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Du Y, Zhao H, Feng N, Zheng D, Khan A, Zhou H, Deng P, Wang Y, Lu X, Jiang W. Alginate Oligosaccharides Alleviate Salt Stress in Rice Seedlings by Regulating Cell Wall Metabolism to Maintain Cell Wall Structure and Improve Lodging Resistance. PLANTS (BASEL, SWITZERLAND) 2024; 13:1215. [PMID: 38732430 PMCID: PMC11085217 DOI: 10.3390/plants13091215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 04/23/2024] [Accepted: 04/25/2024] [Indexed: 05/13/2024]
Abstract
Salt stress is one of the major abiotic stresses that damage the structure and composition of cell walls. Alginate oligosaccharides (AOS) have been advocated to significantly improve plant stress tolerance. The metabolic mechanism by which AOS induces salt tolerance in rice cell walls remains unclear. Here, we report the impact of AOS foliar application on the cell wall composition of rice seedlings using the salt-tolerant rice variety FL478 and the salt-sensitive variety IR29. Data revealed that salt stress decreased biomass, stem basal width, stem breaking strength, and lodging resistance; however, it increased cell wall thickness. In leaves, exogenous AOS up-regulated the expression level of OSCESA8, increased abscisic acid (ABA) and brassinosteroids (BR) content, and increased β-galacturonic activity, polygalacturonase activity, xylanase activity, laccase activity, biomass, and cellulose content. Moreover, AOS down-regulated the expression levels of OSMYB46 and OSIRX10 and decreased cell wall hemicellulose, pectin, and lignin content to maintain cell wall stability under salt stress. In stems, AOS increased phenylalamine ammonia-lyase and tyrosine ammonia-lyase activities, while decreasing cellulase, laccase, and β-glucanase activities. Furthermore, AOS improved the biomass and stem basal width and also enhanced the cellulose, pectin, and lignin content of the stem, As a result, increased resistance to stem breakage strength and alleviated salt stress-induced damage, thus enhancing the lodging resistance. Under salt stress, AOS regulates phytohormones and modifies cellulose, hemicellulose, lignin, and pectin metabolism to maintain cell wall structure and improve stem resistance to lodging. This study aims to alleviate salt stress damage to rice cell walls, enhance resistance to lodging, and improve salt tolerance in rice by exogenous application of AOS.
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Affiliation(s)
- Youwei Du
- College of Coastal Agriculture Sciences, Guangdong Ocean University, Zhanjiang 524088, China; (Y.D.); (H.Z.); (A.K.); (H.Z.); (P.D.); (Y.W.); (X.L.); (W.J.)
- South China Center of National Saline-Tolerant Rice Technology Innovation Center, Zhanjiang 524088, China
| | - Huimin Zhao
- College of Coastal Agriculture Sciences, Guangdong Ocean University, Zhanjiang 524088, China; (Y.D.); (H.Z.); (A.K.); (H.Z.); (P.D.); (Y.W.); (X.L.); (W.J.)
- South China Center of National Saline-Tolerant Rice Technology Innovation Center, Zhanjiang 524088, China
| | - Naijie Feng
- College of Coastal Agriculture Sciences, Guangdong Ocean University, Zhanjiang 524088, China; (Y.D.); (H.Z.); (A.K.); (H.Z.); (P.D.); (Y.W.); (X.L.); (W.J.)
- South China Center of National Saline-Tolerant Rice Technology Innovation Center, Zhanjiang 524088, China
- Shenzhen Research Institute of Guangdong Ocean University, Shenzhen 518108, China
| | - Dianfeng Zheng
- College of Coastal Agriculture Sciences, Guangdong Ocean University, Zhanjiang 524088, China; (Y.D.); (H.Z.); (A.K.); (H.Z.); (P.D.); (Y.W.); (X.L.); (W.J.)
- South China Center of National Saline-Tolerant Rice Technology Innovation Center, Zhanjiang 524088, China
- Shenzhen Research Institute of Guangdong Ocean University, Shenzhen 518108, China
| | - Aaqil Khan
- College of Coastal Agriculture Sciences, Guangdong Ocean University, Zhanjiang 524088, China; (Y.D.); (H.Z.); (A.K.); (H.Z.); (P.D.); (Y.W.); (X.L.); (W.J.)
| | - Hang Zhou
- College of Coastal Agriculture Sciences, Guangdong Ocean University, Zhanjiang 524088, China; (Y.D.); (H.Z.); (A.K.); (H.Z.); (P.D.); (Y.W.); (X.L.); (W.J.)
- South China Center of National Saline-Tolerant Rice Technology Innovation Center, Zhanjiang 524088, China
| | - Peng Deng
- College of Coastal Agriculture Sciences, Guangdong Ocean University, Zhanjiang 524088, China; (Y.D.); (H.Z.); (A.K.); (H.Z.); (P.D.); (Y.W.); (X.L.); (W.J.)
- South China Center of National Saline-Tolerant Rice Technology Innovation Center, Zhanjiang 524088, China
| | - Yaxing Wang
- College of Coastal Agriculture Sciences, Guangdong Ocean University, Zhanjiang 524088, China; (Y.D.); (H.Z.); (A.K.); (H.Z.); (P.D.); (Y.W.); (X.L.); (W.J.)
- South China Center of National Saline-Tolerant Rice Technology Innovation Center, Zhanjiang 524088, China
| | - Xutong Lu
- College of Coastal Agriculture Sciences, Guangdong Ocean University, Zhanjiang 524088, China; (Y.D.); (H.Z.); (A.K.); (H.Z.); (P.D.); (Y.W.); (X.L.); (W.J.)
- South China Center of National Saline-Tolerant Rice Technology Innovation Center, Zhanjiang 524088, China
| | - Wenxin Jiang
- College of Coastal Agriculture Sciences, Guangdong Ocean University, Zhanjiang 524088, China; (Y.D.); (H.Z.); (A.K.); (H.Z.); (P.D.); (Y.W.); (X.L.); (W.J.)
- South China Center of National Saline-Tolerant Rice Technology Innovation Center, Zhanjiang 524088, China
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Ma R, Zhang M, Yang X, Guo J, Fan Y. Transcriptome analysis reveals genes related to the synthesis and metabolism of cell wall polysaccharides in goji berry (Lycium barbarum L.) from various regions. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2023; 103:7050-7060. [PMID: 37340801 DOI: 10.1002/jsfa.12791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 06/06/2023] [Accepted: 06/14/2023] [Indexed: 06/22/2023]
Abstract
BACKGROUND In goji berries (Lycium barbarum L.), the cell wall properties and ripening environment affect fruit quality and their economic benefits. However, the mechanism underlying the cell wall remains to be fully elucidated. RESULTS The results showed that total sugar content was higher in Qinghai berries (13.87%, P < 0.01), whereas cellulose content peaked in Zhongning berries (28%, P < 0.05). Arabinose, galactose, and galacturonic acid were the principal components of the cell wall polysaccharides in goji berries. Among them, the content of galactose in Zhongning was significantly the highest (P < 0.05). Interestingly, we found that highly expressed β-glucosidase and lowly expressed endoglucanase led to cellulose accumulation by RNA-sequencing analysis. The expression analysis results suggested that pectate lyase and pectinesterase enzymes could be major factors related to higher galactose and galacturonic acid contents in Zhongning compared to in Qinghai and Gansu. The starch and sucrose metabolism pathway, pentose and glucuronate interconversions pathway, and galactose metabolism pathway played a significant role in cell wall polysaccharide synthesis and metabolism. CONCLUSION In the present study, we aimed to provide some insights into the cell wall on polysaccharide composition, structural features, and gene analysis in goji berries from Zhongning, Qinghai, and Gansu in China. These results might help to clarify the molecular function of the major genes in the cell wall polysaccharides of goji berries and provide a solid foundation for further study. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Ruixue Ma
- School of Food Science and Engineering, Ningxia University, Yinchuan, China
| | - Meng Zhang
- School of Food Science and Engineering, Ningxia University, Yinchuan, China
| | - Xiaohua Yang
- School of Food Science and Engineering, Ningxia University, Yinchuan, China
| | - Jia Guo
- School of Food Science and Engineering, Ningxia University, Yinchuan, China
| | - Yanli Fan
- School of Food Science and Engineering, Ningxia University, Yinchuan, China
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Song F, Li Z, Wang C, Jiang Y, Wang Z, He L, Ma X, Zhang Y, Song X, Liu J, Wu L. CsMYB15 positively regulates Cs4CL2-mediated lignin biosynthesis during juice sac granulation in navel orange. FRONTIERS IN PLANT SCIENCE 2023; 14:1223820. [PMID: 37457356 PMCID: PMC10348809 DOI: 10.3389/fpls.2023.1223820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 06/19/2023] [Indexed: 07/18/2023]
Abstract
'Lane Late', a late-maturing navel orange cultivar, is mainly distributed in the Three Gorges Reservoir area, which matures in the late March of the next year and needs overwintering cultivation. Citrus fruit granulation is a physiological disorder, which is characterized by lignification and dehydration of juice sac cells, seriously affecting the commercial value of citrus fruits. The pre-harvest granulation of late-maturing navel orange is main caused by low temperature in the winter, but its mechanism and regulation pattern remain unclear. In this study, a SG2-type R2R3-MYB transcription factor, CsMYB15, was identified from Citrus sinensis, which was significantly induced by both juice sac granulation and low temperature treatment. Subcellular localization analysis and transcriptional activation assay revealed that CsMYB15 protein was localized to the nucleus, and it exhibited transcriptional activation activity in yeast. Over-expression of CsMYB15 by stable transformation in navel orange calli and transient transformation in kumquat fruits and navel orange juice sacs significantly increased lignin content in the transgenic lines. Further, Yeast one hybrid, EMSA, and LUC assays demonstrated that CsMYB15 directly bound to the Cs4CL2 promoter and activated its expression, thereby causing a high accumulation of lignin in citrus. Taken together, these results elucidated the biological function of CsMYB15 in regulating Cs4CL2-mediated lignin biosynthesis, and provided novel insight into the transcriptional regulation mechanism underlying the juice sac granulation of late-maturing navel orange.
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Affiliation(s)
- Fang Song
- Hubei Key Laboratory of Germplasm Innovation and Utilization of Fruit Trees, Institute of Fruit and Tea, Hubei Academy of Agricultural Science, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Zixuan Li
- Hubei Key Laboratory of Germplasm Innovation and Utilization of Fruit Trees, Institute of Fruit and Tea, Hubei Academy of Agricultural Science, Wuhan, China
| | - Ce Wang
- Hubei Key Laboratory of Germplasm Innovation and Utilization of Fruit Trees, Institute of Fruit and Tea, Hubei Academy of Agricultural Science, Wuhan, China
| | - Yingchun Jiang
- Hubei Key Laboratory of Germplasm Innovation and Utilization of Fruit Trees, Institute of Fruit and Tea, Hubei Academy of Agricultural Science, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Zhijing Wang
- Hubei Key Laboratory of Germplasm Innovation and Utilization of Fruit Trees, Institute of Fruit and Tea, Hubei Academy of Agricultural Science, Wuhan, China
| | - Ligang He
- Hubei Key Laboratory of Germplasm Innovation and Utilization of Fruit Trees, Institute of Fruit and Tea, Hubei Academy of Agricultural Science, Wuhan, China
| | - Xiaofang Ma
- Hubei Key Laboratory of Germplasm Innovation and Utilization of Fruit Trees, Institute of Fruit and Tea, Hubei Academy of Agricultural Science, Wuhan, China
| | - Yu Zhang
- Hubei Key Laboratory of Germplasm Innovation and Utilization of Fruit Trees, Institute of Fruit and Tea, Hubei Academy of Agricultural Science, Wuhan, China
| | - Xin Song
- Hubei Key Laboratory of Germplasm Innovation and Utilization of Fruit Trees, Institute of Fruit and Tea, Hubei Academy of Agricultural Science, Wuhan, China
| | - Jihong Liu
- Hubei Hongshan Laboratory, Wuhan, China
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Liming Wu
- Hubei Key Laboratory of Germplasm Innovation and Utilization of Fruit Trees, Institute of Fruit and Tea, Hubei Academy of Agricultural Science, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
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Shen Q, Weng Y. Alternative Splicing of NAC Transcription Factor Gene CmNST1 Is Associated with Naked Seed Mutation in Pumpkin, Cucurbita moschata. Genes (Basel) 2023; 14:genes14050962. [PMID: 37239322 DOI: 10.3390/genes14050962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 04/16/2023] [Accepted: 04/21/2023] [Indexed: 05/28/2023] Open
Abstract
In pumpkin (Cucurbita moschata), the naked or hull-less seed phenotype has great benefits for breeding this crop for oil or snack use. We previously identified a naked seed mutant in this crop. In this study, we report genetic mapping, identification, and characterization of a candidate gene for this mutation. We showed that the naked seed phenotype is controlled by a single recessive gene (N). The bulked segregant analysis identified a 2.4 Mb region on Chromosome 17 with 15 predicted genes. Multiple lines of evidence suggested that CmoCh17G004790 is the most probable candidate gene for the N locus which encodes a NAC transcription factor WALL THICKENING PROMOTING FACTOR 1 (CmNST1). No nucleotide polymorphism or structural variation was found in the genomic DNA sequences of CmNST1 between the mutant and the wildtype inbred line (hulled seed). However, the cDNA sequence cloned from developing seed coat samples of the naked seed mutant was 112 bp shorter than that from the wildtype which is due to seed coat-specific alternative splicing in the second exon of the mutant CmNST1 transcript. The expression level of CmNST1 in the developing seed coat was higher in the mutant than in the wildtype during early seed coat development which was reversed later. Transcriptomic profiling with RNA-Seq at different stages of seed development in the mutant and wildtype revealed a critical role of CmNST1 as a master regulator for the lignin biosynthesis pathway during seed coat development while other NAC and MYB transcription factors were also involved in forming a regulatory network for the building of secondary cell walls. This work provides a novel mechanism for the well-characterized NST1 transcription factor gene in regulating secondary cell wall development. The cloned gene also provides a useful tool for marker-assisted breeding of hull-less C. moschata varieties.
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Affiliation(s)
- Qiong Shen
- College of Horticulture, Shanxi Agricultural University, Taiyuan 030031, China
| | - Yiqun Weng
- USDA-ARS Vegetable Crops Research Unit, Horticulture Department, University of Wisconsin, Madison, WI 53706, USA
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Li F, Zhang Y, Tian C, Wang X, Zhou L, Jiang J, Wang L, Chen F, Chen S. Molecular module of CmMYB15-like-Cm4CL2 regulating lignin biosynthesis of chrysanthemum (Chrysanthemum morifolium) in response to aphid (Macrosiphoniella sanborni) feeding. THE NEW PHYTOLOGIST 2023; 237:1776-1793. [PMID: 36444553 DOI: 10.1111/nph.18643] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 11/23/2022] [Indexed: 05/22/2023]
Abstract
Lignin is a major component of plant cell walls and a conserved basic defense mechanism in higher plants deposited in response to aphid infection. However, the molecular mechanisms of lignin biosynthesis in response to aphid infection and the effect of lignin on aphid feeding behavior remain unclear. We report that 4-Coumarate:coenzyme A ligase 2 (Cm4CL2), a gene encoding a key enzyme in the lignin biosynthesis pathway, is induced by aphid feeding, resulting in lignin deposition and reduced aphid attack. Upstream regulator analysis showed that the expression of Cm4CL2 in response to aphid feeding was directly upregulated by CmMYB15-like, an SG2-type R2R3-MYB transcription factor. CmMYB15-like binds directly to the AC cis-element in the promoter region of Cm4CL2. Genetic validation demonstrated that CmMYB15-like was induced by aphid infection and contributed to lignin deposition and cell wall thickening, which consequently enhanced aphid resistance in a Cm4CL2-dependent manner. This study is the first to show that the CmMYB15-like-Cm4CL2 module regulates lignin biosynthesis in response to aphid feeding.
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Affiliation(s)
- Fei Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement / Key Laboratory of Flower Biology and Germplasm Innovation, Ministry of Agriculture and Rural Affairs / Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration / College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yi Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement / Key Laboratory of Flower Biology and Germplasm Innovation, Ministry of Agriculture and Rural Affairs / Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration / College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chang Tian
- State Key Laboratory of Crop Genetics and Germplasm Enhancement / Key Laboratory of Flower Biology and Germplasm Innovation, Ministry of Agriculture and Rural Affairs / Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration / College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xinhui Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement / Key Laboratory of Flower Biology and Germplasm Innovation, Ministry of Agriculture and Rural Affairs / Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration / College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Lijie Zhou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement / Key Laboratory of Flower Biology and Germplasm Innovation, Ministry of Agriculture and Rural Affairs / Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration / College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiafu Jiang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement / Key Laboratory of Flower Biology and Germplasm Innovation, Ministry of Agriculture and Rural Affairs / Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration / College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - LiKai Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement / Key Laboratory of Flower Biology and Germplasm Innovation, Ministry of Agriculture and Rural Affairs / Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration / College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Fadi Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement / Key Laboratory of Flower Biology and Germplasm Innovation, Ministry of Agriculture and Rural Affairs / Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration / College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Sumei Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement / Key Laboratory of Flower Biology and Germplasm Innovation, Ministry of Agriculture and Rural Affairs / Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration / College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
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Kong Y, Wang G, Tang H, Yang J, Yang Y, Wang J, Li G, Li Y, Yuan J. Multi-omics analysis provides insight into the phytotoxicity of chicken manure and cornstalk on seed germination. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 861:160611. [PMID: 36460104 DOI: 10.1016/j.scitotenv.2022.160611] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/21/2022] [Accepted: 11/27/2022] [Indexed: 06/17/2023]
Abstract
To minimize environmental risks and the phytotoxic influence of organic materials on crop growth, it is necessary to test their phytotoxicity and maturity when they were used in farmland. However, the stress response of seed germination to chicken manure and cornstalks is not clear. This study used multi-omics analysis to investigate the inhibition mechanism of seed germination by chicken manure and cornstalk. Chicken manure caused destructive inhibition of seed germination with higher phytotoxicity (GI = 0). Cornstalk also had a low GI (8.81 %), while it mainly inhibited radicle growth (RL = 9.39 %) rather than seed germination (GR = 93.33 %). The response of radish seed germination to chicken manure and cornstalk phytotoxic stresses was accompanied by metabolic adjustments of storage substance accumulation, antioxidant enzyme activity change, phytohormone induction, and expression of specific proteins and gene regulation. Combined transcriptomic and proteomic analysis revealed that differential expression of 13,090 (5944 upregulated/7146 downregulated) and 3850 (2389 upregulated/1461 downregulated) genes (DEGs), and 1041 (82 upregulated/932 downregulated) and 575 (111 upregulated/464 downregulated) proteins (DEPs) at chicken manure and cornstalk treatment, respectively. Most down-regulated genes and proteins were involved in phenylpropanoid biosynthesis under chicken manure stress, which caused irreversible inhibition of seed germination. Down-regulation of phytohormone signal transduction-related genes under cornstalk stress resulted in inhibition of radicle growth, but the inhibitory stress was restorable. These findings provide new insight into the phytotoxicity of livestock manure and cornstalk on seed germination.
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Affiliation(s)
- Yilin Kong
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Science, China Agricultural University, Beijing 100193, China
| | - Guoying Wang
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Science, China Agricultural University, Beijing 100193, China
| | - Huan Tang
- Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Jia Yang
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Science, China Agricultural University, Beijing 100193, China
| | - Yan Yang
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Science, China Agricultural University, Beijing 100193, China
| | - Jiani Wang
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Science, China Agricultural University, Beijing 100193, China
| | - Guoxue Li
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Science, China Agricultural University, Beijing 100193, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, Suzhou 215128, China
| | - Yun Li
- College of Resources and Environmental Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Jing Yuan
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Science, China Agricultural University, Beijing 100193, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, Suzhou 215128, China.
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Sodium silicate accelerates the deposition of lignin and silicon by activating the biosynthesis of lignin monolignols and increasing the relative silicon content in muskmelon wounds. Lebensm Wiss Technol 2023. [DOI: 10.1016/j.lwt.2023.114605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
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Choi SJ, Lee Z, Kim S, Jeong E, Shim JS. Modulation of lignin biosynthesis for drought tolerance in plants. FRONTIERS IN PLANT SCIENCE 2023; 14:1116426. [PMID: 37152118 PMCID: PMC10157170 DOI: 10.3389/fpls.2023.1116426] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 04/06/2023] [Indexed: 05/09/2023]
Abstract
Lignin is a complex polymer that is embedded in plant cell walls to provide physical support and water protection. For these reasons, the production of lignin is closely linked with plant adaptation to terrestrial regions. In response to developmental cues and external environmental conditions, plants use an elaborate regulatory network to determine the timing and location of lignin biosynthesis. In this review, we summarize the canonical lignin biosynthetic pathway and transcriptional regulatory network of lignin biosynthesis, consisting of NAC and MYB transcription factors, to explain how plants regulate lignin deposition under drought stress. Moreover, we discuss how the transcriptional network can be applied to the development of drought tolerant plants.
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Liu Z, Deng B, Yuan H, Zhang B, Liu J, Meng J, Chang M. Transcription factor FfMYB15 regulates the expression of cellulase gene FfCEL6B during mycelial growth of Flammulina filiformis. Microb Cell Fact 2022; 21:216. [PMID: 36253826 PMCID: PMC9578197 DOI: 10.1186/s12934-022-01932-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 09/25/2022] [Indexed: 11/10/2022] Open
Abstract
Background Cellulose degradation can determine mycelial growth rate and affect yield during the growth of Flammulina filiformis. The degradation of cellulose requires the joint action of a variety of cellulases, and some cellulase-related genes have been detected in mushrooms. However, little is known about the transcriptional regulatory mechanisms of cellulose degradation. Results In this study, FfMYB15 that may regulate the expression of cellulase gene FfCEL6B in F. filiformis was identified. RNA interference (RNAi) showed that FfCEL6B positively regulated mycelial growth. Gene expression analyses indicated that the expression patterns of FfCEL6B and FfMYB15 in mycelia cultured on the 0.9% cellulose medium for different times were similar with a correlation coefficient of 0.953. Subcellular localization and transcriptional activity analyses implied that FfMYB15 was located in the nucleus and was a transcriptional activator. Electrophoretic mobility shift assay (EMSA) and dual-luciferase assays demonstrated that FfMYB15 could bind and activate FfCEL6B promoter by recognizing MYB cis-acting element. Conclusions This study indicated that FfCEL6B played an active role in mycelial growth of F. filiformis and was regulated by FfMYB15. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01932-z.
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Affiliation(s)
- Zongqi Liu
- College of Food Science and Engineering, Shanxi Agricultural University, 1 Mingxian South Road, Taigu, 030801, Shanxi Province, China
| | - Bing Deng
- College of Food Science and Engineering, Shanxi Agricultural University, 1 Mingxian South Road, Taigu, 030801, Shanxi Province, China.,Shanxi Key Laboratory of Edible Fungi for Loess Plateau, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Hui Yuan
- College of Food Science and Engineering, Shanxi Agricultural University, 1 Mingxian South Road, Taigu, 030801, Shanxi Province, China
| | - Benfeng Zhang
- College of Food Science and Engineering, Shanxi Agricultural University, 1 Mingxian South Road, Taigu, 030801, Shanxi Province, China
| | - Jingyu Liu
- College of Food Science and Engineering, Shanxi Agricultural University, 1 Mingxian South Road, Taigu, 030801, Shanxi Province, China.,Shanxi Key Laboratory of Edible Fungi for Loess Plateau, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Junlong Meng
- College of Food Science and Engineering, Shanxi Agricultural University, 1 Mingxian South Road, Taigu, 030801, Shanxi Province, China.,Collaborative Innovation Center of Advancing Quality and Efficiency of Loess Plateau Edible Fungi, Taigu, 030801, Shanxi, China
| | - Mingchang Chang
- College of Food Science and Engineering, Shanxi Agricultural University, 1 Mingxian South Road, Taigu, 030801, Shanxi Province, China. .,Collaborative Innovation Center of Advancing Quality and Efficiency of Loess Plateau Edible Fungi, Taigu, 030801, Shanxi, China.
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The Regulation of Xylem Development by Transcription Factors and Their Upstream MicroRNAs. Int J Mol Sci 2022; 23:ijms231710134. [PMID: 36077531 PMCID: PMC9456210 DOI: 10.3390/ijms231710134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 08/27/2022] [Accepted: 09/01/2022] [Indexed: 11/16/2022] Open
Abstract
Xylem, as a unique organizational structure of vascular plants, bears water transport and supports functions necessary for plant survival. Notably, secondary xylem in the stem (i.e., wood) also has important economic and ecological value. In view of this, the regulation of xylem development has been widely concerned. In recent years, studies on model plants Arabidopsis and poplar have shown that transcription factors play important regulatory roles in various processes of xylem development, including the directional differentiation of procambium and cambium into xylem, xylem arrangement patterns, secondary cell wall formation and programmed cell death. This review focuses on the regulatory roles of widely and thoroughly studied HD-ZIP, MYB and NAC transcription factor gene families in xylem development, and it also pays attention to the regulation of their upstream microRNAs. In addition, the existing questions in the research and future research directions are prospected.
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Zhang Y, Shan X, Zhao Q, Shi F. The MicroRNA397a-LACCASE17 module regulates lignin biosynthesis in Medicago ruthenica (L.). FRONTIERS IN PLANT SCIENCE 2022; 13:978515. [PMID: 36061772 PMCID: PMC9434696 DOI: 10.3389/fpls.2022.978515] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 07/28/2022] [Indexed: 06/15/2023]
Abstract
Mechanical strength is essential for the upright growth habit, which is one of the most important characteristics of terrestrial plants. Lignin, a phenylpropanoid-derived polymer mainly present in secondary cell walls plays critical role in providing mechanical support. Here, we report that the prostrate-stem cultivar of the legume forage Medicago ruthenica cultivar 'Mengnong No. 1' shows compromised mechanical strength compared with the erect-stem cultivar 'Zhilixing'. The erect-stem cultivar, 'Zhilixing' has significantly higher lignin content, leading to higher mechanical strength than the prostrate-stem cultivar. The low abundance of miRNA397a in the Zhiixing cultivar causes reduced cleavage of MrLAC17 transcript, which results in enhanced expression level of MrLAC17 compared to that in the prostrate-stem cultivar Mengnong No. 1. Complementation of the Arabidopsis lac4 lac17 double mutants with MrLAC17 restored the lignin content to wild-type levels, confirming that MrLAC17 perform an exchangeable role with Arabidopsis laccases. LAC17-mediated lignin polymerization is therefore increased in the 'Zhilixing', causing the erect stem phenotype. Our data reveal the importance of the miR397a in the lignin biosynthesis and suggest a strategy for molecular breeding targeting plant architecture in legume forage.
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Affiliation(s)
- Yutong Zhang
- Key Laboratory of Forage Cultivation, Processing and High Efficient Utilization of the Ministry of Agriculture and Key Laboratory of Grassland Resources of the Ministry of Education, College of Grassland Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
| | - Xiaotong Shan
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Qiao Zhao
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Fengling Shi
- Key Laboratory of Forage Cultivation, Processing and High Efficient Utilization of the Ministry of Agriculture and Key Laboratory of Grassland Resources of the Ministry of Education, College of Grassland Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
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Sezen UU, Worthy SJ, Umaña MN, Davies SJ, McMahon SM, Swenson NG. Comparative transcriptomics of tropical woody plants supports fast and furious strategy along the leaf economics spectrum in lianas. Biol Open 2022; 11:276072. [PMID: 35876379 PMCID: PMC9346291 DOI: 10.1242/bio.059184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 05/19/2022] [Indexed: 12/03/2022] Open
Abstract
Lianas, climbing woody plants, influence the structure and function of tropical forests. Climbing traits have evolved multiple times, including ancestral groups such as gymnosperms and pteridophytes, but the genetic basis of the liana strategy is largely unknown. Here, we use a comparative transcriptomic approach for 47 tropical plant species, including ten lianas of diverse taxonomic origins, to identify genes that are consistently expressed or downregulated only in lianas. Our comparative analysis of full-length transcripts enabled the identification of a core interactomic network common to lianas. Sets of transcripts identified from our analysis reveal features related to functional traits pertinent to leaf economics spectrum in lianas, include upregulation of genes controlling epidermal cuticular properties, cell wall remodeling, carbon concentrating mechanism, cell cycle progression, DNA repair and a large suit of downregulated transcription factors and enzymes involved in ABA-mediated stress response as well as lignin and suberin synthesis. All together, these genes are known to be significant in shaping plant morphologies through responses such as gravitropism, phyllotaxy and shade avoidance. Summary: The full-length fraction of liana transcriptomes mapped on a protein–protein interactome revealed the nature of their convergence through distinct sets of expressed and downregulated genes not observed in free-standing plants.
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Affiliation(s)
- U Uzay Sezen
- Smithsonian Environmental Research Center, 647 Contees Wharf Rd, Edgewater, MD, 21037, USA
| | - Samantha J Worthy
- Department of Evolution and Ecology, University of California, Davis, CA, 95616USA
| | - Maria N Umaña
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Stuart J Davies
- Forest Global Earth Observatory, Smithsonian Tropical Research Institute, Gamboa, Panama.,Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington DC, 20560, USA
| | - Sean M McMahon
- Smithsonian Environmental Research Center, 647 Contees Wharf Rd, Edgewater, MD, 21037, USA
| | - Nathan G Swenson
- Department of Evolution and Ecology, University of California, Davis, CA, 95616USA.,Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
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Liu Z, Gao S, Zhang H, Xu Z, Qian W. Genome-Wide Association Study Reveals That PvGUX1_1 Is Associated with Pod Stringlessness in Snap Bean (Phaseolus vulgaris L.). BIOLOGY 2022; 11:biology11040611. [PMID: 35453811 PMCID: PMC9024788 DOI: 10.3390/biology11040611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 04/10/2022] [Accepted: 04/12/2022] [Indexed: 11/16/2022]
Abstract
Simple Summary Using 138 snap bean accessions as plant materials, we investigated their suture strings across two years. With the goal of identifying the gene(s) responsible for the formation of suture strings, we conducted a genome-wide association study. A strong association signal was found in a 266.19 kb region on Chr02. Within the region, 23 candidate genes were identified. Importantly, the sequence and gene expression of PvGUX1_1 differed significantly between sutured pods and non-sutured pods. In addition, PvGUX1_1 was also a domesticated locus that diverged from PvGUX1_2 during an early stage. The results obtained in this study can provide important information for the improvement of pod quality in snap beans. Abstract Suture strings are a particularly important pod trait that determine the quality and texture of snap beans (Phaseolus vulgaris L.). The St locus on chromosome 2 has been described as a major locus associated with suture strings. However, the gene and genetic basis underlying this locus remain unknown. Here, we investigated the suture strings of 138 snap bean accessions across two years. A total of 3.66 million single-nucleotide polymorphisms (SNPs) were obtained by deep resequencing. Based on these SNPs, we identified a strong association signal on Chr02 and a promising candidate gene, PvGUX1_1. Further analysis revealed that the 2 bp deletion in the exon of PvGUX1_1 was significantly associated with stringlessness. Comparative mapping indicated that PvGUX1_1 was a domesticated locus and diverged from PvGUX1_2 during an early stage. Our study provides important insights into the genetic mechanism of suture string formation and useful information for snap bean improvement.
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Chen P, Li R, Zhu L, Hao Q, Yao S, Liu J, Ji K. Characterization and Interaction Analysis of the Secondary Cell Wall Synthesis-Related Transcription Factor PmMYB7 in Pinus massoniana Lamb. Int J Mol Sci 2022; 23:ijms23042079. [PMID: 35216196 PMCID: PMC8877852 DOI: 10.3390/ijms23042079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/02/2022] [Accepted: 02/07/2022] [Indexed: 02/01/2023] Open
Abstract
In vascular plants, the importance of R2R3-myeloblastosis (R2R3-MYB) transcription factors (TFs) in the formation of secondary cell walls (SCWs) has long been a controversial topic due to the lack of empirical evidence of an association between TFs and downstream target genes. Here, we found that the transcription factor PmMYB7, which belongs to the R2R3-MYB subfamily, is involved in lignin biosynthesis in Pinus massoniana. PmMYB7 was highly expressed in lignified tissues and upon abiotic stress. As a bait carrier, the PmMYB7 protein had no toxicity or autoactivation in the nucleus. Forty-seven proteins were screened from the P. massoniana yeast library. These proteins were predicted to be mainly involved in resistance, abiotic stress, cell wall biosynthesis, and cell development. We found that the PmMYB7 protein interacted with caffeoyl CoA 3-O-methyltransferase-2 (PmCCoAOMT2)—which is involved in lignin biosynthesis—but not with beta-1, 2-xylosyltransferase (PmXYXT1) yeast two-hybrid (Y2H) studies. Our in vivo coimmunoprecipitation (Co-IP) assay further showed that the PmMYB7 and PmCCoAOMT2 proteins could interact. Therefore, we concluded that PmMYB7 is an upstream TF that can interact with PmCCoAOMT2 in plant cells. These findings lay a foundation for further research on the function of PmMYB7, lignin biosynthesis and molecular breeding in P. massoniana.
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Nookaraju A, Pandey SK, Ahlawat YK, Joshi CP. Understanding the Modus Operandi of Class II KNOX Transcription Factors in Secondary Cell Wall Biosynthesis. PLANTS (BASEL, SWITZERLAND) 2022; 11:493. [PMID: 35214825 PMCID: PMC8880547 DOI: 10.3390/plants11040493] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/27/2022] [Accepted: 02/07/2022] [Indexed: 06/14/2023]
Abstract
Lignocellulosic biomass from the secondary cell walls of plants has a veritable potential to provide some of the most appropriate raw materials for producing second-generation biofuels. Therefore, we must first understand how plants synthesize these complex secondary cell walls that consist of cellulose, hemicellulose, and lignin in order to deconstruct them later on into simple sugars to produce bioethanol via fermentation. Knotted-like homeobox (KNOX) genes encode homeodomain-containing transcription factors (TFs) that modulate various important developmental processes in plants. While Class I KNOX TF genes are mainly expressed in the shoot apical meristems of both monocot and eudicot plants and are involved in meristem maintenance and/or formation, Class II KNOXTF genes exhibit diverse expression patterns and their precise functions have mostly remained unknown, until recently. The expression patterns of Class II KNOX TF genes in Arabidopsis, namely KNAT3, KNAT4, KNAT5, and KNAT7, suggest that TFs encoded by at least some of these genes, such as KNAT7 and KNAT3, may play a significant role in secondary cell wall formation. Specifically, the expression of the KNAT7 gene is regulated by upstream TFs, such as SND1 and MYB46, while KNAT7 interacts with other cell wall proteins, such as KNAT3, MYB75, OFPs, and BLHs, to regulate secondary cell wall formation. Moreover, KNAT7 directly regulates the expression of some xylan synthesis genes. In this review, we summarize the current mechanistic understanding of the roles of Class II KNOX TFs in secondary cell wall formation. Recent success with the genetic manipulation of Class II KNOX TFs suggests that this may be one of the biotechnological strategies to improve plant feedstocks for bioethanol production.
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Affiliation(s)
- Akula Nookaraju
- Department of Biological Sciences, Michigan Technological University, Houghton, MI 49931, USA; (A.N.); (S.K.P.); (Y.K.A.)
- Kaveri Seed Company Limited, Secunderabad 500003, Telangana, India
| | - Shashank K. Pandey
- Department of Biological Sciences, Michigan Technological University, Houghton, MI 49931, USA; (A.N.); (S.K.P.); (Y.K.A.)
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 87 Umeå, Sweden
| | - Yogesh K. Ahlawat
- Department of Biological Sciences, Michigan Technological University, Houghton, MI 49931, USA; (A.N.); (S.K.P.); (Y.K.A.)
- Department of Horticultural Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Chandrashekhar P. Joshi
- Department of Biological Sciences, Michigan Technological University, Houghton, MI 49931, USA; (A.N.); (S.K.P.); (Y.K.A.)
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Shi J, Yan X, Sun T, Shen Y, Shi Q, Wang W, Bao M, Luo H, Nian F, Ning G. Homeostatic regulation of flavonoid and lignin biosynthesis in phenylpropanoid pathway of transgenic tobacco. Gene 2022; 809:146017. [PMID: 34655725 DOI: 10.1016/j.gene.2021.146017] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 05/16/2021] [Accepted: 10/11/2021] [Indexed: 11/04/2022]
Abstract
Flavonoids and lignin consist of a large number of secondarymetabolites which are derived from the phenylpropanoid pathway, and they act as a significant role in plant growth, development, and stress response. However, few reports have documented that how different subbranches of phenylpropanoid metablolic pathway mutually interact. In Arabidopsis, AtCPC (AtCAPRICE) is known to play a negative role in anthocyanin accumulation. Nonetheless, whether AtCPC could control the biosynthesis of lignin is largely unknown. Additionally, whether the RrFLS and RrANR, flavonol synthase and anthocyanidin reductase, from Rosa rugosa regulate different branches of phenylpropanoid pathway is unclear. Here, we performed a series of transgenic experiments with short life cycle tobacco and RNA-Seq analysis. Finally, a series of assays related to biological, physiological, and phenotypic characteristics were undertaken. Our results indicated that ectopic expression of AtCPC in tobacco not only decreased the flavonoid compound accumulation, but also up-regulated several lignin biosynthetic genes, and significantly increased the accumulation of lignin. Our results also revealed that although they respectively improved the flavonol and proanthocyanidin contents, the overexpression of RrFLS and RrANR plays positive roles in lignin biosynthesis in transgenic tobacco plants. Our findings provide a novel insight into the mechanism underlying homeostatic regulation of flavonoid and lignin biosynthesis in phenylpropanoid pathway of plants.
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Affiliation(s)
- Jiewei Shi
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Xu Yan
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Tingting Sun
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuxiao Shen
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Qi Shi
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Wenen Wang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Manzhu Bao
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Hong Luo
- Department of Genetics and Biochemistry, Clemson University, 110 Biosystems Research Complex, Clemson, SC 29634-0318, USA
| | - Fuzhao Nian
- College of Tobacco Science, Yunnan Agricultural University, No.452, Fengyuan Road, Kunming, China.
| | - Guogui Ning
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China.
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Kim MH, Cho JS, Bae EK, Choi YI, Eom SH, Lim YJ, Lee H, Park EJ, Ko JH. PtrMYB120 functions as a positive regulator of both anthocyanin and lignin biosynthetic pathway in a hybrid poplar. TREE PHYSIOLOGY 2021; 41:2409-2423. [PMID: 34100089 DOI: 10.1093/treephys/tpab082] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 06/01/2021] [Indexed: 06/12/2023]
Abstract
Both anthocyanins and lignins are essential secondary metabolites in plant growth and development. Their biosynthesis is metabolically interconnected and diverges in the central metabolite 4-coumaroyl CoA of the phenylpropanoid pathway. Considerable progress has been made in understanding transcriptional regulation of genes involved in lignin and anthocyanin synthesis pathways, but the concerted regulation of these pathways is not yet fully understood. Here, we functionally characterized PtrMYB120, a R2R3-MYB transcription factor from Populus trichocarpa. Overexpression of PtrMYB120 in a hybrid poplar (i.e., 35S::PtrMYB120) was associated with increased anthocyanin (i.e., cyanidin 3-O-glucoside) accumulation and upregulation of anthocyanin biosynthetic genes. However, transgenic poplars with dominant suppression of PtrMYB120 function achieved by fusing the ERF-associated amphiphilic repression motif to PtrMYB120 (i.e., 35S::PtrMYB120-SRDX) had a dramatic decrease in not only anthocyanin but also Klason lignin content with downregulation of both anthocyanin and lignin biosynthetic genes. Indeed, 35S::PtrMYB120-SRDX poplars had irregularly shaped xylem vessels with reduced S-lignin content in stems, which was proportionally related to the level of the introduced PtrMYB120-SRDX gene. Furthermore, protoplast-based transcriptional activation assay using the PtrMYB120-GR system suggested that PtrMYB120 directly regulates genes involved in both anthocyanin and lignin biosynthesis, including chalcone synthase and ferulate-5 hydroxylase. Interestingly, the saccharification efficiency of line #6 of 35S::PtrMYB120-SRDX poplars, which had slightly reduced lignin content with a normal growth phenotype, was dramatically enhanced (>45%) by NaOH treatment. Taken together, our results suggest that PtrMYB120 functions as a positive regulator of both anthocyanin and lignin biosynthetic pathways and can be targeted to enhance saccharification efficiency in woody perennials.
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Affiliation(s)
- Min-Ha Kim
- Department of Plant & Environmental New Resources, Kyung Hee University, 1732 Deogyeong-daero, Yongin 17104, Republic of Korea
| | - Jin-Seong Cho
- Department of Plant & Environmental New Resources, Kyung Hee University, 1732 Deogyeong-daero, Yongin 17104, Republic of Korea
- Abio materials Co., Ltd., 7-44 Jamsil-gil, Cheonan 31005, Republic of Korea
| | - Eun-Kyung Bae
- Division of Forest Biotechnology, National Institute of Forest Science, 39 Onjeong-ro, Suwon 16631, Republic of Korea
| | - Young-Im Choi
- Division of Forest Biotechnology, National Institute of Forest Science, 39 Onjeong-ro, Suwon 16631, Republic of Korea
| | - Seok Hyun Eom
- Department of Horticultural Biotechnology, 1732 Deogyeong-daero, Yongin 17104, Republic of Korea
| | - You Jin Lim
- Department of Horticultural Biotechnology, 1732 Deogyeong-daero, Yongin 17104, Republic of Korea
| | - Hyoshin Lee
- Department of Horticultural Biotechnology, 1732 Deogyeong-daero, Yongin 17104, Republic of Korea
| | - Eung-Jun Park
- Division of Forest Biotechnology, National Institute of Forest Science, 39 Onjeong-ro, Suwon 16631, Republic of Korea
| | - Jae-Heung Ko
- Department of Plant & Environmental New Resources, Kyung Hee University, 1732 Deogyeong-daero, Yongin 17104, Republic of Korea
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Yao T, Feng K, Xie M, Barros J, Tschaplinski TJ, Tuskan GA, Muchero W, Chen JG. Phylogenetic Occurrence of the Phenylpropanoid Pathway and Lignin Biosynthesis in Plants. FRONTIERS IN PLANT SCIENCE 2021; 12:704697. [PMID: 34484267 PMCID: PMC8416159 DOI: 10.3389/fpls.2021.704697] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 07/19/2021] [Indexed: 05/19/2023]
Abstract
The phenylpropanoid pathway serves as a rich source of metabolites in plants and provides precursors for lignin biosynthesis. Lignin first appeared in tracheophytes and has been hypothesized to have played pivotal roles in land plant colonization. In this review, we summarize recent progress in defining the lignin biosynthetic pathway in lycophytes, monilophytes, gymnosperms, and angiosperms. In particular, we review the key structural genes involved in p-hydroxyphenyl-, guaiacyl-, and syringyl-lignin biosynthesis across plant taxa and consider and integrate new insights on major transcription factors, such as NACs and MYBs. We also review insight regarding a new transcriptional regulator, 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase, canonically identified as a key enzyme in the shikimate pathway. We use several case studies, including EPSP synthase, to illustrate the evolution processes of gene duplication and neo-functionalization in lignin biosynthesis. This review provides new insights into the genetic engineering of the lignin biosynthetic pathway to overcome biomass recalcitrance in bioenergy crops.
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Affiliation(s)
- Tao Yao
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Kai Feng
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Meng Xie
- Biology Department, Brookhaven National Laboratory, Upton, NY, United States
| | - Jaime Barros
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX, United States
| | - Timothy J. Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Gerald A. Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
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Qu G, Peng D, Yu Z, Chen X, Cheng X, Yang Y, Ye T, Lv Q, Ji W, Deng X, Zhou B. Advances in the role of auxin for transcriptional regulation of lignin biosynthesis. FUNCTIONAL PLANT BIOLOGY : FPB 2021; 48:743-754. [PMID: 33663680 DOI: 10.1071/fp20381] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 02/13/2021] [Indexed: 06/12/2023]
Abstract
Lignin is a natural polymer interlaced with cellulose and hemicellulose in secondary cell walls (SCWs). Auxin acts via its signalling transduction to regulate most of plant physiological processes. Lignification responds to auxin signals likewise and affects the development of anther and secondary xylem in plants. In this review, the research advances of AUXIN RESPONSE FACTOR (ARF)-dependent signalling pathways regulating lignin formation are discussed in detail. In an effort to facilitate the understanding of several key regulators in this process, we present a regulatory framework that comprises protein-protein interactions at the top and protein-gene regulation divided into five tiers. This characterises the regulatory roles of auxin in lignin biosynthesis and links auxin signalling transduction to transcriptional cascade of lignin biosynthesis. Our works further point to several of significant problems that need to be resolved in the future to gain a better understanding of the underlying mechanisms through which auxin regulates lignin biosynthesis.
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Affiliation(s)
- Gaoyi Qu
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology; 410004, Changsha, China
| | - Dan Peng
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology; 410004, Changsha, China; and Huitong National Field Station for Scientific Observation and Research of Chinese Fir Plantation Ecosystem in Hunan Province, Huitong 438107, China; and Forestry Biotechnology Hunan Key Laboratories, Hunan Changsha, 410004, China
| | - Ziqin Yu
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology; 410004, Changsha, China
| | - Xinling Chen
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology; 410004, Changsha, China
| | - Xinrui Cheng
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology; 410004, Changsha, China
| | - Youzhen Yang
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology; 410004, Changsha, China
| | - Tao Ye
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology; 410004, Changsha, China
| | - Qiang Lv
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology; 410004, Changsha, China
| | - Wenjun Ji
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology; 410004, Changsha, China
| | - Xiangwen Deng
- National Engineering Laboratory of Applied Technology for Forestry and Ecology in Southern China, Changsha 410004, Hunan, China
| | - Bo Zhou
- Faculty of Life Science and Biotechnology of Central South University of Forestry and Technology; 410004, Changsha, China; and Huitong National Field Station for Scientific Observation and Research of Chinese Fir Plantation Ecosystem in Hunan Province, Huitong 438107, China; and National Engineering Laboratory of Applied Technology for Forestry and Ecology in Southern China, Changsha 410004, Hunan, China; and Forestry Biotechnology Hunan Key Laboratories, Hunan Changsha, 410004, China; and Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, 410018, Changsha, China; and Corresponding author.
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Innovation, conservation, and repurposing of gene function in root cell type development. Cell 2021; 184:3333-3348.e19. [PMID: 34010619 DOI: 10.1016/j.cell.2021.04.024] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 01/19/2021] [Accepted: 04/14/2021] [Indexed: 12/21/2022]
Abstract
Plant species have evolved myriads of solutions, including complex cell type development and regulation, to adapt to dynamic environments. To understand this cellular diversity, we profiled tomato root cell type translatomes. Using xylem differentiation in tomato, examples of functional innovation, repurposing, and conservation of transcription factors are described, relative to the model plant Arabidopsis. Repurposing and innovation of genes are further observed within an exodermis regulatory network and illustrate its function. Comparative translatome analyses of rice, tomato, and Arabidopsis cell populations suggest increased expression conservation of root meristems compared with other homologous populations. In addition, the functions of constitutively expressed genes are more conserved than those of cell type/tissue-enriched genes. These observations suggest that higher order properties of cell type and pan-cell type regulation are evolutionarily conserved between plants and animals.
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Shi J, Zhang Q, Yan X, Zhang D, Zhou Q, Shen Y, Anupol N, Wang X, Bao M, Larkin RM, Luo H, Ning G. A conservative pathway for coordination of cell wall biosynthesis and cell cycle progression in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:630-648. [PMID: 33547692 DOI: 10.1111/tpj.15187] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 01/27/2021] [Indexed: 06/12/2023]
Abstract
The mechanism that coordinates cell growth and cell cycle progression remains poorly understood; in particular, whether the cell cycle and cell wall biosynthesis are coordinated remains unclear. Recently, cell wall biosynthesis and cell cycle progression were reported to respond to wounding. Nonetheless, no genes are reported to synchronize the biosynthesis of the cell wall and the cell cycle. Here, we report that wounding induces the expression of genes associated with cell wall biosynthesis and the cell cycle, and that two genes, AtMYB46 in Arabidopsis thaliana and RrMYB18 in Rosa rugosa, are induced by wounding. We found that AtMYB46 and RrMYB18 promote the biosynthesis of the cell wall by upregulating the expression of cell wall-associated genes, and that both of them also upregulate the expression of a battery of genes associated with cell cycle progression. Ultimately, this response leads to the development of curled leaves of reduced size. We also found that the coordination of cell wall biosynthesis and cell cycle progression by AtMYB46 and RrMYB18 is evolutionarily conservative in multiple species. In accordance with wounding promoting cell regeneration by regulating the cell cycle, these findings also provide novel insight into the coordination between cell growth and cell cycle progression and a method for producing miniature plants.
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Affiliation(s)
- Jiewei Shi
- Key laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qunxia Zhang
- Key laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xu Yan
- Key laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Delin Zhang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qin Zhou
- Key laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuxiao Shen
- Key laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Nachaisin Anupol
- Key laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiuqing Wang
- Key laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Manzhu Bao
- Key laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Robert M Larkin
- Key laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hong Luo
- Department of Genetics and Biochemistry, Clemson University, 110 Biosystems Research Complex, Clemson, SC, 29634-0318, USA
| | - Guogui Ning
- Key laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
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Nakata MT, Sakamoto S, Nuoendagula, Kajita S, Mitsuda N. Fiber Cell-Specific Expression of the VP16-Fused Ethylene Response Factor 41 Protein Increases Biomass Yield and Alters Lignin Composition. FRONTIERS IN PLANT SCIENCE 2021; 12:654655. [PMID: 33995450 PMCID: PMC8121085 DOI: 10.3389/fpls.2021.654655] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 03/29/2021] [Indexed: 01/06/2024]
Abstract
Arabidopsis thaliana transcription factors belonging to the ERFIIId and ERFIIIe subclade (ERFIIId/e) of the APETALA 2/ethylene response factor (AP2/ERF) family enhance primary cell wall (PCW) formation. These transcription factors activate expression of genes encoding PCW-type cellulose synthase (CESA) subunits and other genes for PCW biosynthesis. In this study, we show that fiber-specific expression of ERF035-VP16 and ERF041-VP16, which are VP16-fused proteins of ERFIIId/e members, promote cell wall thickening in a wild-type background with a concomitant increase of alcohol insoluble residues (cell wall content) per fresh weight (FW) and monosaccharides related to the PCW without affecting plant growth. Furthermore, in the ERF041-VP16 lines, the total amount of lignin and the syringyl (S)/guaiacyl (G) ratio decreased, and the enzymatic saccharification yield of glucose from cellulose per fresh weight improved. In these lines, PCW-type CESA genes were upregulated and ferulate 5-hydropxylase1 (F5H1), which is necessary for production of the S unit lignin, was downregulated. In addition, various changes in the expression levels of transcription factors regulating secondary cell wall (SCW) formation were observed. In conclusion, fiber cell-specific ERF041-VP16 improves biomass yield, increases PCW components, and alters lignin composition and deposition and may be suitable for use in future molecular breeding programs of biomass crops.
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Affiliation(s)
- Miyuki T. Nakata
- Plant Gene Regulation Research Group, Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Shingo Sakamoto
- Plant Gene Regulation Research Group, Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
- Smart CO2 Utilization Research Team, Global Zero Emission Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Nuoendagula
- Graduate School of Bio-Applications and Systems Engineering (BASE), Tokyo University of Agriculture and Technology (TUAT), Koganei, Japan
| | - Shinya Kajita
- Graduate School of Bio-Applications and Systems Engineering (BASE), Tokyo University of Agriculture and Technology (TUAT), Koganei, Japan
| | - Nobutaka Mitsuda
- Plant Gene Regulation Research Group, Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
- Smart CO2 Utilization Research Team, Global Zero Emission Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
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23
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Im JH, Ko JH, Kim WC, Crain B, Keathley D, Han KH. Mitogen-activated protein kinase 6 negatively regulates secondary wall biosynthesis by modulating MYB46 protein stability in Arabidopsis thaliana. PLoS Genet 2021; 17:e1009510. [PMID: 33826618 PMCID: PMC8055014 DOI: 10.1371/journal.pgen.1009510] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 04/19/2021] [Accepted: 03/25/2021] [Indexed: 11/18/2022] Open
Abstract
The R2R3-MYB transcription factor MYB46 functions as a master switch for secondary cell wall biosynthesis, ensuring the exquisite expression of the secondary wall biosynthetic genes in the tissues where secondary walls are critical for growth and development. At the same time, suppression of its function is needed when/where formation of secondary walls is not desirable. Little is known about how this opposing control of secondary cell wall formation is achieved. We used both transient and transgenic expression of MYB46 and mitogen-activated protein kinase 6 (MPK6) to investigate the molecular mechanism of the post-translational regulation of MYB46. We show that MYB46 is phosphorylated by MPK6, leading to site specific phosphorylation-dependent degradation of MYB46 by the ubiquitin-mediated proteasome pathway. In addition, the MPK6-mediated MYB46 phosphorylation was found to regulate in planta secondary wall forming function of MYB46. Furthermore, we provide experimental evidences that MYB83, a paralog of MYB46, is not regulated by MPK6. The coupling of MPK signaling to MYB46 function provides insights into the tissue- and/or condition-specific activity of MYB46 for secondary wall biosynthesis.
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Affiliation(s)
- Jong Hee Im
- Department of Horticulture, Michigan State University, East Lansing, Michigan, United States of America
- National Academy of Agricultural Science, Rural Development Administration, Jeonju, Republic of Korea
| | - Jae-Heung Ko
- Department of Plant & Environmental New Resources, College of Life Science and Graduate School of Biotechnology, Kyung Hee University, Yongin-si, Gyeonggi-do, Republic of Korea
- * E-mail: (J-HK); (K-HH)
| | - Won-Chan Kim
- School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Brent Crain
- Department of Horticulture, Michigan State University, East Lansing, Michigan, United States of America
| | - Daniel Keathley
- Department of Horticulture, Michigan State University, East Lansing, Michigan, United States of America
| | - Kyung-Hwan Han
- Department of Horticulture, Michigan State University, East Lansing, Michigan, United States of America
- Department of Forestry, Michigan State University, East Lansing, Michigan, United States of America
- * E-mail: (J-HK); (K-HH)
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24
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Xiao R, Zhang C, Guo X, Li H, Lu H. MYB Transcription Factors and Its Regulation in Secondary Cell Wall Formation and Lignin Biosynthesis during Xylem Development. Int J Mol Sci 2021; 22:3560. [PMID: 33808132 PMCID: PMC8037110 DOI: 10.3390/ijms22073560] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/26/2021] [Accepted: 03/26/2021] [Indexed: 01/12/2023] Open
Abstract
The secondary wall is the main part of wood and is composed of cellulose, xylan, lignin, and small amounts of structural proteins and enzymes. Lignin molecules can interact directly or indirectly with cellulose, xylan and other polysaccharide molecules in the cell wall, increasing the mechanical strength and hydrophobicity of plant cells and tissues and facilitating the long-distance transportation of water in plants. MYBs (v-myb avian myeloblastosis viral oncogene homolog) belong to one of the largest superfamilies of transcription factors, the members of which regulate secondary cell-wall formation by promoting/inhibiting the biosynthesis of lignin, cellulose, and xylan. Among them, MYB46 and MYB83, which comprise the second layer of the main switch of secondary cell-wall biosynthesis, coordinate upstream and downstream secondary wall synthesis-related transcription factors. In addition, MYB transcription factors other than MYB46/83, as well as noncoding RNAs, hormones, and other factors, interact with one another to regulate the biosynthesis of the secondary wall. Here, we discuss the biosynthesis of secondary wall, classification and functions of MYB transcription factors and their regulation of lignin polymerization and secondary cell-wall formation during wood formation.
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Affiliation(s)
- Ruixue Xiao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China; (R.X.); (H.L.)
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (C.Z.); (X.G.)
| | - Chong Zhang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (C.Z.); (X.G.)
| | - Xiaorui Guo
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (C.Z.); (X.G.)
| | - Hui Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China; (R.X.); (H.L.)
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (C.Z.); (X.G.)
| | - Hai Lu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China; (R.X.); (H.L.)
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (C.Z.); (X.G.)
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25
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Chen L, Wu F, Zhang J. NAC and MYB Families and Lignin Biosynthesis-Related Members Identification and Expression Analysis in Melilotus albus. PLANTS 2021; 10:plants10020303. [PMID: 33562564 PMCID: PMC7914948 DOI: 10.3390/plants10020303] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 11/28/2020] [Accepted: 12/11/2020] [Indexed: 11/26/2022]
Abstract
Melilotus albus is an annual or biennial legume species that adapts to extreme environments via its high stress tolerance. NAC and MYB transcription factors (TFs) are involved in the regulation of lignin biosynthesis, which has not been studied in M. albus. A total of 101 MaNAC and 299 MaMYB members were identified based on M. albus genome. Chromosome distribution and synteny analysis indicated that some genes underwent tandem duplication. Ka/Ks analysis suggested that MaNACs and MaMYBs underwent strong purifying selection. Stress-, hormone- and development-related cis-elements and MYB-binding sites were identified in the promoter regions of MaNACs and MaMYBs. Five MaNACs, two MaMYBs and ten lignin biosynthesis genes were identified as presenting coexpression relationships according to weighted gene coexpression network analysis (WGCNA). Eleven and thirteen candidate MaNAC and MaMYB genes related to lignin biosynthesis were identified, respectively, and a network comprising these genes was constructed which further confirmed the MaNAC and MaMYB relationship. These candidate genes had conserved gene structures and motifs and were highly expressed in the stems and roots, and qRT-PCR further verified the expression patterns. Overall, our results provide a reference for determining the precise role of NAC and MYB genes in M. albus and may facilitate efforts to breed low-lignin-content forage cultivars in the future.
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26
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Chen SP, Sun WH, Xiong YF, Jiang YT, Liu XD, Liao XY, Zhang DY, Jiang SZ, Li Y, Liu B, Ma L, Yu X, He L, Liu B, Feng JL, Feng LZ, Wang ZW, Zou SQ, Lan SR, Liu ZJ. The Phoebe genome sheds light on the evolution of magnoliids. HORTICULTURE RESEARCH 2020; 7:146. [PMID: 32922818 PMCID: PMC7459323 DOI: 10.1038/s41438-020-00368-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 06/04/2020] [Accepted: 06/19/2020] [Indexed: 05/09/2023]
Abstract
Lauraceae includes the genus Phoebe, and the family is linked to the evolution of magnoliids. We sequenced the genome of Phoebe bournei Nanmu. The assembled genome size was 989.19 Mb, with a contig N50 value of 2.05 Mb. A total of 28,198 protein-coding genes were annotated in P. bournei. Whole-genome duplication (WGD) analysis showed that Lauraceae has experienced two WGD events; the older WGD event occurred just before the divergence of Lauraceae and Magnoliales, and the more recent WGD was shared by all lineages of Lauraceae. The phylogenetic tree showed that magnoliids form a sister clade to monocots and eudicots. We also identified 63 MADS-box genes, including AGL12-like genes that may be related to the regulation of P. bournei roots and FIN219-like genes encoding GH3 proteins, which are involved in photomorphogenesis. SAUR50-like genes involved in light signal-mediated pedicel or stem development were also identified. Four ATMYB46- and three PtrEPSP-homologous genes related to lignin biosynthesis were identified. These genes may be associated with the formation of straight trunks in P. bournei. Overall, the P. bournei reference genome provides insight into the origin, evolution, and diversification of Phoebe and other magnoliids.
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Affiliation(s)
- Shi-Pin Chen
- College of Forestry, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at the College of Landscape Architecture, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Wei-Hong Sun
- College of Forestry, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at the College of Landscape Architecture, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Yuan-Fang Xiong
- College of Forestry, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at the College of Landscape Architecture, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Yu-Ting Jiang
- College of Forestry, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at the College of Landscape Architecture, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Xue-Die Liu
- College of Forestry, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at the College of Landscape Architecture, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Xing-Yu Liao
- College of Forestry, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at the College of Landscape Architecture, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Di-Yang Zhang
- College of Forestry, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at the College of Landscape Architecture, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Shu-Zhen Jiang
- College of Forestry, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at the College of Landscape Architecture, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Yu Li
- College of Forestry, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at the College of Landscape Architecture, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Bin Liu
- College of Forestry, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at the College of Landscape Architecture, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Liang Ma
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at the College of Landscape Architecture, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Xia Yu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at the College of Landscape Architecture, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Li He
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at the College of Landscape Architecture, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Bao Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at the College of Landscape Architecture, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Jin-Lin Feng
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at the College of Landscape Architecture, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Li-Zhen Feng
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at the College of Landscape Architecture, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | | | - Shuang-Quan Zou
- College of Forestry, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at the College of Landscape Architecture, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Si-Ren Lan
- College of Forestry, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at the College of Landscape Architecture, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at the College of Landscape Architecture, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, 325005 Wenzhou, China
- Institute of Vegetable and Flowers, Shandong Academy of Agricultural Sciences, 250100 Jinan, China
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Tu M, Wang X, Yin W, Wang Y, Li Y, Zhang G, Li Z, Song J, Wang X. Grapevine VlbZIP30 improves drought resistance by directly activating VvNAC17 and promoting lignin biosynthesis through the regulation of three peroxidase genes. HORTICULTURE RESEARCH 2020; 7:150. [PMID: 32922822 PMCID: PMC7458916 DOI: 10.1038/s41438-020-00372-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 06/19/2020] [Accepted: 06/23/2020] [Indexed: 05/20/2023]
Abstract
Drought stress severely affects grapevine quality and yield, and recent reports have revealed that lignin plays an important role in protection from drought stress. Since little is known about lignin-mediated drought resistance in grapevine, we investigated its significance. Herein, we show that VlbZIP30 mediates drought resistance by activating the expression of lignin biosynthetic genes and increasing lignin deposition. Transgenic grapevine plants overexpressing VlbZIP30 exhibited lignin deposition (mainly G and S monomers) in the stem secondary xylem under control conditions, which resulted from the upregulated expression of VvPRX4 and VvPRX72. Overexpression of VlbZIP30 improves drought tolerance, characterized by a reduction in the water loss rate, maintenance of an effective photosynthesis rate, and increased lignin content (mainly G monomer) in leaves under drought conditions. Electrophoretic mobility shift assay, luciferase reporter assays, and chromatin immunoprecipitation-qPCR assays indicated that VlbZIP30 directly binds to the G-box cis-element in the promoters of lignin biosynthetic (VvPRX N1) and drought-responsive (VvNAC17) genes to regulate their expression. In summary, we report a novel VlbZIP30-mediated mechanism linking lignification and drought tolerance in grapevine. The results of this study may be of value for the development of molecular breeding strategies to produce drought-resistant fruit crops.
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Affiliation(s)
- Mingxing Tu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Xianhang Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
- College of Enology, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Wuchen Yin
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Ya Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Yajuan Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Guofeng Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Zhi Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Junyang Song
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Xiping Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, 712100 Shaanxi China
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28
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Soni N, Hegde N, Dhariwal A, Kushalappa AC. Role of laccase gene in wheat NILs differing at QTL-Fhb1 for resistance against Fusarium head blight. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 298:110574. [PMID: 32771175 DOI: 10.1016/j.plantsci.2020.110574] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 06/16/2020] [Accepted: 06/19/2020] [Indexed: 05/20/2023]
Abstract
Fusarium head blight (FHB), caused mainly by Fusarium graminearum (Fg), is one of the most severe diseases of wheat. It affects grain yield and quality due to mycotoxin contamination, which is harmful for both human and livestock consumption. Cell wall lignification, following pathogen invasion, is one of the innate defense responses. Plant laccases are known to lignify the secondary cell walls. A metabolo-genomics study identified laccase as one of the candidate genes in QTL-Fhb1 of wheat NILs derived from Sumai 3*5/Thatcher cross. Based on phylogenetics, it was named as TaLAC4. Real-time qPCR revealed a strongly induced expression of TaLAC4 in NIL-R. The VIGS based transient silencing of TaLAC4 in NIL-R resulted in an increased susceptibility leading to Fg spread within the entire spike in 15dpi, contrasting to non-silenced where the infection was limited to inoculated spikelets. Histopathology revealed thickened cell walls, mainly due to G-lignin, in non-silenced NIL-R, relative to silenced, in conjunction with higher total lignin content. Metabolic profiling of TaLAC4 silenced NILs identified the accumulation of several precursor metabolites higher in abundances upstream TaLAC4. These results confirm that the resistance function of TaLAC4 in NIL-R is due to pathogen-induced lignification of secondary cell walls in the rachis.
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Affiliation(s)
- Nancy Soni
- Plant Science Department, McGill University, Ste.-Anne-de-Bellevue, QC, Canada
| | - Niranjan Hegde
- Plant Science Department, McGill University, Ste.-Anne-de-Bellevue, QC, Canada
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29
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Bae SY, Kim MH, Cho JS, Park EJ, Lee H, Kim JH, Ko JH. Overexpression of Populus transcription factor PtrTALE12 increases axillary shoot development by regulating WUSCHEL expression. TREE PHYSIOLOGY 2020; 40:1232-1246. [PMID: 32420604 DOI: 10.1093/treephys/tpaa062] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 03/26/2020] [Accepted: 05/13/2020] [Indexed: 06/11/2023]
Abstract
The TALE (Three Amino acid Loop Extension) transcription factor family has been shown to control meristem formation and organogenesis in plants. To understand the functional roles of the TALE family in woody perennials, each of the TALE members of Populus trichocarpa was overexpressed in Arabidopsis as a proxy. Among them, the overexpression of PtrTALE12 (i.e., 35S::PtrTALE12) resulted in a dramatic increase of axillary shoot development with early flowering. Interestingly, expression of WUSCHEL (WUS), a central regulator of both apical and axillary meristem formation, was significantly increased in the 35S::PtrTALE12 Arabidopsis plants. Conversely, WUS expression was downregulated in 35S::PtrTALE12-SRDX (short transcriptional repressor domain) plants. Further analysis found that PtrTALE12, expressed preferentially in meristem tissues, directly regulates WUS expression in transient activation assays using Arabidopsis leaf protoplast. Yeast two-hybrid assays showed that PtrTALE12 interacts with SHOOT MERISTEMLESS (STM); however, the interaction does not affect the WUS expression. In addition, expression of both CIRCADIAN CLOCK ASSOCIATED1 (CCA1) and LATE ELONGATED HYPOCOTYL (LHY) genes was suppressed accordingly for early flowering 35S::PtrTALE12 Arabidopsis. Indeed, transgenic poplars overexpressing PtrTALE12 as well as Arabidopsis plants overexpressing AtBLH11, a close homolog of PtrTALE12, phenocopied the 35S::PtrTALE12 Arabidopsis (i.e., increased axillary shoot development). Taken together, our results suggest that PtrTALE12 functions as a positive regulator of axillary shoot formation in both Arabidopsis and poplar.
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Affiliation(s)
- So-Young Bae
- Department of Plant & Environmental New Resources, Kyung Hee University, 1732 Deogyeong-daero, Yongin 17104, Republic of Korea
| | - Min-Ha Kim
- Department of Plant & Environmental New Resources, Kyung Hee University, 1732 Deogyeong-daero, Yongin 17104, Republic of Korea
| | - Jin-Seong Cho
- Department of Plant & Environmental New Resources, Kyung Hee University, 1732 Deogyeong-daero, Yongin 17104, Republic of Korea
| | - Eung-Jun Park
- Division of Forest Biotechnology, National Institute of Forest Science, 39 Onjeong-ro, Suwon 16631, Republic of Korea
| | - Hyoshin Lee
- Division of Forest Biotechnology, National Institute of Forest Science, 39 Onjeong-ro, Suwon 16631, Republic of Korea
| | - Jeong-Hoe Kim
- Department of Biology, School of Biological Sciences, Kyungpook National University, Daegu 41566, Korea
| | - Jae-Heung Ko
- Department of Plant & Environmental New Resources, Kyung Hee University, 1732 Deogyeong-daero, Yongin 17104, Republic of Korea
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Wang Y, Xu Y, Pei S, Lu M, Kong Y, Zhou G, Hu R. KNAT7 regulates xylan biosynthesis in Arabidopsis seed-coat mucilage. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:4125-4139. [PMID: 32277756 DOI: 10.1093/jxb/eraa189] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 04/09/2020] [Indexed: 05/21/2023]
Abstract
As a major hemicellulose component of plant cell walls, xylans play a determining role in maintaining the wall structure. However, the mechanisms of transcriptional regulation of xylan biosynthesis remain largely unknown. Arabidopsis seed mucilage represents an ideal system for studying polysaccharide biosynthesis and modifications of plant cell walls. Here, we identify KNOTTED ARABIDOPSIS THALIANA 7 (KNAT7) as a positive transcriptional regulator of xylan biosynthesis in seed mucilage. The xylan content was significantly reduced in the mucilage of the knat7-3 mutant and this was accompanied by significantly reduced expression of the xylan biosynthesis-related genes IRREGULAR XYLEM 14 (IRX14) and MUCILAGE MODIFIED 5/MUCILAGE-RELATED 21 (MUM5/MUCI21). Electrophoretic mobility shift assays, yeast one-hybrid assays, and chromatin immunoprecipitation with quantitative PCR verified the direct binding of KNAT7 to the KNOTTED1 (KN1) binding site [KBS,TGACAG(G/C)T] in the promoters of IRX7, IRX14, and MUM5/MUCI21 in vitro, in vivo, and in planta. Furthermore, KNAT7 directly activated the expression of IRX14 and MUM5/MUCI21 in transactivation assays in mesophyll protoplasts, and overexpression of IRX14 or MUM5/MUCI21 in knat7-3 partially rescued the defects in mucilage adherence. Taken together, our results indicate that KNAT7 positively regulates xylan biosynthesis in seed-coat mucilage via direct activation of the expression of IRX14 and MUM5/MUCI21.
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Affiliation(s)
- Yiping Wang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, PR China
- University of Chinese Academy of Sciences, Beijing, PR China
| | - Yan Xu
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, PR China
| | - Shengqiang Pei
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, PR China
| | - Mingmin Lu
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, PR China
| | - Yingzhen Kong
- Agronomy College, College of Resource and Environment, Qingdao Agricultural University, Qingdao, PR China
| | - Gongke Zhou
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, PR China
| | - Ruibo Hu
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, PR China
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Zheng H, Dong L, Han X, Jin H, Yin C, Han Y, Li B, Qin H, Zhang J, Shen Q, Zhang K, Wang D. The TuMYB46L-TuACO3 module regulates ethylene biosynthesis in einkorn wheat defense to powdery mildew. THE NEW PHYTOLOGIST 2020; 225:2526-2541. [PMID: 31675430 PMCID: PMC7065006 DOI: 10.1111/nph.16305] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 10/22/2019] [Indexed: 05/22/2023]
Abstract
Powdery mildew disease, elicited by the obligate fungal pathogen Blumeria graminis f.sp. tritici (Bgt), causes widespread yield losses in global wheat crop. However, the molecular mechanisms governing wheat defense to Bgt are still not well understood. Here we found that TuACO3, encoding the 1-aminocyclopropane-1-carboxylic acid (ACC) oxidase functioning in ethylene (ET) biosynthesis, was induced by Bgt infection of the einkorn wheat Triticum urartu, which was accompanied by increased ET content. Silencing TuACO3 decreased ET production and compromised wheat defense to Bgt, whereas both processes were enhanced in the transgenic wheat overexpressing TuACO3. TuMYB46L, phylogenetically related to Arabidopsis MYB transcription factor AtMYB46, was found to bind to the TuACO3 promoter region in yeast-one-hybrid and EMSA experiments. TuMYB46L expression decreased rapidly following Bgt infection. Silencing TuMYB46L promoted ET content and Bgt defense, but the reverse was observed when TuMYB46L was overexpressed. Hence, decreased expression of TuMYB46L permits elevated function of TuACO3 in ET biosynthesis in Bgt-infected wheat. The TuMYB46L-TuACO3 module regulates ET biosynthesis to promote einkorn wheat defense against Bgt. Furthermore, we found four chitinase genes acting downstream of the TuMYB46L-TuACO3 module. Collectively, our data shed a new light on the molecular mechanisms underlying wheat defense to Bgt.
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Affiliation(s)
- Hongyuan Zheng
- College of AgronomyHenan Agricultural UniversityZhengzhou450002China
- The State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing100101China
| | - Lingli Dong
- The State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing100101China
| | - Xinyun Han
- The State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing100101China
| | - Huaibing Jin
- The State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing100101China
| | - Cuicui Yin
- The State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing100101China
| | - Yali Han
- The State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing100101China
| | - Bei Li
- The State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing100101China
- University of Chinese Academy of SciencesBeijing100049China
| | - Huanju Qin
- The State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing100101China
| | - Jinsong Zhang
- The State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing100101China
- University of Chinese Academy of SciencesBeijing100049China
| | - Qianhua Shen
- The State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing100101China
- University of Chinese Academy of SciencesBeijing100049China
| | - Kunpu Zhang
- The State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing100101China
| | - Daowen Wang
- The State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing100101China
- University of Chinese Academy of SciencesBeijing100049China
- The State Key Laboratory of Wheat and Maize Crop ScienceHenan Agricultural UniversityZhengzhou450002China
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Meneses M, García-Rojas M, Muñoz-Espinoza C, Carrasco-Valenzuela T, Defilippi B, González-Agüero M, Meneses C, Infante R, Hinrichsen P. Transcriptomic study of pedicels from GA 3-treated table grape genotypes with different susceptibility to berry drop reveals responses elicited in cell wall yield, primary growth and phenylpropanoids synthesis. BMC PLANT BIOLOGY 2020; 20:66. [PMID: 32041534 PMCID: PMC7011282 DOI: 10.1186/s12870-020-2260-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 01/20/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND Gibberellins (GA3) are the most sprayed growth regulator for table grape production worldwide, increasing berry size of seedless varieties through pericarp cell expansion. However, these treatments also exacerbate berry drop, which has a detrimental effect on the postharvest quality of commercialized clusters. Several studies have suggested that pedicel stiffening caused by GA3 would have a role in this disorder. Nevertheless, transcriptional and phenotypic information regarding pedicel responses to GA3 is minimal. RESULTS Characterization of responses to GA3 treatments using the lines L23 and Thompson Seedless showed that the former was up to six times more susceptible to berry drop than the latter. GA3 also increased the diameter and dry matter percentage of the pedicel on both genotypes. Induction of lignin biosynthesis-related genes by GA3 has been reported, so the quantity of this polymer was measured. The acetyl bromide method detected a decreased concentration of lignin 7 days after GA3 treatment, due to a higher cell wall yield of the isolated fractions of GA3-treated pedicel samples which caused a dilution effect. Thus, an initial enrichment of primary cell wall components in response to GA3 was suggested, particularly in the L23 background. A transcriptomic profiling was performed to identify which genes were associated with these phenotypic changes. This analysis identified 1281 and 1787 genes differentially upregulated by GA3 in L23 and cv. Thompson Seedless, respectively. Concomitantly, 1202 and 1317 downregulated genes were detected in L23 and cv. Thompson Seedless (FDR < 0.05). Gene ontology analysis of upregulated genes showed enrichment in pathways including phenylpropanoids, cell wall metabolism, xylem development, photosynthesis and the cell cycle at 7 days post GA3 application. Twelve genes were characterized by qPCR and striking differences were observed between genotypes, mainly in genes related to cell wall synthesis. CONCLUSIONS High levels of berry drop are related to an early strong response of primary cell wall synthesis in the pedicel promoted by GA3 treatment. Genetic backgrounds can produce similar phenotypic responses to GA3, although there is considerable variation in the regulation of genes in terms of which are expressed, and the extent of transcript levels achieved within the same time frame.
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Affiliation(s)
- Marco Meneses
- Instituto de Investigaciones Agropecuarias, INIA-La Platina, Santa Rosa 11610, Santiago, Chile
- Programa de Doctorado en Ciencias Silvoagropecuarias y Veterinarias, Campus Sur, Universidad de Chile, Santiago, Chile
| | - Miguel García-Rojas
- Instituto de Investigaciones Agropecuarias, INIA-La Platina, Santa Rosa 11610, Santiago, Chile
| | - Claudia Muñoz-Espinoza
- Instituto de Investigaciones Agropecuarias, INIA-La Platina, Santa Rosa 11610, Santiago, Chile
| | - Tomás Carrasco-Valenzuela
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Bruno Defilippi
- Instituto de Investigaciones Agropecuarias, INIA-La Platina, Santa Rosa 11610, Santiago, Chile
| | | | - Claudio Meneses
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
- FONDAP Center for Genome Regulation, Universidad Andres Bello, Santiago, Chile
| | - Rodrigo Infante
- Programa de Doctorado en Ciencias Silvoagropecuarias y Veterinarias, Campus Sur, Universidad de Chile, Santiago, Chile
| | - Patricio Hinrichsen
- Instituto de Investigaciones Agropecuarias, INIA-La Platina, Santa Rosa 11610, Santiago, Chile.
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Xie M, Zhang J, Singan VR, McGranahan MJ, LaFayette PR, Jawdy SS, Engle N, Doeppke C, Tschaplinski TJ, Davis MF, Lindquist E, Barry K, Schmutz J, Parrott WA, Chen F, Tuskan GA, Chen J, Muchero W. Identification of functional single nucleotide polymorphism of Populus trichocarpa PtrEPSP-TF and determination of its transcriptional effect. PLANT DIRECT 2020; 4:e00178. [PMID: 31911959 PMCID: PMC6941116 DOI: 10.1002/pld3.178] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 09/17/2019] [Accepted: 10/02/2019] [Indexed: 06/10/2023]
Abstract
In plants, the phenylpropanoid pathway is responsible for the synthesis of a diverse array of secondary metabolites that include lignin monomers, flavonoids, and coumarins, many of which are essential for plant structure, biomass recalcitrance, stress defense, and nutritional quality. Our previous studies have demonstrated that Populus trichocarpa PtrEPSP-TF, an isoform of 5-enolpyruvylshikimate 3-phosphate (EPSP) synthase, has transcriptional activity and regulates phenylpropanoid biosynthesis in Populus. In this study, we report the identification of single nucleotide polymorphism (SNP) of PtrEPSP-TF that defines its functionality. Populus natural variants carrying this SNP were shown to have reduced lignin content. Here, we demonstrated that the SNP-induced substitution of 142nd amino acid (PtrEPSP-TFD142E) dramatically impairs the DNA-binding and transcriptional activity of PtrEPSP-TF. When introduced to a monocot species rice (Oryza sativa) in which an EPSP synthase isoform with the DNA-binding helix-turn-helix (HTH) motif is absent, the PtrEPSP-TF, but not PtrEPSP-TFD142E, activated genes in the phenylpropanoid pathway. More importantly, heterologous expression of PtrEPSP-TF uncovered five new transcriptional regulators of phenylpropanoid biosynthesis in rice. Collectively, this study identifies the key amino acid required for PtrEPSP-TF functionality and provides a strategy to uncover new transcriptional regulators in phenylpropanoid biosynthesis.
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Affiliation(s)
- Meng Xie
- Center for Bioenergy InnovationOak Ridge National LaboratoryOak RidgeTNUSA
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
| | - Jin Zhang
- Center for Bioenergy InnovationOak Ridge National LaboratoryOak RidgeTNUSA
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
| | | | | | | | - Sara S. Jawdy
- Center for Bioenergy InnovationOak Ridge National LaboratoryOak RidgeTNUSA
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
| | - Nancy Engle
- Center for Bioenergy InnovationOak Ridge National LaboratoryOak RidgeTNUSA
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
| | - Crissa Doeppke
- Center for Bioenergy InnovationOak Ridge National LaboratoryOak RidgeTNUSA
- National Renewable Energy LaboratoryGoldenCOUSA
| | - Timothy J. Tschaplinski
- Center for Bioenergy InnovationOak Ridge National LaboratoryOak RidgeTNUSA
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
| | - Mark F. Davis
- Center for Bioenergy InnovationOak Ridge National LaboratoryOak RidgeTNUSA
- National Renewable Energy LaboratoryGoldenCOUSA
| | - Erika Lindquist
- U.S. Department of EnergyJoint Genome InstituteWalnut CreekCAUSA
| | - Kerrie Barry
- U.S. Department of EnergyJoint Genome InstituteWalnut CreekCAUSA
| | - Jeremy Schmutz
- U.S. Department of EnergyJoint Genome InstituteWalnut CreekCAUSA
- HudsonAlpha Institute for BiotechnologyHuntsvilleALUSA
| | - Wayne A. Parrott
- Department of Crop and Soil SciencesUniversity of GeorgiaAthensGAUSA
| | - Feng Chen
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
| | - Gerald A. Tuskan
- Center for Bioenergy InnovationOak Ridge National LaboratoryOak RidgeTNUSA
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
| | - Jin‐Gui Chen
- Center for Bioenergy InnovationOak Ridge National LaboratoryOak RidgeTNUSA
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
| | - Wellington Muchero
- Center for Bioenergy InnovationOak Ridge National LaboratoryOak RidgeTNUSA
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
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Zhang J, Tuskan GA, Tschaplinski TJ, Muchero W, Chen JG. Transcriptional and Post-transcriptional Regulation of Lignin Biosynthesis Pathway Genes in Populus. FRONTIERS IN PLANT SCIENCE 2020; 11:652. [PMID: 32528504 PMCID: PMC7262965 DOI: 10.3389/fpls.2020.00652] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 04/28/2020] [Indexed: 05/04/2023]
Abstract
Lignin is a heterogeneous polymer of aromatic subunits derived from phenylalanine. It is polymerized in intimate proximity to the polysaccharide components in plant cell walls and provides additional rigidity and compressive strength for plants. Understanding the regulatory mechanisms of lignin biosynthesis is important for genetic modification of the plant cell wall for agricultural and industrial applications. Over the past 10 years the transcriptional regulatory model of lignin biosynthesis has been established in plants. However, the role of post-transcriptional regulation is still largely unknown. Increasing evidence suggests that lignin biosynthesis pathway genes are also regulated by alternative splicing, microRNA, and long non-coding RNA. In this review, we briefly summarize recent progress on the transcriptional regulation, then we focus on reviewing progress on the post-transcriptional regulation of lignin biosynthesis pathway genes in the woody model plant Populus.
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Affiliation(s)
- Jin Zhang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- *Correspondence: Jin Zhang,
| | - Gerald A. Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Timothy J. Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Jin-Gui Chen,
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Chen K, Song M, Guo Y, Liu L, Xue H, Dai H, Zhang Z. MdMYB46 could enhance salt and osmotic stress tolerance in apple by directly activating stress-responsive signals. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:2341-2355. [PMID: 31077628 PMCID: PMC6835124 DOI: 10.1111/pbi.13151] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 04/25/2019] [Accepted: 05/05/2019] [Indexed: 05/02/2023]
Abstract
To expand the cultivation area of apple (Malus×domestica Borkh.) and select resistant varieties by genetic engineering, it is necessary to clarify the mechanism of salt and osmotic stress tolerance in apple. The MdMYB46 transcription factor was identified, and the stress treatment test of MdMYB46-overexpressing and MdMYB46-RNAi apple lines indicated that MdMYB46 could enhance the salt and osmotic stress tolerance in apple. In transgenic Arabidopsis and apple, MdMYB46 promoted the biosynthesis of secondary cell wall and deposition of lignin by directly binding to the promoter of lignin biosynthesis-related genes. To explore whether MdMYB46 could coordinate stress signal transduction pathways to cooperate with the formation of secondary walls to enhance the stress tolerance of plants, MdABRE1A, MdDREB2A and dehydration-responsive genes MdRD22 and MdRD29A were screened out for their positive correlation with osmotic stress, salt stress and the transcriptional level of MdMYB46. The further verification test demonstrated that MdMYB46 could activate their transcription by directly binding to the promoters of these genes. The above results indicate that MdMYB46 could enhance the salt and osmotic stress tolerance in apple not only by activating secondary cell wall biosynthesis pathways, but also by directly activating stress-responsive signals.
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Affiliation(s)
- Keqin Chen
- Group of Molecular Biology of Fruit TreesCollege of HorticultureShenyang Agricultural UniversityShenyangLiaoningChina
| | - Mengru Song
- Group of Fruit Germplasm Evaluation & UtilizationCollege of HorticultureShenyang Agricultural UniversityShenyangLiaoningChina
| | - Yunna Guo
- Group of Fruit Germplasm Evaluation & UtilizationCollege of HorticultureShenyang Agricultural UniversityShenyangLiaoningChina
| | - Lifu Liu
- Group of Fruit Germplasm Evaluation & UtilizationCollege of HorticultureShenyang Agricultural UniversityShenyangLiaoningChina
| | - Hao Xue
- Group of Molecular Biology of Fruit TreesCollege of HorticultureShenyang Agricultural UniversityShenyangLiaoningChina
| | - Hongyan Dai
- Group of Fruit Germplasm Evaluation & UtilizationCollege of HorticultureShenyang Agricultural UniversityShenyangLiaoningChina
| | - Zhihong Zhang
- Group of Molecular Biology of Fruit TreesCollege of HorticultureShenyang Agricultural UniversityShenyangLiaoningChina
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BplMYB46 from Betula platyphylla Can Form Homodimers and Heterodimers and Is Involved in Salt and Osmotic Stresses. Int J Mol Sci 2019; 20:ijms20051171. [PMID: 30866467 PMCID: PMC6429157 DOI: 10.3390/ijms20051171] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 02/26/2019] [Accepted: 03/04/2019] [Indexed: 12/21/2022] Open
Abstract
MYB proteins play important roles in the regulation of plant growth, development, and stress responses. Overexpression of BplMYB46 from Betula platyphylla improved plant salt and osmotic tolerances. In the present study, the interaction of eight avian myeloblastosis viral oncogene homolog (MYB) transcription factors with BplMYB46 was investigated using the yeast two-hybrid system, which showed that BplMYB46 could form homodimers and heterodimers with BplMYB6, BplMYB8, BplMYB11, BplMYB12, and BplMYB13. Relative beta-glucuronidase activity and chromatin immunoprecipitation assays showed that the interaction between BplMYB46 and the five MYBs increased the binding of BplMYB46 to the MYBCORE motif. A subcellular localization study showed that these MYBs were all located in the nucleus. Real-time fluorescence quantitative PCR results indicated that the expressions of BplMYB46 and the five MYB genes could be induced by salt and osmotic stress, and the BplMYB46 and BplMYB13 exhibited the most similar expression patterns. BplMYB46 and BplMYB13 co-overexpression in tobacco using transient transformation technology improved tobacco’s tolerance to salt and osmotic stresses compared with overexpressing BplMYB13 or BplMYB46 alone. Taken together, these results demonstrated that BplMYB46 could interact with five other MYBs to form heterodimers that activate the transcription of target genes via an enhanced binding ability to the MYBCORE motif to mediate reactive oxygen species scavenging in response to salt and osmotic stresses.
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Zhao K, Lin F, Romero-Gamboa SP, Saha P, Goh HJ, An G, Jung KH, Hazen SP, Bartley LE. Rice Genome-Scale Network Integration Reveals Transcriptional Regulators of Grass Cell Wall Synthesis. FRONTIERS IN PLANT SCIENCE 2019; 10:1275. [PMID: 31681374 PMCID: PMC6813959 DOI: 10.3389/fpls.2019.01275] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 09/12/2019] [Indexed: 05/07/2023]
Abstract
Grasses have evolved distinct cell wall composition and patterning relative to dicotyledonous plants. However, despite the importance of this plant family, transcriptional regulation of its cell wall biosynthesis is poorly understood. To identify grass cell wall-associated transcription factors, we constructed the Rice Combined mutual Ranked Network (RCRN). The RCRN covers >90% of annotated rice (Oryza sativa) genes, is high quality, and includes most grass-specific cell wall genes, such as mixed-linkage glucan synthases and hydroxycinnamoyl acyltransferases. Comparing the RCRN and an equivalent Arabidopsis network suggests that grass orthologs of most genetically verified eudicot cell wall regulators also control this process in grasses, but some transcription factors vary significantly in network connectivity between these divergent species. Reverse genetics, yeast-one-hybrid, and protoplast-based assays reveal that OsMYB61a activates a grass-specific acyltransferase promoter, which confirms network predictions and supports grass-specific cell wall synthesis genes being incorporated into conserved regulatory circuits. In addition, 10 of 15 tested transcription factors, including six novel Wall-Associated regulators (WAP1, WACH1, WAHL1, WADH1, OsMYB13a, and OsMYB13b), alter abundance of cell wall-related transcripts when transiently expressed. The results highlight the quality of the RCRN for examining rice biology, provide insight into the evolution of cell wall regulation, and identify network nodes and edges that are possible leads for improving cell wall composition.
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Affiliation(s)
- Kangmei Zhao
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - Fan Lin
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | | | - Prasenjit Saha
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - Hyung-Jung Goh
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, South Korea
| | - Gynheung An
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, South Korea
| | - Ki-Hong Jung
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, South Korea
| | - Samuel P. Hazen
- Department of Biology, University of Massachusetts, Amherst, MA, United States
| | - Laura E. Bartley
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
- *Correspondence: Laura E. Bartley,
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Ma X, Zhao H, Xu W, You Q, Yan H, Gao Z, Su Z. Co-expression Gene Network Analysis and Functional Module Identification in Bamboo Growth and Development. Front Genet 2018; 9:574. [PMID: 30542370 PMCID: PMC6277748 DOI: 10.3389/fgene.2018.00574] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Accepted: 11/08/2018] [Indexed: 11/27/2022] Open
Abstract
Bamboo is one of the fastest-growing non-timber forest plants. Moso bamboo (Phyllostachys edulis) is the most economically valuable bamboo in Asia, especially in China. With the release of the whole-genome sequence of moso bamboo, there are increasing demands for refined annotation of bamboo genes. Recently, large amounts of bamboo transcriptome data have become available, including data on the multiple growth stages of tissues. It is now feasible for us to construct co-expression networks to improve bamboo gene annotation and reveal the relationships between gene expression and growth traits. We integrated the genome sequence of moso bamboo and 78 transcriptome data sets to build genome-wide global and conditional co-expression networks. We overlaid the gene expression results onto the network with multiple dimensions (different development stages). Through combining the co-expression network, module classification and function enrichment tools, we identified 1,896 functional modules related to bamboo development, which covered functions such as photosynthesis, hormone biosynthesis, signal transduction, and secondary cell wall biosynthesis. Furthermore, an online database (http://bioinformatics.cau.edu.cn/bamboo) was built for searching the moso bamboo co-expression network and module enrichment analysis. Our database also includes cis-element analysis, gene set enrichment analysis, and other tools. In summary, we integrated public and in-house bamboo transcriptome data sets and carried out co-expression network analysis and functional module identification. Through data mining, we have yielded some novel insights into the regulation of growth and development. Our established online database might be convenient for the bamboo research community to identify functional genes or modules with important traits.
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Affiliation(s)
- Xuelian Ma
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Hansheng Zhao
- State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene Science for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing, China
| | - Wenying Xu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Qi You
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Hengyu Yan
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Zhimin Gao
- State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene Science for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing, China
| | - Zhen Su
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
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Handakumbura PP, Brow K, Whitney IP, Zhao K, Sanguinet KA, Lee SJ, Olins J, Romero-Gamboa SP, Harrington MJ, Bascom CJ, MacKinnon KJM, Veling MT, Liu L, Lee JE, Vogel JP, O'Malley RC, Bezanilla M, Bartley LE, Hazen SP. SECONDARY WALL ASSOCIATED MYB1 is a positive regulator of secondary cell wall thickening in Brachypodium distachyon and is not found in the Brassicaceae. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 96:532-545. [PMID: 30054951 DOI: 10.1111/tpj.14047] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 07/14/2018] [Accepted: 07/18/2018] [Indexed: 05/11/2023]
Abstract
Grass biomass is comprised chiefly of secondary walls that surround fiber and xylem cells. A regulatory network of interacting transcription factors in part regulates cell wall thickening. We identified Brachypodium distachyon SECONDARY WALL ASSOCIATED MYB1 (SWAM1) as a potential regulator of secondary cell wall biosynthesis based on gene expression, phylogeny, and transgenic plant phenotypes. SWAM1 interacts with cellulose and lignin gene promoters with preferential binding to AC-rich sequence motifs commonly found in the promoters of cell wall-related genes. SWAM1 overexpression (SWAM-OE) lines had greater above-ground biomass with only a slight change in flowering time while SWAM1 dominant repressor (SWAM1-DR) plants were severely dwarfed with a striking reduction in lignin of sclerenchyma fibers and stem epidermal cell length. Cellulose, hemicellulose, and lignin genes were significantly down-regulated in SWAM1-DR plants and up-regulated in SWAM1-OE plants. There was no reduction in bioconversion yield in SWAM1-OE lines; however, it was significantly increased for SWAM1-DR samples. Phylogenetic and syntenic analyses strongly suggest that the SWAM1 clade was present in the last common ancestor between eudicots and grasses, but is not in the Brassicaceae. Collectively, these data suggest that SWAM1 is a transcriptional activator of secondary cell wall thickening and biomass accumulation in B. distachyon.
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Affiliation(s)
- Pubudu P Handakumbura
- Biology Department, University of Massachusetts, Amherst, MA 01003, USA
- Plant Biology Graduate Program, University of Massachusetts, Amherst, MA 01003, USA
| | - Kathryn Brow
- Biology Department, University of Massachusetts, Amherst, MA 01003, USA
| | - Ian P Whitney
- Biology Department, University of Massachusetts, Amherst, MA 01003, USA
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA 01003, USA
| | - Kangmei Zhao
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Karen A Sanguinet
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164, USA
| | - Scott J Lee
- Biology Department, University of Massachusetts, Amherst, MA 01003, USA
- Plant Biology Graduate Program, University of Massachusetts, Amherst, MA 01003, USA
| | - Jennifer Olins
- Biology Department, University of Massachusetts, Amherst, MA 01003, USA
| | - Sandra P Romero-Gamboa
- Biology Department, University of Massachusetts, Amherst, MA 01003, USA
- Plant Biology Graduate Program, University of Massachusetts, Amherst, MA 01003, USA
| | | | - Carlisle J Bascom
- Biology Department, University of Massachusetts, Amherst, MA 01003, USA
- Plant Biology Graduate Program, University of Massachusetts, Amherst, MA 01003, USA
| | - Kirk J-M MacKinnon
- Biology Department, University of Massachusetts, Amherst, MA 01003, USA
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA 01003, USA
| | - Michael T Veling
- Biology Department, University of Massachusetts, Amherst, MA 01003, USA
| | - Lifeng Liu
- DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Ji E Lee
- DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - John P Vogel
- DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
| | | | | | - Laura E Bartley
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Samuel P Hazen
- Biology Department, University of Massachusetts, Amherst, MA 01003, USA
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Xie M, Zhang J, Tschaplinski TJ, Tuskan GA, Chen JG, Muchero W. Regulation of Lignin Biosynthesis and Its Role in Growth-Defense Tradeoffs. FRONTIERS IN PLANT SCIENCE 2018; 9:1427. [PMID: 30323825 PMCID: PMC6172325 DOI: 10.3389/fpls.2018.01427] [Citation(s) in RCA: 157] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 09/07/2018] [Indexed: 05/20/2023]
Abstract
Plant growth-defense tradeoffs are fundamental for optimizing plant performance and fitness in a changing biotic/abiotic environment. This process is thought to involve readjusting resource allocation to different pathways. It has been frequently observed that among secondary cell wall components, alteration in lignin biosynthesis results in changes in both growth and defense. How this process is regulated, leading to growth or defense, remains largely elusive. In this article, we review the canonical lignin biosynthesis pathway, the recently discovered tyrosine shortcut pathway, and the biosynthesis of unconventional C-lignin. We summarize the current model of the hierarchical transcriptional regulation of lignin biosynthesis. Moreover, the interface between recently identified transcription factors and the hierarchical model are also discussed. We propose the existence of a transcriptional co-regulation mechanism coordinating energy allowance among growth, defense and lignin biosynthesis.
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Affiliation(s)
- Meng Xie
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Department of Plant Sciences, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Jin Zhang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Timothy J. Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Gerald A. Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
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New Genomic Approaches to Enhance Biomass Degradation by the Industrial Fungus Trichoderma reesei. Int J Genomics 2018; 2018:1974151. [PMID: 30345291 PMCID: PMC6174759 DOI: 10.1155/2018/1974151] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 06/20/2018] [Accepted: 07/29/2018] [Indexed: 11/17/2022] Open
Abstract
The filamentous fungi Trichoderma reesei is one of the most well-studied cellulolytic microorganisms. It is the most important fungus for the industrial production of enzymes to biomass deconstruction being widely used in the biotechnology industry, mainly in the production of biofuels. Here, we performed an analytic review of the holocellulolytic system presented by T. reesei as well as the transcriptional and signaling mechanisms involved with holocellulase expression in this fungus. We also discuss new perspectives about control of secretion and cellulase expression based on RNA-seq and functional characterization data of T. reesei growth in different carbon sources, which comprise glucose, cellulose, sophorose, and sugarcane bagasse.
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Kim DH, Park S, Lee JY, Ha SH, Lee JG, Lim SH. A Rice B-Box Protein, OsBBX14, Finely Regulates Anthocyanin Biosynthesis in Rice. Int J Mol Sci 2018; 19:ijms19082190. [PMID: 30060460 PMCID: PMC6121638 DOI: 10.3390/ijms19082190] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 07/22/2018] [Accepted: 07/24/2018] [Indexed: 11/16/2022] Open
Abstract
Anthocyanins are responsible pigments for giving attractive colors of plant organs and nutraceutical benefits of grains. Anthocyanin biosynthesis is known to be regulated by transcription factors and other regulatory proteins. In rice (Oryza sativa), the R2R3 MYB transcription factor (TF) OsC1 and a bHLH TF, OsB2, were previously reported to control anthocyanin biosynthesis in vegetative tissues and seeds, respectively; however, the regulatory mechanisms of the anthocyanin biosynthesis by TFs remain largely unknown. In this study, we identified OsBBX14, a homolog of Arabidopsis thaliana B-box domain protein 22 (AtBBX22), and investigated its function. The transcript level of OsBBX14 was high in pigmented rice seeds and gradually increased as the seeds matured. The ectopic expression of OsBBX14 in Arabidopsis resulted in a dramatic increase in anthocyanin accumulation in its seedlings. Using a steroid receptor-based inducible activation system, OsBBX14 and OsHY5 were found to directly activate OsC1 or OsB2 in an independent or collaborative manner. Yeast two hybrid revealed that the second B-box domain of OsBBX14 physically interacts with the bZIP domain of OsHY5. These results suggest that the anthocyanin biosynthesis in rice is induced and finely tuned by OsBBX14 in collaboration with OsHY5.
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Affiliation(s)
- Da-Hye Kim
- National Institute of Agricultural Science, Rural Development Administration, Jeonju 54874, Korea.
| | - Sangkyu Park
- National Institute of Agricultural Science, Rural Development Administration, Jeonju 54874, Korea.
| | - Jong-Yeol Lee
- National Institute of Agricultural Science, Rural Development Administration, Jeonju 54874, Korea.
| | - Sun-Hwa Ha
- Department of Genetic Engineering and Graduate School of Biotechnology, Kyung Hee University, Yongin 17104, Korea.
| | - Jun-Gu Lee
- Department of Horticulture, College of Agriculture & Life Sciences, Chonbuk National University, Jeonju 54896, Korea.
| | - Sun-Hyung Lim
- National Institute of Agricultural Science, Rural Development Administration, Jeonju 54874, Korea.
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Zhang J, Xie M, Tuskan GA, Muchero W, Chen JG. Recent Advances in the Transcriptional Regulation of Secondary Cell Wall Biosynthesis in the Woody Plants. FRONTIERS IN PLANT SCIENCE 2018; 9:1535. [PMID: 30405670 PMCID: PMC6206300 DOI: 10.3389/fpls.2018.01535] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 09/28/2018] [Indexed: 05/19/2023]
Abstract
Plant cell walls provide structural support for growth and serve as a barrier for pathogen attack. Plant cell walls are also a source of renewable biomass for conversion to biofuels and bioproducts. Understanding plant cell wall biosynthesis and its regulation is of critical importance for the genetic modification of plant feedstocks for cost-effective biofuels and bioproducts conversion and production. Great progress has been made in identifying enzymes involved in plant cell wall biosynthesis, and in Arabidopsis it is generally recognized that the regulation of genes encoding these enzymes is under a transcriptional regulatory network with coherent feedforward and feedback loops. However, less is known about the transcriptional regulation of plant secondary cell wall (SCW) biosynthesis in woody species despite of its high relevance to biofuels and bioproducts conversion and production. In this article, we synthesize recent progress on the transcriptional regulation of SCW biosynthesis in Arabidopsis and contrast to what is known in woody species. Furthermore, we evaluate progress in related emerging regulatory machineries targeting transcription factors in this complex regulatory network of SCW biosynthesis.
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Affiliation(s)
- Jin Zhang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Meng Xie
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, United States
| | - Gerald A. Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- *Correspondence: Wellington Muchero, Jin-Gui Chen,
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- *Correspondence: Wellington Muchero, Jin-Gui Chen,
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Tissue-Specific Transcriptome Analysis Reveals Multiple Responses to Salt Stress in Populus euphratica Seedlings. Genes (Basel) 2017; 8:genes8120372. [PMID: 29292723 PMCID: PMC5748690 DOI: 10.3390/genes8120372] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 11/24/2017] [Accepted: 11/29/2017] [Indexed: 01/05/2023] Open
Abstract
Salt stress is one of the most crucial factors impacting plant growth, development and reproduction. However, information regarding differences in tissue-specific gene expression patterns, which may improve a plant’s tolerance to salt stress, is limited. Here, we investigated the gene expression patterns in tissues of Populus euphratica Oliv. seedlings using RNA sequencing (RNA-Seq) technology. A total of 109.3 million, 125bp paired-end clean reads were generated, and 6428, 4797, 2335 and 3358 differentially expressed genes (DEGs) were identified in leaf, phloem, xylem and root tissues, respectively. While the tissue-specific DEGs under salt stress had diverse functions, “membrane transporter activity” was the most significant leaf function, whereas “oxidation–reduction process” was the most significant function in root tissue. Further analysis of the tissue-specific DEGs showed that the expression patterns or functions of gene families, such as SOS, NHX, GolS, GPX, APX, RBOHF and CBL, were diverse, suggesting that calcium signaling, reactive oxygen species (ROS) and salt overly sensitive (SOS) pathways are all involved in ionic homeostasis in tissues from P. euphratica seedlings. The DEGs, for example the up-regulated antioxidant genes, contribute to ROS-scavenging induced by salt stress but result in decreased Na+ concentrations in root vasculature cells and in xylem sap, while the down-regulated rbohF leads to the reverse results. These results suggest that the divergence of DEGs expression patterns contribute to maintenance of ionic and ROS homeostasis in tissues and improve plant salinity tolerance. We comprehensively analyzed the response of P. euphratica seedlings to salt stress and provide helpful genetic resources for studying plant-abiotic stress interactions.
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Reciprocal cross-regulation of VND and SND multigene TF families for wood formation in Populus trichocarpa. Proc Natl Acad Sci U S A 2017; 114:E9722-E9729. [PMID: 29078399 DOI: 10.1073/pnas.1714422114] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Secondary cell wall (SCW) biosynthesis is the biological process that generates wood, an important renewable feedstock for materials and energy. NAC domain transcription factors, particularly Vascular-Related NAC-Domain (VND) and Secondary Wall-Associated NAC Domain (SND) proteins, are known to regulate SCW differentiation. The regulation of VND and SND is important to maintain homeostasis for plants to avoid abnormal growth and development. We previously identified a splice variant, PtrSND1-A2IR , derived from PtrSND1-A2 as a dominant-negative regulator, which suppresses the transactivation of all PtrSND1 family members. PtrSND1-A2IR also suppresses the self-activation of the PtrSND1 family members except for its cognate transcription factor, PtrSND1-A2, suggesting the existence of an unknown factor needed to regulate PtrSND1-A2 Here, a splice variant, PtrVND6-C1IR , derived from PtrVND6-C1 was discovered that suppresses the protein functions of all PtrVND6 family members. PtrVND6-C1IR also suppresses the expression of all PtrSND1 members, including PtrSND1-A2, demonstrating that PtrVND6-C1IR is the previously unidentified regulator of PtrSND1-A2 We also found that PtrVND6-C1IR cannot suppress the expression of its cognate transcription factor, PtrVND6-C1PtrVND6-C1 is suppressed by PtrSND1-A2IR Both PtrVND6-C1IR and PtrSND1-A2IR cannot suppress their cognate transcription factors but can suppress all members of the other family. The results indicate that the splice variants from the PtrVND6 and PtrSND1 family may exert reciprocal cross-regulation for complete transcriptional regulation of these two families in wood formation. This reciprocal cross-regulation between families suggests a general mechanism among NAC domain proteins and likely other transcription factors, where intron-retained splice variants provide an additional level of regulation.
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Becker MG, Walker PL, Pulgar-Vidal NC, Belmonte MF. SeqEnrich: A tool to predict transcription factor networks from co-expressed Arabidopsis and Brassica napus gene sets. PLoS One 2017; 12:e0178256. [PMID: 28575075 PMCID: PMC5456048 DOI: 10.1371/journal.pone.0178256] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 05/10/2017] [Indexed: 01/08/2023] Open
Abstract
Transcription factors and their associated DNA binding sites are key regulatory elements of cellular differentiation, development, and environmental response. New tools that predict transcriptional regulation of biological processes are valuable to researchers studying both model and emerging-model plant systems. SeqEnrich predicts transcription factor networks from co-expressed Arabidopsis or Brassica napus gene sets. The networks produced by SeqEnrich are supported by existing literature and predicted transcription factor–DNA interactions that can be functionally validated at the laboratory bench. The program functions with gene sets of varying sizes and derived from diverse tissues and environmental treatments. SeqEnrich presents as a powerful predictive framework for the analysis of Arabidopsis and Brassica napus co-expression data, and is designed so that researchers at all levels can easily access and interpret predicted transcriptional circuits. The program outperformed its ancestral program ChipEnrich, and produced detailed transcription factor networks from Arabidopsis and Brassica napus gene expression data. The SeqEnrich program is ideal for generating new hypotheses and distilling biological information from large-scale expression data.
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Affiliation(s)
- Michael G. Becker
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Philip L. Walker
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | | | - Mark F. Belmonte
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
- * E-mail:
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Cosio C, Ranocha P, Francoz E, Burlat V, Zheng Y, Perry SE, Ripoll JJ, Yanofsky M, Dunand C. The class III peroxidase PRX17 is a direct target of the MADS-box transcription factor AGAMOUS-LIKE15 (AGL15) and participates in lignified tissue formation. THE NEW PHYTOLOGIST 2017; 213:250-263. [PMID: 27513887 DOI: 10.1111/nph.14127] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 07/03/2016] [Indexed: 05/22/2023]
Abstract
Several physiological functions have been attributed to class III peroxidases (PRXs) in plants, but the in planta role of most members of this family still remains undetermined. Here, we report the first functional characterization of PRX17 (At2g22420), one of the 73 members of this family in Arabidopsis thaliana. Localization of PRX17 was examined by transient expression in Nicotiana benthamiana. Loss- and gain-of-function mutants in A. thaliana were studied. Regulation at the gene and protein levels was analyzed using β-glucuronidase (GUS) activity, quantitative reverse transcriptase (qRT)-PCR, zymography, and chromatin immunoprecipitation. Phenotypes were characterized including lignin and xylan contents. PRX17 was expressed in various tissues, including vascular tissues, and PRX17 was localized to the cell wall. In prx17, the lignin content was reduced in the stem and siliques and bolting was delayed, while the opposite phenotype was observed in 35S:PRX17 plants, together with a significant increase of lignin and xylan immunofluorescence signal. Finally, we demonstrated that the transcription factor AGAMOUS-LIKE15 (AGL15) binds to the PRX17 promoter and regulates PRX17 expression level. This converging set of structural, transcriptomic and physiological data suggests that PRX17, under the control of AGL15, contributes to developmental programs by playing an essential role in regulating age-dependent lignified tissue formation, including changes in cell wall properties.
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Affiliation(s)
- Claudia Cosio
- Division of Biological Sciences, Section Cell & Developmental Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Philippe Ranocha
- Laboratoire de Recherche en Sciences Végétales, CNRS, UPS, Université de Toulouse, 24 chemin de Borde Rouge, Auzeville, BP42617, Castanet Tolosan, 31326, France
| | - Edith Francoz
- Laboratoire de Recherche en Sciences Végétales, CNRS, UPS, Université de Toulouse, 24 chemin de Borde Rouge, Auzeville, BP42617, Castanet Tolosan, 31326, France
| | - Vincent Burlat
- Laboratoire de Recherche en Sciences Végétales, CNRS, UPS, Université de Toulouse, 24 chemin de Borde Rouge, Auzeville, BP42617, Castanet Tolosan, 31326, France
| | - Yumei Zheng
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, 40546-0091, USA
| | - Sharyn E Perry
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, 40546-0091, USA
| | - Juan-Jose Ripoll
- Division of Biological Sciences, Section Cell & Developmental Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Martin Yanofsky
- Division of Biological Sciences, Section Cell & Developmental Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Christophe Dunand
- Laboratoire de Recherche en Sciences Végétales, CNRS, UPS, Université de Toulouse, 24 chemin de Borde Rouge, Auzeville, BP42617, Castanet Tolosan, 31326, France
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48
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Co-expression network analyses identify functional modules associated with development and stress response in Gossypium arboreum. Sci Rep 2016; 6:38436. [PMID: 27922095 PMCID: PMC5138846 DOI: 10.1038/srep38436] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 11/09/2016] [Indexed: 11/22/2022] Open
Abstract
Cotton is an economically important crop, essential for the agriculture and textile industries. Through integrating transcriptomic data, we discovered that multi-dimensional co-expression network analysis was powerful for predicting cotton gene functions and functional modules. Here, the recently available transcriptomic data on Gossypium arboreum, including data on multiple growth stages of tissues and stress treatment samples were applied to construct a co-expression network exploring multi-dimensional expression (development and stress) through multi-layered approaches. Based on differential gene expression and network analysis, a fibre development regulatory module of the gene GaKNL1 was found to regulate the second cell wall through repressing the activity of REVOLUTA, and a tissue-selective module of GaJAZ1a was examined in response to water stress. Moreover, comparative genomics analysis of the JAZ1-related regulatory module revealed high conservation across plant species. In addition, 1155 functional modules were identified through integrating the co-expression network, module classification and function enrichment tools, which cover functions such as metabolism, stress responses, and transcriptional regulation. In the end, an online platform was built for network analysis (http://structuralbiology.cau.edu.cn/arboreum), which could help to refine the annotation of cotton gene function and establish a data mining system to identify functional genes or modules with important agronomic traits.
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49
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Chan AC, Khan D, Girard IJ, Becker MG, Millar JL, Sytnik D, Belmonte MF. Tissue-specific laser microdissection of the Brassica napus funiculus improves gene discovery and spatial identification of biological processes. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:3561-71. [PMID: 27194740 PMCID: PMC4892738 DOI: 10.1093/jxb/erw179] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The three primary tissue systems of the funiculus each undergo unique developmental programs to support the growth and development of the filial seed. To understand the underlying transcriptional mechanisms that orchestrate development of the funiculus at the globular embryonic stage of seed development, we used laser microdissection coupled with RNA-sequencing to produce a high-resolution dataset of the mRNAs present in the epidermis, cortex, and vasculature of the Brassica napus (canola) funiculus. We identified 7761 additional genes in these tissues compared with the whole funiculus organ alone using this technology. Differential expression and enrichment analyses were used to identify several biological processes associated with each tissue system. Our data show that cell wall modification and lipid metabolism are prominent in the epidermis, cell growth and modification occur in the cortex, and vascular tissue proliferation and differentiation occur in the central vascular strand. We provide further evidence that each of the three tissue systems of the globular stage funiculus are involved in specific biological processes that all co-ordinate to support seed development. The identification of genes and gene regulators responsible for tissue-specific developmental processes of the canola funiculus now serves as a valuable resource for seed improvement research.
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Affiliation(s)
- Ainsley C Chan
- University of Manitoba, Department of Biological Sciences, 50 Sifton Road, Winnipeg, MB R3T 2N2, Canada
| | - Deirdre Khan
- University of Manitoba, Department of Biological Sciences, 50 Sifton Road, Winnipeg, MB R3T 2N2, Canada
| | - Ian J Girard
- University of Manitoba, Department of Biological Sciences, 50 Sifton Road, Winnipeg, MB R3T 2N2, Canada
| | - Michael G Becker
- University of Manitoba, Department of Biological Sciences, 50 Sifton Road, Winnipeg, MB R3T 2N2, Canada
| | - Jenna L Millar
- University of Manitoba, Department of Biological Sciences, 50 Sifton Road, Winnipeg, MB R3T 2N2, Canada
| | - David Sytnik
- University of Manitoba, Department of Biological Sciences, 50 Sifton Road, Winnipeg, MB R3T 2N2, Canada
| | - Mark F Belmonte
- University of Manitoba, Department of Biological Sciences, 50 Sifton Road, Winnipeg, MB R3T 2N2, Canada
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Kamimura N, Mori T, Nakabayashi R, Tsuji Y, Hishiyama S, Saito K, Masai E, Kajita S. Expression and functional analyses of a putative phenylcoumaran benzylic ether reductase in Arabidopsis thaliana. PLANT CELL REPORTS 2016; 35:513-526. [PMID: 26601823 DOI: 10.1007/s00299-015-1899-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 10/19/2015] [Accepted: 11/04/2015] [Indexed: 06/05/2023]
Abstract
A candidate gene for phenylcoumaran benzylic ether reductase in Arabidopsis thaliana encodes a peptide with predicted functional activity and plays a crucial role in secondary metabolism. Phenylcoumaran benzylic ether reductase (PCBER) is thought to be an enzyme crucial in the biosynthesis of 8-5'-linked neolignans. Genes of the enzyme have been isolated and characterized in several plant species. In this study, we cloned cDNA and the 5'-untranslated region of one PCBER candidate gene (At4g39230, designated AtPCBER1) from Arabidopsis thaliana. At the amino acid level, AtPCBER1 shows high sequence identity (64-71 %) with PCBERs identified from other plant species. Expression analyses of AtPCBER1 by reverse transcriptase-polymerase chain reaction and histochemical analysis of transgenic plants harboring the 5'-untranslated region of AtPCBER1 linked with gus coding sequence indicate that expression is induced by wounding and is expressed in most tissues, including flower, stem, leaf, and root. Catalytic analysis of recombinant AtPCBER1 with neolignan and lignans in the presence of NADPH suggests that the protein can reduce not only the 8-5'-linked neolignan, dehydrodiconiferyl alcohol, but also 8-8' linked lignans, pinoresinol, and lariciresinol, with lower activities. To investigate further, we performed metabolomic analyses of transgenic plants in which the target gene was up- or down-regulated. Our results indicate no significant effects of AtPCBER1 gene regulation on plant growth and development; however, levels of some secondary metabolites, including lignans, flavonoids, and glucosinolates, differ between wild-type and transgenic plants. Taken together, our findings indicate that AtPCBER1 encodes a polypeptide with PCBER activity and has a critical role in the biosynthesis of secondary metabolites in A. thaliana.
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Affiliation(s)
- Naofumi Kamimura
- Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka-cho, Nagaoka, Niigata, 940-2188, Japan
| | - Tetsuya Mori
- Metabolomics Research Group, Center for Sustainable Resource Science, RIKEN, 1-7-22 Tsurumi, Kanagawa, 230-0045, Japan
| | - Ryo Nakabayashi
- Metabolomics Research Group, Center for Sustainable Resource Science, RIKEN, 1-7-22 Tsurumi, Kanagawa, 230-0045, Japan
| | - Yukiko Tsuji
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53726-4084, USA
| | - Shojiro Hishiyama
- Forestry and Forest Products Research Institute, 1 Matsunosato, Ibaraki, 305-8687, Japan
| | - Kazuki Saito
- Metabolomics Research Group, Center for Sustainable Resource Science, RIKEN, 1-7-22 Tsurumi, Kanagawa, 230-0045, Japan
| | - Eiji Masai
- Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka-cho, Nagaoka, Niigata, 940-2188, Japan
| | - Shinya Kajita
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan.
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