTA), an effective Ca2+ chelator, and used morphology indicators, spectroscopic analysis, histochemical staining, electron microscopy, and proteomic techniques to investigate the role of Ca2+ in inflorescence stem mechanical strength. The EGTA treatment reduced the mechanical strength of inflorescence stems, triggered the loss of Ca2+ from cell walls, and reduced lignin in thickened secondary walls in xylem cells as determined by spectroscopic analysis and histochemical staining. Electron microscopy showed that the EGTA treatment also resulted in significantly fewer xylem cell layers with thickened secondary walls as well as in reducing the thickness of these secondary walls. The proteomic analysis showed 1065 differentially expressed proteins (DEPs) at the full-flowering stage (S4). By overlapping the Kyoto encyclopedia of genes and genomes (KEGG) and gene ontology (GO) analysis results, we identified 43 DEPs involved in signal transduction, transport, energy metabolism, carbohydrate metabolism, and secondary metabolite biosynthesis. Using quantitative real-time polymerase chain reaction (qRT-PCR) analysis, we showed that EGTA treatment inhibited Ca2+ sensors and secondary wall biosynthesis-related genes. Our findings revealed that EGTA treatment reduced the inflorescence stem mechanical strength by reducing lignin deposition in xylem cells through altering the expression of genes involved in Ca2+ binding and secondary wall biosynthesis.
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Affiliation(s)
- Yuhan Tang
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Daqiu Zhao
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Jiasong Meng
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Jun Tao
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009 Jiangsu China
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19
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The regulatory role of shikimate in plant phenylalanine metabolism. J Theor Biol 2018; 462:158-170. [PMID: 30412698 DOI: 10.1016/j.jtbi.2018.11.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Revised: 10/31/2018] [Accepted: 11/06/2018] [Indexed: 01/19/2023]
Abstract
In higher plants, the amino acid phenylalanine is a substrate of both primary and secondary metabolic pathways. The primary pathway that consumes phenylalanine, protein biosynthesis, is essential for the viability of all cells. Meanwhile, the secondary pathways are not necessary for the survival of individual cells, but benefit of the plant as a whole. Here we focus on the monolignol pathway, a secondary metabolic pathway in the cytosol that rapidly consumes phenylalanine to produce the precursors of lignin during wood formation. In planta monolignol biosynthesis involves a series of seemingly redundant steps wherein shikimate, a precursor of phenylalanine synthesized in the plastid, is transiently ligated to the main substrate of the pathway. However, shikimate is not catalytically involved in the reactions of the monolignol pathway, and is only needed for pathway enzymes to recognize their main substrates. After some steps the shikimate moiety is removed unaltered, and the main substrate continues along the pathway. It has been suggested that this portion of the monolignol pathway fulfills a regulatory role in the following way. Low phenylalanine concentrations (viz. availability) correlate with low shikimate concentrations. When shikimate concentratios are low, flux into the monolignol pathway will be limited by means of the steps requiring shikimate. Thus, when the concentration of phenylalanine is low it will be reserved for protein biosynthesis. Here we employ a theoretical approach to test this hypothesis. Simplified versions of plant phenylalanine metabolism are modelled as systems of ordinary differential equations. Our analysis shows that the seemingly redundant steps can be sufficient for the prioritization of protein biosynthesis over the monolignol pathway when the availability of phenylalanine is low, depending on system parameters. Thus, the phenylalanine precursor shikimate may signal low phenylalanine availability to secondary pathways. Because our models have been abstracted from plant phenylalanine metabolism, this mechanism of metabolic signalling, which we call the Precursor Shutoff Valve (PSV), may also be present in other biochemical networks comprised of two pathways that share a common substrate.
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Faraji M, Fonseca LL, Escamilla-Treviño L, Barros-Rios J, Engle NL, Yang ZK, Tschaplinski TJ, Dixon RA, Voit EO. A dynamic model of lignin biosynthesis in Brachypodium distachyon. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:253. [PMID: 30250505 PMCID: PMC6145374 DOI: 10.1186/s13068-018-1241-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/27/2018] [Indexed: 05/31/2023]
Abstract
BACKGROUND Lignin is a crucial molecule for terrestrial plants, as it offers structural support and permits the transport of water over long distances. The hardness of lignin reduces plant digestibility by cattle and sheep; it also makes inedible plant materials recalcitrant toward the enzymatic fermentation of cellulose, which is a potentially valuable substrate for sustainable biofuels. Targeted attempts to change the amount or composition of lignin in relevant plant species have been hampered by the fact that the lignin biosynthetic pathway is difficult to understand, because it uses several enzymes for the same substrates, is regulated in an ill-characterized manner, may operate in different locations within cells, and contains metabolic channels, which the plant may use to funnel initial substrates into specific monolignols. RESULTS We propose a dynamic mathematical model that integrates various datasets and other information regarding the lignin pathway in Brachypodium distachyon and permits explanations for some counterintuitive observations. The model predicts the lignin composition and label distribution in a BdPTAL knockdown strain, with results that are quite similar to experimental data. CONCLUSION Given the present scarcity of available data, the model resulting from our analysis is presumably not final. However, it offers proof of concept for how one may design integrative pathway models of this type, which are necessary tools for predicting the consequences of genomic or other alterations toward plants with lignin features that are more desirable than in their wild-type counterparts.
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Affiliation(s)
- Mojdeh Faraji
- The Wallace H. Coulter, Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 950 Atlantic Drive, Atlanta, GA 30332-2000 USA
- BioEnergy Sciences Center (BESC), Oak Ridge National Lab, Oak Ridge, TN USA
| | - Luis L. Fonseca
- The Wallace H. Coulter, Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 950 Atlantic Drive, Atlanta, GA 30332-2000 USA
- BioEnergy Sciences Center (BESC), Oak Ridge National Lab, Oak Ridge, TN USA
| | - Luis Escamilla-Treviño
- BioEnergy Sciences Center (BESC), Oak Ridge National Lab, Oak Ridge, TN USA
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX 76203-5017 USA
| | - Jaime Barros-Rios
- BioEnergy Sciences Center (BESC), Oak Ridge National Lab, Oak Ridge, TN USA
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX 76203-5017 USA
| | - Nancy L. Engle
- BioEnergy Sciences Center (BESC), Oak Ridge National Lab, Oak Ridge, TN USA
- Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831 USA
| | - Zamin K. Yang
- BioEnergy Sciences Center (BESC), Oak Ridge National Lab, Oak Ridge, TN USA
- Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831 USA
| | - Timothy J. Tschaplinski
- BioEnergy Sciences Center (BESC), Oak Ridge National Lab, Oak Ridge, TN USA
- Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831 USA
| | - Richard A. Dixon
- BioEnergy Sciences Center (BESC), Oak Ridge National Lab, Oak Ridge, TN USA
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX 76203-5017 USA
| | - Eberhard O. Voit
- The Wallace H. Coulter, Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 950 Atlantic Drive, Atlanta, GA 30332-2000 USA
- BioEnergy Sciences Center (BESC), Oak Ridge National Lab, Oak Ridge, TN USA
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Wang JP, Liu B, Sun Y, Chiang VL, Sederoff RR. Enzyme-Enzyme Interactions in Monolignol Biosynthesis. FRONTIERS IN PLANT SCIENCE 2018; 9:1942. [PMID: 30693007 PMCID: PMC6340093 DOI: 10.3389/fpls.2018.01942] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 12/13/2018] [Indexed: 05/18/2023]
Abstract
The enzymes that comprise the monolignol biosynthetic pathway have been studied intensively for more than half a century. A major interest has been the role of pathway in the biosynthesis of lignin and the role of lignin in the formation of wood. The pathway has been typically conceived as linear steps that convert phenylalanine into three major monolignols or as a network of enzymes in a metabolic grid. Potential interactions of enzymes have been investigated to test models of metabolic channeling or for higher order interactions. Evidence for enzymatic or physical interactions has been fragmentary and limited to a few enzymes studied in different species. Only recently the entire pathway has been studied comprehensively in any single plant species. Support for interactions comes from new studies of enzyme activity, co-immunoprecipitation, chemical crosslinking, bimolecular fluorescence complementation, yeast 2-hybrid functional screening, and cell type-specific gene expression based on light amplification by stimulated emission of radiation capture microdissection. The most extensive experiments have been done on differentiating xylem of Populus trichocarpa, where genomic, biochemical, chemical, and cellular experiments have been carried out. Interactions affect the rate, direction, and specificity of both 3 and 4-hydroxylation in the monolignol biosynthetic pathway. Three monolignol P450 mono-oxygenases form heterodimeric and heterotetrameric protein complexes that activate specific hydroxylation of cinnamic acid derivatives. Other interactions include regulatory kinetic control of 4-coumarate CoA ligases through subunit specificity and interactions between a cinnamyl alcohol dehydrogenase and a cinnamoyl-CoA reductase. Monolignol enzyme interactions with other pathway proteins have been associated with biotic and abiotic stress response. Evidence challenging or supporting metabolic channeling in this pathway will be discussed.
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Affiliation(s)
- Jack P. Wang
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Baoguang Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- Department of Forestry, Beihua University, Jilin, China
| | - Yi Sun
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Vincent L. Chiang
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Ronald R. Sederoff
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
- *Correspondence: Ronald R. Sederoff,
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