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Riseh RS, Fathi F, Lagzian A, Vatankhah M, Kennedy JF. Modifying lignin: A promising strategy for plant disease control. Int J Biol Macromol 2024; 271:132696. [PMID: 38823737 DOI: 10.1016/j.ijbiomac.2024.132696] [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: 03/09/2024] [Revised: 05/02/2024] [Accepted: 05/26/2024] [Indexed: 06/03/2024]
Abstract
Lignin is a complex polymer found in the cell walls of plants, providing structural support and protection against pathogens. By modifying lignin composition and structure, scientists aim to optimize plant defense responses and increase resistance to pathogens. This can be achieved through various genetic engineering techniques which involve manipulating the genes responsible for lignin synthesis. By either up regulating or down regulating specific genes, researchers can alter the lignin content, composition, or distribution in plant tissues. Reducing lignin content in specific tissues like leaves can improve the effectiveness of defense mechanisms by allowing for better penetration of antimicrobial compounds. Overall, Lignin modification through techniques has shown promising results in enhancing various plants resistance against pathogens. Furthermore, lignin modification can have additional benefits beyond pathogen resistance. It can improve biomass processing for biofuel production by reducing lignin recalcitrance, making the extraction of sugars from cellulose more efficient. The complexity of lignin biosynthesis and its interactions with other plant components make it a challenging target for modification. Additionally, the potential environmental impact and regulatory considerations associated with genetically modified organisms (GMOs) require careful evaluation. Ongoing research aims to further optimize this approach and develop sustainable solutions for crop protection.
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Affiliation(s)
- Roohallah Saberi Riseh
- Department of Plant Protection, Faculty of Agriculture, Vali-e-Asr University of Rafsanjan, 7718897111 Rafsanjan, Iran.
| | - Fariba Fathi
- Department of Plant Protection, Faculty of Agriculture, Vali-e-Asr University of Rafsanjan, 7718897111 Rafsanjan, Iran
| | - Arezoo Lagzian
- Department of Plant Protection, Faculty of Agriculture, Vali-e-Asr University of Rafsanjan, 7718897111 Rafsanjan, Iran
| | - Masoumeh Vatankhah
- Department of Plant Protection, Faculty of Agriculture, Vali-e-Asr University of Rafsanjan, 7718897111 Rafsanjan, Iran
| | - John F Kennedy
- Chembiotech Laboratories Ltd, WR15 8FF Tenbury Wells, United Kingdom.
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Wang R, Wu M, Zhang X, Jiang T, Wei Z. Methylation of microRNA genes and its effect on secondary xylem development of stem in poplar. THE PLANT GENOME 2024:e20446. [PMID: 38528365 DOI: 10.1002/tpg2.20446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 02/21/2024] [Accepted: 02/27/2024] [Indexed: 03/27/2024]
Abstract
MicroRNAs (miRNAs) and DNA methylation are both vital regulators of gene expression. DNA methylation can affect the transcription of miRNAs, just like coding genes, through methylating the CpG islands in the gene regions of miRNAs. Although previous studies have shown that DNA methylation and miRNAs can each be involved in the process of wood formation, the relationship between the two has been relatively little studied in plant wood formation. Studies have shown that the second internode (IN2) (from top to bottom) of 3-month-old poplar trees can represent the primary stage of poplar stem development and IN8 can represent the secondary stage. There were also significant differences in DNA methylation patterns and miRNA expression patterns obtained from PS and SS. In this study, we first interactively analyzed methylation and miRNA sequencing data to identify 43 differentially expressed miRNAs regulated by differential methylation from the primary stage and secondary stage, which were found to be involved in multiple biological processes related to wood formation by enrichment analysis. In addition, six miRNA/target gene modules were finally identified as potentially involved in secondary xylem development of poplar stems through degradome sequencing and functional analysis. In conclusion, this study provides important reference information on the mechanism of interaction between different regulatory pathways of wood formation.
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Affiliation(s)
- Ruiqi Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Meixuan Wu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Xiao Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Tingbo Jiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Zhigang Wei
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin, China
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Kruse LH, Sunstrum FG, Garcia D, López Pérez G, Jancsik S, Bohlmann J, Irmisch S. Improved production of the antidiabetic metabolite montbretin A in Nicotiana benthamiana: discovery, characterization, and use of Crocosmia shikimate shunt genes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:766-785. [PMID: 37960967 DOI: 10.1111/tpj.16528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 09/20/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023]
Abstract
The plant-specialized metabolite montbretin A (MbA) is being developed as a new treatment option for type-2 diabetes, which is among the ten leading causes of premature death and disability worldwide. MbA is a complex acylated flavonoid glycoside produced in small amounts in below-ground organs of the perennial plant Montbretia (Crocosmia × crocosmiiflora). The lack of a scalable production system limits the development and potential application of MbA as a pharmaceutical or nutraceutical. Previous efforts to reconstruct montbretin biosynthesis in Nicotiana benthamiana (Nb) resulted in low yields of MbA and higher levels of montbretin B (MbB) and montbretin C (MbC). MbA, MbB, and MbC are nearly identical metabolites differing only in their acyl moieties, derived from caffeoyl-CoA, coumaroyl-CoA, and feruloyl-CoA, respectively. In contrast to MbA, MbB and MbC are not pharmaceutically active. To utilize the montbretia caffeoyl-CoA biosynthesis for improved MbA engineering in Nb, we cloned and characterized enzymes of the shikimate shunt of the general phenylpropanoid pathway, specifically hydroxycinnamoyl-CoA: shikimate hydroxycinnamoyl transferase (CcHCT), p-coumaroylshikimate 3'-hydroxylase (CcC3'H), and caffeoylshikimate esterase (CcCSE). Gene expression patterns suggest that CcCSE enables the predominant formation of MbA, relative to MbB and MbC, in montbretia. This observation is supported by results from in vitro characterization of CcCSE and reconstruction of the shikimate shunt in yeast. Using CcHCT together with montbretin biosynthetic genes in multigene constructs resulted in a 30-fold increase of MbA in Nb. This work advances our understanding of the phenylpropanoid pathway and features a critical step towards improved MbA production in bioengineered Nb.
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Affiliation(s)
- Lars H Kruse
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Frederick G Sunstrum
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Daniela Garcia
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Guillermo López Pérez
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Sharon Jancsik
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Joerg Bohlmann
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
- Department of Forest and Conservation Science, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Sandra Irmisch
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
- Plant Sciences, Institute of Biology, Leiden University, Leiden, 2333 BE, Netherlands
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4
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Yu G, Sun B, Zhu Z, Mehareb EM, Teng A, Han J, Zhang H, Liu J, Liu X, Raza G, Zhang B, Zhang Y, Wang K. Genome-wide DNase I-hypersensitive site assay reveals distinct genomic distributions and functional features of open chromatin in autopolyploid sugarcane. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:573-589. [PMID: 37897092 DOI: 10.1111/tpj.16513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 09/15/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023]
Abstract
The characterization of cis-regulatory DNA elements (CREs) is essential for deciphering the regulation of gene expression in eukaryotes. Although there have been endeavors to identify CREs in plants, the properties of CREs in polyploid genomes are still largely unknown. Here, we conducted the genome-wide identification of DNase I-hypersensitive sites (DHSs) in leaf and stem tissues of the auto-octoploid species Saccharum officinarum. We revealed that DHSs showed highly similar distributions in the genomes of these two S. officinarum tissues. Notably, we observed that approximately 74% of DHSs were located in distal intergenic regions, suggesting considerable differences in the abundance of distal CREs between S. officinarum and other plants. Leaf- and stem-dependent transcriptional regulatory networks were also developed by mining the binding motifs of transcription factors (TFs) from tissue-specific DHSs. Four TEOSINTE BRANCHED 1, CYCLOIDEA, and PCF1 (TCP) TFs (TCP2, TCP4, TCP7, and TCP14) and two ethylene-responsive factors (ERFs) (ERF109 and ERF03) showed strong causal connections with short binding distances from each other, pointing to their possible roles in the regulatory networks of leaf and stem development. Through functional validation in transiently transgenic protoplasts, we isolate a set of tissue-specific promoters. Overall, the DHS maps presented here offer a global view of the potential transcriptional regulatory elements in polyploid sugarcane and can be expected to serve as a valuable resource for both transcriptional network elucidation and genome editing in sugarcane breeding.
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Affiliation(s)
- Guangrun Yu
- School of Life Sciences, Nantong University, Nantong, 226019, China
| | - Bo Sun
- School of Life Sciences, Nantong University, Nantong, 226019, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhiying Zhu
- School of Life Sciences, Nantong University, Nantong, 226019, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Eid M Mehareb
- Sugar Crops Research Institute (SRCI), Agricultural Research Center (ARC), Giza, 12619, Egypt
| | - Ailing Teng
- School of Life Sciences, Nantong University, Nantong, 226019, China
| | - Jinlei Han
- School of Life Sciences, Nantong University, Nantong, 226019, China
| | - Hui Zhang
- School of Life Sciences, Nantong University, Nantong, 226019, China
| | - Jiayong Liu
- Sugarcane Institute, Yunnan Academy of Agricultural Sciences, Kaiyuan, 661699, China
| | - Xinlong Liu
- Sugarcane Institute, Yunnan Academy of Agricultural Sciences, Kaiyuan, 661699, China
| | - Ghulam Raza
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, 38000, Pakistan
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, North Carolina, 27858, USA
| | - Yuebin Zhang
- Sugarcane Institute, Yunnan Academy of Agricultural Sciences, Kaiyuan, 661699, China
| | - Kai Wang
- School of Life Sciences, Nantong University, Nantong, 226019, China
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Wang Q, Lei S, Yan J, Song Y, Qian J, Zheng M, Hsu YF. UBC6, a ubiquitin-conjugating enzyme, participates in secondary cell wall thickening in the inflorescence stem of Arabidopsis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 205:108152. [PMID: 37944242 DOI: 10.1016/j.plaphy.2023.108152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 10/22/2023] [Accepted: 10/29/2023] [Indexed: 11/12/2023]
Abstract
Secondary cell wall (SCW) thickening in plant inflorescence stems is a complicated cellular process that is essential for stem strength and biomass. Although Arabidopsis NAC transcription factor (TF) 1 (NST1) regulates the SCW thickening in anther walls, the single T-DNA-insertion mutant (nst1) does not show disrupted SCW thickening in anther endothecium, interfascicular fibers or xylem. To better understand the regulatory mechanism of this process, we generated an ethyl methanesulfonate (EMS)-mutagenized Arabidopsis population with the nst1 background. scd5 (SCW-defective mutant 5) was isolated in a forward genetic screen from the EMS mutant library, which displayed not only less lignin deposition in the interfascicular fiber and xylem than the wild type but also a pendent inflorescence stem. The EMS-induced mutation associated with the scd5 phenotype was found in the 5th exon of At2G46030 that encodes a ubiquitin-conjugating enzyme (UBC6), we thereby renamed the allele nst1 ubc6. Overexpressing UBC6 in nst1 ubc6 rescued the defective SCW, whereas disrupting UBC6 in nst1 by the CRISPR/Cas9 system caused a phenotype similar to that observed in nst1 ubc6. UBC6 was localized to the nucleus and plasma membrane, and possessed E2 ubiquitin-conjugating activity in vitro. MYB7 and MYB32 are considered as transcription repressors in the phenylpropanoid pathway and are involved in NAC TF-related transcriptional regulation in SCW thickening. UBC6 can interact with MYB7 and MYB32 and positively mediate the degradation of MYB7 and MYB32 by the 26S proteasome. Overall, these results indicated the contribution of UBC6 to SCW thickening in Arabidopsis inflorescence stems.
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Affiliation(s)
- Qingzhu Wang
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Shikang Lei
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Jiawen Yan
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Yu Song
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Jie Qian
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Min Zheng
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, 400715, China.
| | - Yi-Feng Hsu
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, 400715, China.
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Baldi P, Asquini E, Nicolussi Golo G, Populin F, Moser M. Isoenzymes of the Flavonoid and Phenylpropanoid Pathways Show Organ-Specific Regulation during Apple Fruit Development. Int J Mol Sci 2023; 24:14353. [PMID: 37762656 PMCID: PMC10532258 DOI: 10.3390/ijms241814353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 09/14/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023] Open
Abstract
Elucidating the molecular mechanisms controlling fruit development is a primary target for the improvement of new apple (Malus × domestica Borkh.) cultivars. The first two weeks of development following pollination are crucial to determine fruit characteristics. During this period, a lot of changes take place in apple fruit, going from rapid cell division to the production of important metabolites. In this work, attention was focused on the phenylpropanoid and flavonoid pathways responsible for the production of numerous compounds contributing to fruit quality, such as flavonols, catechins, dihydrochalcones and anthocyanins. A total of 17 isoenzymes were identified, belonging to seven classes of the phenylpropanoid and flavonoid pathways that, despite showing more than 80% sequence identity, showed differential expression regulation during the first two weeks of apple fruit development. This feature seems to be quite common for most of the enzymes of both pathways. Differential regulation of isoenzymes was shown to be present in both 'Golden Delicious' and a wild relative (Malus mandshurica), even though differences were also present. Each isoenzyme showed a specific pattern of expression in the flower and fruit organs, suggesting that genes coding for enzymes with the same function may control different aspects of plant biology. Finally, promoter analysis was performed in order to highlight differences in the number and type of regulatory motifs. Overall, our results indicate that the control of the expression of genes involved in the phenylpropanoid and flavonoid pathways may be very complex as not only enzymes belonging to the same class, but even putative isoenzymes, can have different roles for the plant. Such genes may represent an important regulatory mechanism, as they would allow the plant to fine-tune the processing of metabolic intermediates towards different branches of the pathway, for example, in an organ-specific way.
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Affiliation(s)
- Paolo Baldi
- Department of Genomics and Biology of Fruit Crops, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, 38098 Trento, Italy; (E.A.); (G.N.G.); (F.P.); (M.M.)
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7
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Duan R, Zhang X, Liu Y, Wang L, Yang J, Wang L, Wang S, Su Y, Xue H. Transcriptome and Physiological Analysis Highlight Lignin Metabolism of the Fruit Dots Disordering during Postharvest Cold Storage in 'Danxiahong' Pear. Genes (Basel) 2023; 14:1785. [PMID: 37761925 PMCID: PMC10531081 DOI: 10.3390/genes14091785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/07/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
Pear (Pyrus L.) is one of the most important fruits in the world. Fruit dots are an important trait that affects pear quality. Abnormal fruit dots usually reduce the merchantability of pears. In this research, during cold storage, 'Danxiahong' pear fruit exhibited protrudent fruit dots on the peels. Microscopy system measurement showed that fruit dots size and height on the abnormal fruit peel were bigger and higher than the normal ones. Likewise, scanning electron microscopy observations indicated that the abnormal fruit peel, in contrast to the normal pear peel, exhibited an abnormal cell structure and fruit dots. Physiological analysis showed that the lignin content in abnormal fruit peel was significantly higher than in normal fruit peel. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis revealed that the top-enriched pathways were mainly associated with lignin synthesis and metabolism. The transcripts of lignin biosynthesis-associated genes were analyzed, and the results showed that the expression of a cascade of structural genes, including PpyPAL, PpyCCR, PpyC3H, PpyC4H, PpyHCT, PpyCAD, PpyLAC, and PpyPOD, was significantly induced in the protrudent peels. Furthermore, the expression of regulatory genes involved in lignin biosynthesis, especially the NAC-MYB-based gene regulatory network, was significantly upregulated in the abnormal peels. Real-time quantitative PCR (RT-qPCR) analysis confirmed the induction of lignin biosynthesis genes. Overall, this research revealed that the abnormal fruit surface was caused by fruit dots disorder during cold storage. This research provides insights into the fine regulation pathways in the prevention of fruit dots protrusion, especially in modulating lignin synthesis and metabolism during postharvest storage.
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Affiliation(s)
- Ruiwei Duan
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crop, Zhengzhou 450009, China; (R.D.); (X.Z.); (L.W.); (J.Y.); (L.W.); (S.W.); (Y.S.)
- Key Laboratory of Fruit Breeding Technology of Ministry of Agriculture and Rural Affairs, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
- Henan Key Laboratory of Fruit and Cucurbit Biology, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Xiangzhan Zhang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crop, Zhengzhou 450009, China; (R.D.); (X.Z.); (L.W.); (J.Y.); (L.W.); (S.W.); (Y.S.)
- Key Laboratory of Fruit Breeding Technology of Ministry of Agriculture and Rural Affairs, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
- Henan Key Laboratory of Fruit and Cucurbit Biology, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Yudong Liu
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China;
| | - Lei Wang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crop, Zhengzhou 450009, China; (R.D.); (X.Z.); (L.W.); (J.Y.); (L.W.); (S.W.); (Y.S.)
- Key Laboratory of Fruit Breeding Technology of Ministry of Agriculture and Rural Affairs, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
- Henan Key Laboratory of Fruit and Cucurbit Biology, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Jian Yang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crop, Zhengzhou 450009, China; (R.D.); (X.Z.); (L.W.); (J.Y.); (L.W.); (S.W.); (Y.S.)
- Key Laboratory of Fruit Breeding Technology of Ministry of Agriculture and Rural Affairs, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
- Henan Key Laboratory of Fruit and Cucurbit Biology, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Long Wang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crop, Zhengzhou 450009, China; (R.D.); (X.Z.); (L.W.); (J.Y.); (L.W.); (S.W.); (Y.S.)
- Key Laboratory of Fruit Breeding Technology of Ministry of Agriculture and Rural Affairs, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
- Henan Key Laboratory of Fruit and Cucurbit Biology, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Suke Wang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crop, Zhengzhou 450009, China; (R.D.); (X.Z.); (L.W.); (J.Y.); (L.W.); (S.W.); (Y.S.)
- Key Laboratory of Fruit Breeding Technology of Ministry of Agriculture and Rural Affairs, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
- Henan Key Laboratory of Fruit and Cucurbit Biology, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Yanli Su
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crop, Zhengzhou 450009, China; (R.D.); (X.Z.); (L.W.); (J.Y.); (L.W.); (S.W.); (Y.S.)
- Key Laboratory of Fruit Breeding Technology of Ministry of Agriculture and Rural Affairs, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
- Henan Key Laboratory of Fruit and Cucurbit Biology, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Huabai Xue
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crop, Zhengzhou 450009, China; (R.D.); (X.Z.); (L.W.); (J.Y.); (L.W.); (S.W.); (Y.S.)
- Key Laboratory of Fruit Breeding Technology of Ministry of Agriculture and Rural Affairs, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
- Henan Key Laboratory of Fruit and Cucurbit Biology, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
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Chen J, Liu M, Meng X, Zhang Y, Wang Y, Jiao N, Chen J. Multiomics studies with co-transformation reveal microRNAs via miRNA-TF-mRNA network participating in wood formation in Hevea brasiliensis. FRONTIERS IN PLANT SCIENCE 2023; 14:1068796. [PMID: 37645463 PMCID: PMC10461101 DOI: 10.3389/fpls.2023.1068796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 05/17/2023] [Indexed: 08/31/2023]
Abstract
Introduction MicroRNAs (miRNAs) are small endogenous non-coding RNAs that play an important role in wood formation in plants. However, the significance of the link between miRNAs and their target transcripts in wood formation remains unclear in rubber tree (Hevea brasiliensis). Methods In this study, we induced the formation of reaction wood by artificially bending rubber trees for 300 days and performed small RNA sequencing and transcriptome deep sequencing (RNA-seq) to describe the complement of miRNAs and their targets contributing to this process. Results and discussion We identified 5, 11, and 2 differentially abundant miRNAs in normal wood (NW) compared to tension wood (TW), in NW relative to opposite wood (OW), and between TW and OW, respectively. We also identified 12 novel miRNAs and 39 potential miRNA-mRNA pairs with different accumulation patterns in NW, TW, and OW. We noticed that many miRNAs targeted transcription factor genes, which were enriched in KEGG pathways associated with phenylpropanoid biosynthesis, phenylalanine metabolism, and pyruvate metabolism. Thus, miRNA-TF-mRNA network involved in wood formation via tension wood model were constructed. We validated the differential accumulation of miRNAs and their targets by RT-qPCR analysis and overexpressed miRNA in Nicotiana benthamiana with its potential target gene. These results will provide a reference for a deep exploration of growth and development in rubber tree.
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Affiliation(s)
- Jinhui Chen
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory/Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, School of Forestry, Hainan University, Sanya, China
- Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, Haikou, China
| | - Mingming Liu
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory/Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, School of Forestry, Hainan University, Sanya, China
- School of Tropical Crops, Hainan University, Haikou, China
| | - Xiangxu Meng
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory/Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, School of Forestry, Hainan University, Sanya, China
- Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, Haikou, China
| | - Yuanyuan Zhang
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
- State Centre for Rubber Breeding, Haikou, Hainan, China
| | - Yue Wang
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory/Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, School of Forestry, Hainan University, Sanya, China
- Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, Haikou, China
| | - Nanbo Jiao
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory/Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, School of Forestry, Hainan University, Sanya, China
- Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, Haikou, China
| | - Jianmiao Chen
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory/Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, School of Forestry, Hainan University, Sanya, China
- School of Tropical Crops, Hainan University, Haikou, China
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9
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Zhang YS, Xu Y, Xing WT, Wu B, Huang DM, Ma FN, Zhan RL, Sun PG, Xu YY, Song S. Identification of the passion fruit ( Passiflora edulis Sims) MYB family in fruit development and abiotic stress, and functional analysis of PeMYB87 in abiotic stresses. FRONTIERS IN PLANT SCIENCE 2023; 14:1124351. [PMID: 37215287 PMCID: PMC10196401 DOI: 10.3389/fpls.2023.1124351] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 03/21/2023] [Indexed: 05/24/2023]
Abstract
Environmental stresses are ubiquitous in agricultural cultivation, and they affect the healthy growth and development of edible tissues in passion fruit. The study of resistance mechanisms is important in understanding the adaptation and resistance of plants to environmental stresses. In this work, two differently resistant passion fruit varieties were selected, using the expression characteristics of the transcription factor MYB, to explore the resistance mechanism of the MYB gene under various environmental stresses. A total of 174 MYB family members were identified using high-quality passion fruit genomes: 98 2R-MYB, 5 3R-MYB, and 71 1R-MYB (MYB-relate). Their family information was systematically analyzed, including subcellular localization, physicochemical properties, phylogeny at the genomic level, promoter function, encoded proteins, and reciprocal regulation. In this study, bioinformatics and transcriptome sequencing were used to identify members of the PeMYB genes in passion fruit whole-genome data, and biological techniques, such as qPCR, gene clone, and transient transformation of yeast, were used to determine the function of the passion fruit MYB genes in abiotic stress tolerance. Transcriptomic data were obtained for differential expression characteristics of two resistant and susceptible varieties, three expression patterns during pulp development, and four induced expression patterns under abiotic stress conditions. We further focused on the resistance mechanism of PeMYB87 in environmental stress, and we selected 10 representative PeMYB genes for quantitative expression verification. Most of the genes were differentially induced by four abiotic stresses, among which PeMYB87 responded significantly to high-temperature-induced expression and overexpression of the PeMYB87 gene in the yeast system. The transgenic PeMYB87 in yeast showed different degrees of stress resistance under exposure to cold, high temperatures, drought, and salt stresses. These findings lay the foundation for further analysis of the biological functions of PeMYBs involved in stress resistance in passion fruit.
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Affiliation(s)
- Yan-shu Zhang
- National Key Laboratory for Tropical Crop Breeding, Haikou Experimental Station, Tropical Crops Genetic Resources Institute, CATAS/ Germplasm Repository of Passiflora, Haikou, Hainan, China
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, China
- College of Landscape and Horticulture, Southwest Forestry University, Kunming, Yunnan, China
| | - Yi Xu
- National Key Laboratory for Tropical Crop Breeding, Haikou Experimental Station, Tropical Crops Genetic Resources Institute, CATAS/ Germplasm Repository of Passiflora, Haikou, Hainan, China
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, China
| | - Wen-ting Xing
- National Key Laboratory for Tropical Crop Breeding, Haikou Experimental Station, Tropical Crops Genetic Resources Institute, CATAS/ Germplasm Repository of Passiflora, Haikou, Hainan, China
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
| | - Bin Wu
- National Key Laboratory for Tropical Crop Breeding, Haikou Experimental Station, Tropical Crops Genetic Resources Institute, CATAS/ Germplasm Repository of Passiflora, Haikou, Hainan, China
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
| | - Dong-mei Huang
- National Key Laboratory for Tropical Crop Breeding, Haikou Experimental Station, Tropical Crops Genetic Resources Institute, CATAS/ Germplasm Repository of Passiflora, Haikou, Hainan, China
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
| | - Fu-ning Ma
- National Key Laboratory for Tropical Crop Breeding, Haikou Experimental Station, Tropical Crops Genetic Resources Institute, CATAS/ Germplasm Repository of Passiflora, Haikou, Hainan, China
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, China
| | - Ru-lin Zhan
- National Key Laboratory for Tropical Crop Breeding, Haikou Experimental Station, Tropical Crops Genetic Resources Institute, CATAS/ Germplasm Repository of Passiflora, Haikou, Hainan, China
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, China
| | - Pei-guang Sun
- National Key Laboratory for Tropical Crop Breeding, Haikou Experimental Station, Tropical Crops Genetic Resources Institute, CATAS/ Germplasm Repository of Passiflora, Haikou, Hainan, China
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, China
| | - Yong-yan Xu
- College of Landscape and Horticulture, Southwest Forestry University, Kunming, Yunnan, China
| | - Shun Song
- National Key Laboratory for Tropical Crop Breeding, Haikou Experimental Station, Tropical Crops Genetic Resources Institute, CATAS/ Germplasm Repository of Passiflora, Haikou, Hainan, China
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, China
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10
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Zhang M, Sun Y, Di P, Han M, Yang L. Combining Metabolomics and Transcriptomics to Reveal the Regulatory Mechanism of Taproot Enlargement in Panax ginseng. Int J Mol Sci 2023; 24:ijms24065590. [PMID: 36982666 PMCID: PMC10058914 DOI: 10.3390/ijms24065590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/11/2023] [Accepted: 03/13/2023] [Indexed: 03/17/2023] Open
Abstract
Ginseng is regarded as the “king of herbs” in China, with its roots and rhizomes used as medicine, and it has a high medicinal value. In order to meet the market demand, the artificial cultivation of ginseng emerged, but different growth environments significantly affect the root morphology of garden ginseng. In this study, we used ginseng cultivated in deforested land (CF-CG) and ginseng cultivated in farmland (F-CG) as experimental materials. These two phenotypes were explored at the transcriptomic and metabolomic levels so as to understand the regulatory mechanism of taproot enlargement in garden ginseng. The results show that, compared with those of F-CG, the thickness of the main roots in CF-CG was increased by 70.5%, and the fresh weight of the taproots was increased by 305.4%. Sucrose, fructose and ginsenoside were significantly accumulated in CF-CG. During the enlargement of the taproots of CF-CG, genes related to starch and sucrose metabolism were significantly up-regulated, while genes related to lignin biosynthesis were significantly down-regulated. Auxin, gibberellin and abscisic acid synergistically regulated the enlargement of the taproots of the garden ginseng. In addition, as a sugar signaling molecule, T6P might act on the auxin synthesis gene ALDH2 to promote the synthesis of auxin and, thus, participate in the growth and development of garden ginseng roots. In summary, our study is conducive to clarifying the molecular regulation mechanism of taproot enlargement in garden ginseng, and it provides new insights for the further exploration of the morphogenesis of ginseng roots.
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Affiliation(s)
| | | | | | - Mei Han
- Correspondence: (M.H.); (L.Y.)
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11
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Li Y, Zhang T, Kang Y, Wang P, Yu W, Wang J, Li W, Jiang X, Zhou Y. Integrated metabolome, transcriptome analysis, and multi-flux full-length sequencing offer novel insights into the function of lignin biosynthesis as a Sesuvium portulacastrum response to salt stress. Int J Biol Macromol 2023; 237:124222. [PMID: 36990407 DOI: 10.1016/j.ijbiomac.2023.124222] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/21/2023] [Accepted: 03/24/2023] [Indexed: 03/30/2023]
Abstract
Sesuvium portulacastrum is a typical halophyte. However, few studies have investigated its salt-tolerant molecular mechanism. In this study, metabolome, transcriptome, and multi-flux full-length sequencing analysis were conducted to investigate the significantly different metabolites (SDMs) and differentially expressed genes (DEGs) of S. portulacastrum samples under salinity. The complete-length transcriptome of S. portulacastrum was developed, which contained 39,659 non-redundant unigenes. RNA-seq results showed that 52 DEGs involved in lignin biosynthesis may be responsible for S. portulacastrum salt tolerance. Furthermore, 130 SDMs were identified, and the salt response could be attributed to the p-coumaryl alcohol-rich in lignin biosynthesis. The co-expression network that was constructed after comparing the different salt treatment processes showed that the p-Coumaryl alcohol was linked to 30 DEGs. Herein, 8 structures genes, i.e., Sp4CL, SpCAD, SpCCR, SpCOMT, SpF5H, SpCYP73A, SpCCoAOMT, and SpC3'H were identified as significant factors in regulating lignin biosynthesis. Further investigation revealed that 64 putative transcription factors (TFs) may interact with the promoters of the above-mentioned genes. Together, the data revealed a potential regulatory network comprising important genes, putative TFs, and metabolites involved in the lignin biosynthesis of S. portulacastrum roots under salt stress, which could serve as a rich useful genetic resource for breeding excellent salt-tolerant plants.
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12
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Wang P, Guo L, Morgan J, Dudareva N, Chapple C. Transcript and metabolite network perturbations in lignin biosynthetic mutants of Arabidopsis. PLANT PHYSIOLOGY 2022; 190:2828-2846. [PMID: 35880844 PMCID: PMC9706439 DOI: 10.1093/plphys/kiac344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 06/24/2022] [Indexed: 06/01/2023]
Abstract
Lignin, one of the most abundant polymers in plants, is derived from the phenylpropanoid pathway, which also gives rise to an array of metabolites that are essential for plant fitness. Genetic engineering of lignification can cause drastic changes in transcription and metabolite accumulation with or without an accompanying development phenotype. To understand the impact of lignin perturbation, we analyzed transcriptome and metabolite data from the rapidly lignifying stem tissue in 13 selected phenylpropanoid mutants and wild-type Arabidopsis (Arabidopsis thaliana). Our dataset contains 20,974 expressed genes, of which over 26% had altered transcript levels in at least one mutant, and 18 targeted metabolites, all of which displayed altered accumulation in at least one mutant. We found that lignin biosynthesis and phenylalanine supply via the shikimate pathway are tightly co-regulated at the transcriptional level. The hierarchical clustering analysis of differentially expressed genes (DEGs) grouped the 13 mutants into 5 subgroups with similar profiles of mis-regulated genes. Functional analysis of the DEGs in these mutants and correlation between gene expression and metabolite accumulation revealed system-wide effects on transcripts involved in multiple biological processes.
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Affiliation(s)
- Peng Wang
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Longyun Guo
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - John Morgan
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, Indiana 47907, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907, USA
| | - Natalia Dudareva
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907, USA
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13
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Kim S, Wengier DL, Ragland CJ, Sattely ES. Transcriptional Reactivation of Lignin Biosynthesis for the Heterologous Production of Etoposide Aglycone in Nicotiana benthamiana. ACS Synth Biol 2022; 11:3379-3387. [PMID: 36122905 PMCID: PMC9594330 DOI: 10.1021/acssynbio.2c00289] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Nicotiana benthamiana is a valuable plant chassis for heterologous production of medicinal plant natural products. This host is well suited for the processing of organelle-localized plant enzymes, and the conservation of the primary metabolism across the plant kingdom often provides required plant-specific precursor molecules that feed a given pathway. Despite this commonality in metabolism, limited precursor supply and/or competing host pathways can interfere with yields of heterologous products. Here, we use transient transcriptional reprogramming of endogenous N. benthamiana metabolism to drastically improve flux through the etoposide pathway derived from the medicinal plant Podophyllum spp. Specifically, coexpression of a single lignin-associated transcription factor, MYB85, with pathway genes results in unprecedented levels of heterologous product accumulation in N. benthamiana leaves: 1 mg/g dry weight (DW) of the etoposide aglycone, 35 mg/g DW (-)-deoxypodophyllotoxin, and 3.5 mg/g DW (-)-epipodophyllotoxin─up to two orders of magnitude above previously reported biosynthetic yields for the etoposide aglycone and eight times higher than what is observed for (-)-deoxypodophyllotoxin in the native medicinal plant. Unexpectedly, transient activation of lignin metabolism by transcription factor overexpression also reduces the production of undesired side products that likely result from competing N. benthamiana metabolism. Our work demonstrates that synthetic activation of lignin biosynthesis in leaf tissue is an effective strategy for optimizing the production of medicinal compounds derived from phenylpropanoid precursors in the plant chassis N. benthamiana. Furthermore, our results highlight the engineering value of MYB85, an early switch in lignin biosynthesis, for on-demand modulation of monolignol flux and support the role of MYB46 as a master regulator of lignin polymer deposition.
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Affiliation(s)
- Stacie
S. Kim
- Department
of Chemical Engineering, Stanford University, Stanford, California 94305, United States
| | - Diego L. Wengier
- Department
of Chemical Engineering, Stanford University, Stanford, California 94305, United States
| | - Carin J. Ragland
- Department
of Biology, Stanford University, Stanford, California 94305, United States
| | - Elizabeth S. Sattely
- Department
of Chemical Engineering, Stanford University, Stanford, California 94305, United States,Howard
Hughes Medical Institute, Stanford University, Stanford, California 94305, United States,
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14
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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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15
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Ranade SS, Seipel G, Gorzsás A, García-Gil MR. Enhanced lignin synthesis and ecotypic variation in defense-related gene expression in response to shade in Norway spruce. PLANT, CELL & ENVIRONMENT 2022; 45:2671-2681. [PMID: 35775408 DOI: 10.1111/pce.14387] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/25/2022] [Accepted: 05/29/2022] [Indexed: 05/12/2023]
Abstract
During the growth season, northern forests in Sweden daily receive more hours of far-red (FR)-enriched light or twilight (shade) as compared to southern forests. Norway spruce (shade-tolerant) are adapted to latitudinal variation in twilight characterized by a northward increase in FR requirement to maintain growth. Shade is a stressful condition that affects plant growth and increases plant's susceptibility to pathogen attack. Lignin plays a central role in plant defense and its metabolism is regulated by light wavelength composition (light quality). In the current work, we studied regulation of lignin synthesis and defense-related genes (growth-defense trade-offs) in response to shade in Norway spruce. In most angiosperms, light promotes lignin synthesis, whereas shade decreases lignin production leading to weaker stem, which may make plants more disease susceptible. In contrast, enhanced lignin synthesis was detected in response to shade in Norway spruce. We detected a higher number of immunity/defense-related genes up-regulated in northern populations as compared to south ones in response to shade. Enhanced lignin synthesis coupled with higher defense-related gene expression can be interpreted as an adaptive strategy for better survival in northern populations. Findings will contribute to ensuring deployment of well-adapted genetic material and identifying tree families with enhanced disease resistance.
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Affiliation(s)
- Sonali Sachin Ranade
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - George Seipel
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
| | | | - María Rosario García-Gil
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
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16
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Kaur B, Garcha KS, Bhatia D, Khosa JS, Sharma M, Mittal A, Verma N, Dhatt AS. Identification of single major QTL and candidate gene(s) governing hull-less seed trait in pumpkin. FRONTIERS IN PLANT SCIENCE 2022; 13:948106. [PMID: 36035714 PMCID: PMC9406289 DOI: 10.3389/fpls.2022.948106] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 07/12/2022] [Indexed: 06/01/2023]
Abstract
The hull-less pumpkin (Cucurbita pepo) seed does not require de-hulling before use for human consumption, as a result highly preferred by the oil, nut, and baking industries. In hull-less seeds, a single recessive gene is responsible for the absence of outer thick seed coat layers; however, the genomic region and gene(s) controlling the trait are unclear to date. In this study, four crosses attempted to derive F2 and backcross populations confirmed the single recessive gene inheritance of hull-less seed trait in populations adapted to the sub-tropical climate. The candidate genomic region for hull-less seed trait was identified through the BSA-QTLseq approach using bulks of F2:3 progenies from a cross of HP111 (hulled) and HLP36 (hull-less). A novel genomic region on chromosome 12 ranging from 1.80 to 3.86 Mb was associated with the hull-less seed trait. The re-sequencing data identified a total of 396 SNPs within this region and eight were successfully converted into polymorphic KASP assays. The genotyping of segregating F2 (n = 160) with polymorphic KASP assays resulted in a 40.3 cM partial linkage map and identified Cp_3430407 (10 cM) and Cp_3498687 (16.1 cM) as flanking markers for hull-less locus (Cphl-1). These flanking markers correspond to the 68.28 kb region in the reference genome, and the marker, Cp_3430407 successfully predicted the genotype in 93.33% of the C. pepo hull-less germplasm lines, thus can be used for marker-assisted selection in parents polymorphic for the hull-less seed trait. The Cphl-1-linked genomic region (2.06 Mb) encompasses a total of 182 genes, including secondary cell wall and lignin biosynthesis-related transcriptional factors viz., "NAC" (Cp4.1LG12g04350) and "MYB" (Cp4.1LG12g03120). These genes were differentially expressed in the seeds of hulled and hull-less genotypes, and therefore could be the potential candidate genes governing the hull-less seed trait in pumpkin.
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Affiliation(s)
- Barinder Kaur
- Department of Vegetable Science, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Karmvir Singh Garcha
- Department of Vegetable Science, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Dharminder Bhatia
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Jiffinvir Singh Khosa
- Department of Vegetable Science, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Madhu Sharma
- Department of Vegetable Science, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Amandeep Mittal
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Neha Verma
- Department of Vegetable Science, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Ajmer Singh Dhatt
- Directorate of Research, Punjab Agricultural University, Ludhiana, Punjab, India
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Wang H, Feng X, Zhang Y, Wei D, Zhang Y, Jin Q, Cai Y. PbUGT72AJ2-Mediated Glycosylation Plays an Important Role in Lignin Formation and Stone Cell Development in Pears (Pyrus bretschneideri). Int J Mol Sci 2022; 23:ijms23147893. [PMID: 35887241 PMCID: PMC9318811 DOI: 10.3390/ijms23147893] [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: 06/03/2022] [Revised: 07/08/2022] [Accepted: 07/11/2022] [Indexed: 12/04/2022] Open
Abstract
Glycosylation is necessary for many processes of plant secondary metabolism. It can maintain plant homeostasis and is of great significance to normal plant growth and development. At present, the significance of glycosylation for lignin biosynthesis has been proven in some plants, but it has not yet been reported in pears. We used in situ hybridization, in vitro expression, substrate catalysis, transgenic Arabidopsisthaliana, and transient transformation of pear fruit in our investigation, which was predicated on the identification of a gene PbUGT72AJ2 that may be involved in lignin monolignol glycosylation according to our previous work. These results revealed that PbUGT72AJ2 transcripts were localized to some pulp cell walls, lignin deposition, and stone cell areas of pear fruit. The recombinant PbUGT72AJ2-pGEX4T-1 protein had activity against coniferyl alcohol and sinapyl alcohol, and its catalytic efficiency against coniferyl alcohol was higher than that against sinapyl alcohol. When PbUGT72AJ2 was transferred into Arabidopsisthaliana mutants, it was found that some characteristics of Arabidopsisthalianaugt72e3 mutants were restored. In Arabidopsisthaliana, overexpression of PbUGT72AJ2 enhanced the contents of coniferin and syringin, whereas lignification did not change significantly. Transient transformation of pear fruit showed that when PbUGT72AJ2 in pear fruit was silenced by RNA interference, the content of lignin and stone cells in pear fruit increased, whereas the gene PbUGT72AJ2 was overexpressed in pear fruit, and there was almost no change in the pear fruit compared with the control. Lignin deposition in pear fruit was closely related to stone cell development. In this study, we proved that PbUGT72AJ2 plays an important role in lignin deposition and stone cell development in pear fruit, which provides a molecular biological basis for improving pear fruit quality at the molecular level.
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Affiliation(s)
- Han Wang
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China; (H.W.); (X.F.); (Y.Z.); (D.W.); (Y.Z.); (Q.J.)
- Anhui Provincial Engineering Technology Research Center for Development & Utilization of Regional Characteristic Plants, Anhui Agricultural University, No. 130, Changjiang West Road, Hefei 230036, China
| | - Xiaofeng Feng
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China; (H.W.); (X.F.); (Y.Z.); (D.W.); (Y.Z.); (Q.J.)
- Anhui Provincial Engineering Technology Research Center for Development & Utilization of Regional Characteristic Plants, Anhui Agricultural University, No. 130, Changjiang West Road, Hefei 230036, China
| | - Yingjie Zhang
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China; (H.W.); (X.F.); (Y.Z.); (D.W.); (Y.Z.); (Q.J.)
- Anhui Provincial Engineering Technology Research Center for Development & Utilization of Regional Characteristic Plants, Anhui Agricultural University, No. 130, Changjiang West Road, Hefei 230036, China
| | - Dongyi Wei
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China; (H.W.); (X.F.); (Y.Z.); (D.W.); (Y.Z.); (Q.J.)
- Anhui Provincial Engineering Technology Research Center for Development & Utilization of Regional Characteristic Plants, Anhui Agricultural University, No. 130, Changjiang West Road, Hefei 230036, China
| | - Yang Zhang
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China; (H.W.); (X.F.); (Y.Z.); (D.W.); (Y.Z.); (Q.J.)
- Anhui Provincial Engineering Technology Research Center for Development & Utilization of Regional Characteristic Plants, Anhui Agricultural University, No. 130, Changjiang West Road, Hefei 230036, China
| | - Qing Jin
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China; (H.W.); (X.F.); (Y.Z.); (D.W.); (Y.Z.); (Q.J.)
- Anhui Provincial Engineering Technology Research Center for Development & Utilization of Regional Characteristic Plants, Anhui Agricultural University, No. 130, Changjiang West Road, Hefei 230036, China
| | - Yongping Cai
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China; (H.W.); (X.F.); (Y.Z.); (D.W.); (Y.Z.); (Q.J.)
- Anhui Provincial Engineering Technology Research Center for Development & Utilization of Regional Characteristic Plants, Anhui Agricultural University, No. 130, Changjiang West Road, Hefei 230036, China
- Correspondence:
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18
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Genome-wide analysis of the CAD gene family reveals two bona fide CAD genes in oil palm. 3 Biotech 2022; 12:149. [PMID: 35747504 PMCID: PMC9209623 DOI: 10.1007/s13205-022-03208-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 05/21/2022] [Indexed: 11/01/2022] Open
Abstract
Cinnamyl alcohol dehydrogenase (CAD) is the key enzyme for lignin biosynthesis in plants. In this study, genome-wide analysis was performed to identify CAD genes in oil palm (Elaeis guineensis). Phylogenetic analysis was then conducted to select the bona fide EgCADs. The bona fide EgCAD genes and their respective 5' flanking regions were cloned and analysed. Their expression profiles were evaluated in various organs using RT-PCR. Seven EgCAD genes (EgCAD1-7) were identified and divided into four phylogenetic groups. EgCAD1 and EgCAD2 display high sequence similarities with other bona fide CADs and possess all the signature motifs of the bona fide CAD. They also display similar 3D protein structures. Gene expression analysis showed that EgCAD1 was expressed most abundantly in the root tissues, while EgCAD2 was expressed constitutively in all the tissues studied. EgCAD1 possesses only one transcription start site, while EgCAD2 has five. Interestingly, a TC microsatellite was found in the 5' flanking region of EgCAD2. The 5' flanking regions of EgCAD1 and EgCAD2 contain lignin-associated regulatory elements i.e. AC-elements, and other defence-related motifs, including W-box, GT-1 motif and CGTCA-motif. Altogether, these results imply that EgCAD1 and EgCAD2 are bona fide CAD involved in lignin biosynthesis during the normal development of oil palm and in response to stresses. Our findings shed some light on the roles of the bona fide CAD genes in oil palm and pave the way for manipulating lignin content in oil palm through a genetic approach. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03208-0.
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Liu L, Chao N, Yidilisi K, Kang X, Cao X. Comprehensive analysis of the MYB transcription factor gene family in Morus alba. BMC PLANT BIOLOGY 2022; 22:281. [PMID: 35676625 PMCID: PMC9175366 DOI: 10.1186/s12870-022-03626-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 05/03/2022] [Indexed: 05/30/2023]
Abstract
BACKGROUND The V-myb myeloblastosis viral oncogene homolog (MYB) family of proteins is large, containing functionally diverse transcription factors. However, MYBs in Morus are still poorly annotated and a comprehensive functional analysis of these transcription factors is lacking. RESULTS In the present study, a genome-wide identification of MYBs in Morus alba was performed. In total 166 MaMYBs were identified, including 103 R2R3-MYBs and four 3R-MaMYBs. Comprehensive analyses, including the phylogenetic analysis with putative functional annotation, motif and structure analysis, gene structure organization, promoter analysis, chromosomal localization, and syntenic relationships of R2R3-MaMYBs and 3R-MaMYBs, provided primary characterization for these MaMYBs. R2R3-MaMYBs covered the subgroups reported for R2R3-MYBs in Arabidopsis and Populus, and had two Morus-specific subgroups, indicating the high retention of MYBs in Morus. Motif analysis revealed high conservative residues at the start and end of each helix and residues consisting of the third helix in R2 and R3 repeats. Thirteen intron/exon patterns (a-m) were summarized, and the intron/exon pattern of two introns with phase numbers of 0 and 2 was the prevalent pattern for R2R3-MaMYBs. Various cis-elements in promoter regions were identified, and were mainly related to light response, development, phytohormone response, and abiotic and biotic stress response and secondary metabolite production. Expression patterns of R2R3-MaMYBs in different organs showed that MaMYBs involved in secondary cell wall components and stress responsiveness were preferentially expressed in roots or stems. R2R3-MaMYBs involved in flavonoid biosynthesis and anthocyanin accumulation were identified and characterized based on functional annotation and correlation of their expression levels with anthocyanin contents. CONCLUSION Based on a comprehensive analysis, this work provided functional annotation for R2R3-MYBs and an informative reference for further functional dissection of MYBs in Morus.
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Affiliation(s)
- Li Liu
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212018, Jiangsu, China.
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, 212018, Jiangsu, China.
| | - Nan Chao
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212018, Jiangsu, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, 212018, Jiangsu, China
| | - Keermula Yidilisi
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212018, Jiangsu, China
| | - Xiaoru Kang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212018, Jiangsu, China
| | - Xu Cao
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212018, Jiangsu, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, 212018, Jiangsu, China
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20
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Li X, Huang H, Rizwan HM, Wang N, Jiang J, She W, Zheng G, Pan H, Guo Z, Pan D, Pan T. Transcriptome Analysis Reveals Candidate Lignin-Related Genes and Transcription Factors during Fruit Development in Pomelo ( Citrus maxima). Genes (Basel) 2022; 13:845. [PMID: 35627230 PMCID: PMC9140673 DOI: 10.3390/genes13050845] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/27/2022] [Accepted: 05/03/2022] [Indexed: 02/01/2023] Open
Abstract
Juice sac granulation (a physiological disorder) leads to large postharvest losses of pomelo (Citrus maxima). Previous studies have shown that juice sac granulation is closely related to lignin accumulation, while the molecular mechanisms underlying this disorder remain elusive in pomelo. Our results showed that the lignin content in NC (near the core) and FC (far away from the core) juice sacs overall increased from 157 DPA (days post anthesis) to 212 DPA and reached a maximum at 212 DPA. Additionally, the lignin content of NC juice sacs was higher than that of FC juice sacs. In this study, we used transcriptome-based weighted gene co-expression network analysis (WGCNA) to address how lignin formation in NC and FC juice sacs is generated during the development of pomelo. After data assembly and bioinformatic analysis, we found a most correlated module (black module) to the lignin content, then we used the 11 DEGs in this module as hub genes for lignin biosynthesis. Among these DEGs, PAL (phenylalanine ammonia lyase), HCT (hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyl transferase), 4CL2 (4-coumarate: CoA ligase), C4H (cinnamate 4-hydroxylase), C3'H (p-coumarate 3-hydroxylase), and CCoAOMT1 (caffeoyl CoA 3-Omethyltransferase) were the most distinct DEGs in granulated juice sacs. Co-expression analysis revealed that the expression patterns of several transcription factors such as MYB, NAC, OFP6, and bHLH130 are highly correlated with lignin formation. In addition, the expression patterns of the DEGs related to lignin biosynthesis and transcription factors were validated by qRT-PCR, and the results were highly concordant with the RNA-seq results. These results would be beneficial for further studies on the molecular mechanism of lignin accumulation in pomelo juice sacs and would help with citrus breeding.
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Affiliation(s)
- Xiaoting Li
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.L.); (H.M.R.); (N.W.); (J.J.); (W.S.); (G.Z.); (H.P.); (Z.G.); (T.P.)
| | - Hantang Huang
- College of Horticulture, China Agricultural University, Beijing 100083, China;
| | - Hafiz Muhammad Rizwan
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.L.); (H.M.R.); (N.W.); (J.J.); (W.S.); (G.Z.); (H.P.); (Z.G.); (T.P.)
| | - Naiyu Wang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.L.); (H.M.R.); (N.W.); (J.J.); (W.S.); (G.Z.); (H.P.); (Z.G.); (T.P.)
| | - Jingyi Jiang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.L.); (H.M.R.); (N.W.); (J.J.); (W.S.); (G.Z.); (H.P.); (Z.G.); (T.P.)
| | - Wenqin She
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.L.); (H.M.R.); (N.W.); (J.J.); (W.S.); (G.Z.); (H.P.); (Z.G.); (T.P.)
| | - Guohua Zheng
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.L.); (H.M.R.); (N.W.); (J.J.); (W.S.); (G.Z.); (H.P.); (Z.G.); (T.P.)
| | - Heli Pan
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.L.); (H.M.R.); (N.W.); (J.J.); (W.S.); (G.Z.); (H.P.); (Z.G.); (T.P.)
| | - Zhixiong Guo
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.L.); (H.M.R.); (N.W.); (J.J.); (W.S.); (G.Z.); (H.P.); (Z.G.); (T.P.)
| | - Dongming Pan
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.L.); (H.M.R.); (N.W.); (J.J.); (W.S.); (G.Z.); (H.P.); (Z.G.); (T.P.)
| | - Tengfei Pan
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.L.); (H.M.R.); (N.W.); (J.J.); (W.S.); (G.Z.); (H.P.); (Z.G.); (T.P.)
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21
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Jhu MY, Farhi M, Wang L, Philbrook RN, Belcher MS, Nakayama H, Zumstein KS, Rowland SD, Ron M, Shih PM, Sinha NR. Heinz-resistant tomato cultivars exhibit a lignin-based resistance to field dodder (Cuscuta campestris) parasitism. PLANT PHYSIOLOGY 2022; 189:129-151. [PMID: 35099559 PMCID: PMC9070836 DOI: 10.1093/plphys/kiac024] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 12/20/2021] [Indexed: 05/27/2023]
Abstract
Cuscuta species (dodders) are agriculturally destructive, parasitic angiosperms. These parasitic plants use haustoria as physiological bridges to extract nutrients and water from hosts. Cuscuta campestris has a broad host range and wide geographical distribution. While some wild tomato relatives are resistant, cultivated tomatoes are generally susceptible to C. campestris infestations. However, some specific Heinz tomato (Solanum lycopersicum) hybrid cultivars exhibit resistance to dodders in the field, but their defense mechanism was previously unknown. Here, we discovered that the stem cortex in these resistant lines responds with local lignification upon C. campestris attachment, preventing parasite entry into the host. Lignin Induction Factor 1 (LIF1, an AP2-like transcription factor), SlMYB55, and Cuscuta R-gene for Lignin-based Resistance 1, a CC-NBS-LRR (CuRLR1) are identified as factors that confer host resistance by regulating lignification. SlWRKY16 is upregulated upon C. campestris infestation and potentially negatively regulates LIF1 function. Intriguingly, CuRLR1 may play a role in signaling or function as an intracellular receptor for receiving Cuscuta signals or effectors, thereby regulating lignification-based resistance. In summary, these four regulators control the lignin-based resistance response in specific Heinz tomato cultivars, preventing C. campestris from parasitizing resistant tomatoes. This discovery provides a foundation for investigating multilayer resistance against Cuscuta species and has potential for application in other essential crops attacked by parasitic plants.
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Affiliation(s)
| | | | - Li Wang
- Department of Plant Biology, University of California, Davis, CA 95616, USA
- College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Richard N Philbrook
- Department of Plant Biology, University of California, Davis, CA 95616, USA
- Dark Heart Nursery, 630 Pena Dr, Davis, CA 95616, USA
| | - Michael S Belcher
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Hokuto Nakayama
- Department of Plant Biology, University of California, Davis, CA 95616, USA
- Graduate School of Science, Department of Biological Sciences, University of Tokyo, Hongo Bunkyo-ku, Tokyo, 113-0033, Japan
| | | | - Sarah D Rowland
- Department of Plant Biology, University of California, Davis, CA 95616, USA
| | - Mily Ron
- Department of Plant Biology, University of California, Davis, CA 95616, USA
| | - Patrick M Shih
- Department of Plant Biology, University of California, Davis, CA 95616, USA
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Genome Center, University of California, Davis, CA 95616, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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22
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Ren M, Zhang Y, Wang R, Liu Y, Li M, Wang X, Chen X, Luan X, Zhang H, Wei H, Yang C, Wei Z. PtrHAT22, as a higher hierarchy regulator, coordinately regulates secondary cell wall component biosynthesis in Populus trichocarpa. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 316:111170. [PMID: 35151454 DOI: 10.1016/j.plantsci.2021.111170] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 12/20/2021] [Accepted: 12/25/2021] [Indexed: 06/14/2023]
Abstract
Homeodomain-leucine zipper (HD-Zip) II transcription factors (TFs) have been reported to play vital roles in diverse biological processes of plants. However, it remains unclear whether HD-Zip II TFs regulate secondary cell wall (SCW) in woody plants. In this study, we performed the functional characterization of a Populus trichocarpa HD-Zip II TF, PtrHAT22, which encodes a nuclear localized transcription repressor predominantly expressing in secondary developing tissues. Overexpression of PtrHAT22 showed arrested growths, including reduced heights and diameters above the ground, small leaves, and decreased biomass. Meanwhile, the contents of lignin, cellulose, and thickness of SCW significantly decreased, whilst the content of hemicellulose obviously increased in PtrHAT22 transgenic poplar. The expressions of some wood-associated TFs and structural genes significantly changed accordingly with the alternations of SCW characteristics in PtrHAT22 transgenic poplar. Furthermore, PtrHAT22 directly repressed the promoter activities of PtrMYB20, PtrMYB28, and PtrCOMT2, and bind two cis-acting elements that were specifically enriched in their promoter regions. Taken together, our results suggested that PtrHAT22, as a higher hierarchy TF like PtrWNDs, exerted coordination regulation of poplar SCW component biosynthesis through directly and indirectly regulating structural genes and different hierarchy TFs of SCW formation network.
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Affiliation(s)
- Mengxuan Ren
- Research Center of Saline and Alkali Land of State Forestry and Grassland Administration, Chinese Academy of Forestry, Beijing, 100091, PR China
| | - Yang Zhang
- Research Center of Saline and Alkali Land of State Forestry and Grassland Administration, Chinese Academy of Forestry, Beijing, 100091, PR China; State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Heilongjiang, Harbin, 150040, PR China
| | - Ruiqi Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Heilongjiang, Harbin, 150040, PR China
| | - Yingying Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Heilongjiang, Harbin, 150040, PR China
| | - Meiliang Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Heilongjiang, Harbin, 150040, PR China
| | - Xueying Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Heilongjiang, Harbin, 150040, PR China
| | - Xuebing Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Heilongjiang, Harbin, 150040, PR China
| | - Xue Luan
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Heilongjiang, Harbin, 150040, PR China
| | - Huaxin Zhang
- Research Center of Saline and Alkali Land of State Forestry and Grassland Administration, Chinese Academy of Forestry, Beijing, 100091, PR China
| | - Hairong Wei
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA
| | - Chuanping Yang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Heilongjiang, Harbin, 150040, PR China.
| | - Zhigang Wei
- Research Center of Saline and Alkali Land of State Forestry and Grassland Administration, Chinese Academy of Forestry, Beijing, 100091, PR China.
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23
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Xue Y, Shen Z, Tao F, Zhou J, Xu B. Transcriptomic Analysis Reveal the Molecular Mechanisms of Seed Coat Development in Cucurbita pepo L. FRONTIERS IN PLANT SCIENCE 2022; 13:772685. [PMID: 35283914 PMCID: PMC8912962 DOI: 10.3389/fpls.2022.772685] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 01/06/2022] [Indexed: 05/24/2023]
Abstract
Cucurbita pepo is one of the earliest cultivated crops. It is native to Central and South America and is now widely cultivated all over the world for its rich nutrition, short growth period, and high yield, which make it suitable for intercropping. Hull-less C. pepo L. (HLCP) is a rare variant in nature that is easier to consume. Its seed has a seed kernel but lacks a seed coat. The molecular mechanism underlying the lack of seed coat development in the HLCP variety is not clear yet. The BGISEQ-500 sequencing platform was used to sequence 18 cDNA libraries of seed coats from hulled C. pepo (CP) and HLCP at three developmental stages (8, 18, and 28 days) post-pollination. We found that lignin accumulation in the seed coat of the HLCP variety was much lower than that of the CP variety. A total of 2,099 DEGs were identified in the CP variety, which were enriched mainly in the phenylpropanoid biosynthesis pathway, amino sugar, and nucleotide sugar metabolism pathways. A total of 1,831 DEGs were identified in the HLCP variety and found to be enriched mainly in the phenylpropanoid biosynthesis and metabolism pathways of starch and sucrose. Among the DEGs, hub proteins (FusA), protein kinases (IRAK4), and several transcription factors related to seed coat development (MYB, bHLH, NAC, AP2/EREBP, WRKY) were upregulated in the CP variety. The relative expression levels of 12 randomly selected DEGs were determined using quantitative real-time PCR analysis and found to be consistent with those obtained using RNA-Seq, with a correlation coefficient of 0.9474. We found that IRAK4 protein kinases, AP2/EREBP, MYB, bHLH, and NAC transcription factors may play important roles in seed coat development, leading to the formation of HLCP.
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Affiliation(s)
- Yingyu Xue
- College of Plant Protection, Gansu Agricultural University, Lanzhou, China
- Biocontrol Engineering Laboratory of Crop Diseases and Pests of Gansu Province, College of Plant Protection, Gansu Agricultural University, Lanzhou, China
| | - Zhiyan Shen
- College of Plant Protection, Gansu Agricultural University, Lanzhou, China
- Biocontrol Engineering Laboratory of Crop Diseases and Pests of Gansu Province, College of Plant Protection, Gansu Agricultural University, Lanzhou, China
| | - Fei Tao
- College of Plant Protection, Gansu Agricultural University, Lanzhou, China
- Biocontrol Engineering Laboratory of Crop Diseases and Pests of Gansu Province, College of Plant Protection, Gansu Agricultural University, Lanzhou, China
| | - Jingjiang Zhou
- Biocontrol Engineering Laboratory of Crop Diseases and Pests of Gansu Province, College of Plant Protection, Gansu Agricultural University, Lanzhou, China
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, China
| | - Bingliang Xu
- College of Plant Protection, Gansu Agricultural University, Lanzhou, China
- Biocontrol Engineering Laboratory of Crop Diseases and Pests of Gansu Province, College of Plant Protection, Gansu Agricultural University, Lanzhou, China
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24
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Jiang PF, Lin XY, Bian XY, Zeng QY, Liu YJ. Ectopic expression of Populus MYB10 promotes secondary cell wall thickening and inhibits anthocyanin accumulation. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 172:24-32. [PMID: 35016103 DOI: 10.1016/j.plaphy.2022.01.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 12/16/2021] [Accepted: 01/03/2022] [Indexed: 06/14/2023]
Abstract
Secondary cell wall (SCW) formation is regulated by a multilevel transcriptional regulatory network, in which MYB transcription factors (TFs) play key roles. In woody plants, hundreds of MYB TFs have been identified, most of which have unknown functions in wood SCW biosynthesis. Here, we characterized the function of a Populus MYB gene, PtoMYB10. PtoMYB10 was found to encode an R2R3-MYB TF and exhibit dominant expression in xylem tissues. PtoMYB10 was determined to be located in the nucleus with the ability to activate transcription. Overexpression of PtoMYB10 in Populus resulted in a drastic increase in SCW thickening in xylem fiber cells as well as ectopic deposition of lignin in cortex cells. The expression of genes associated with lignin biosynthesis was induced in PtoMYB10 overexpressing plants, whereas repressed gene expression was found with the anthocyanin biosynthesis pathway. Lignin and anthocyanin are both produced from metabolites of the phenylpropanoid pathway. Accordingly, the anthocyanin content of Populus overexpressing PtoMYB10 decreased by more than 68%. These results indicate that PtoMYB10 can positively regulate xylary fiber SCW thickening, accompanied by the reprogramming of phenylpropanoid metabolism, which redirects metabolic flux from anthocyanin biosynthesis to monolignol biosynthesis.
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Affiliation(s)
- Peng-Fei Jiang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
| | - Xiao-Yang Lin
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Xiu-Yan Bian
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
| | - Qing-Yin Zeng
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
| | - Yan-Jing Liu
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China.
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25
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Yu J, Zhou C, Li D, Li S, Jimmy Lin YC, Wang JP, Chiang VL, Li W. A PtrLBD39-mediated transcriptional network regulates tension wood formation in Populus trichocarpa. PLANT COMMUNICATIONS 2022; 3:100250. [PMID: 35059630 PMCID: PMC8760142 DOI: 10.1016/j.xplc.2021.100250] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 09/10/2021] [Accepted: 10/19/2021] [Indexed: 05/29/2023]
Abstract
Tension wood (TW) is a specialized xylem tissue formed in angiosperm trees under gravitational stimulus or mechanical stresses (e.g., bending). The genetic regulation that underlies this important mechanism remains poorly understood. Here, we used laser capture microdissection of stem xylem cells coupled with full transcriptome RNA-sequencing to analyze TW formation in Populus trichocarpa. After tree bending, PtrLBD39 was the most significantly induced transcription factor gene; it has a phylogenetically paired homolog, PtrLBD22. CRISPR-based knockout of PtrLBD39/22 severely inhibited TW formation, reducing cellulose and increasing lignin content. Transcriptomic analyses of CRISPR-based PtrLBD39/22 double mutants showed that these two genes regulate a set of TW-related genes. Chromatin immunoprecipitation sequencing (ChIP-seq) was used to identify direct targets of PtrLBD39. We integrated transcriptomic analyses and ChIP-seq assays to construct a transcriptional regulatory network (TRN) mediated by PtrLBD39. In this TRN, PtrLBD39 directly regulates 26 novel TW-responsive transcription factor genes. Our work suggests that PtrLBD39 and PtrLBD22 specifically control TW formation by mediating a TW-specific TRN in Populus.
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Affiliation(s)
- Jing Yu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Chenguang Zhou
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Danning Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Shuang Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Ying-Chung Jimmy Lin
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- Department of Life Sciences and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, Taiwan 10617, China
| | - Jack P. Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- Department of Forestry and Environmental Resources, Forest Biotechnology Group, North Carolina State University, Raleigh, NC 27695, USA
| | - Vincent L. Chiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- Department of Forestry and Environmental Resources, Forest Biotechnology Group, North Carolina State University, Raleigh, NC 27695, USA
| | - Wei Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
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26
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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: 11] [Impact Index Per Article: 3.7] [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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Meng X, Wang Y, Li J, Jiao N, Zhang X, Zhang Y, Chen J, Tu Z. RNA Sequencing Reveals Phenylpropanoid Biosynthesis Genes and Transcription Factors for Hevea brasiliensis Reaction Wood Formation. Front Genet 2021; 12:763841. [PMID: 34777481 PMCID: PMC8585928 DOI: 10.3389/fgene.2021.763841] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 10/08/2021] [Indexed: 11/13/2022] Open
Abstract
Given the importance of wood in many industrial applications, much research has focused on wood formation, especially lignin biosynthesis. However, the mechanisms governing the regulation of lignin biosynthesis in the rubber tree (Hevea brasiliensis) remain to be elucidated. Here, we gained insight into the mechanisms of rubber tree lignin biosynthesis using reaction wood (wood with abnormal tissue structure induced by gravity or artificial mechanical treatment) as an experimental model. We performed transcriptome analysis of rubber tree mature xylem from tension wood (TW), opposite wood (OW), and normal wood (NW) using RNA sequencing (RNA-seq). A total of 214, 1,280, and 32 differentially expressed genes (DEGs) were identified in TW vs. NW, OW vs. NW, and TW vs. OW, respectively. GO and KEGG enrichment analysis of DEGs from different comparison groups showed that zeatin biosynthesis, plant hormone signal transduction, phenylpropanoid biosynthesis, and plant-pathogen interaction pathways may play important roles in reaction wood formation. Sixteen transcripts involved in phenylpropanoid biosynthesis and 129 transcripts encoding transcription factors (TFs) were used to construct a TF-gene regulatory network for rubber tree lignin biosynthesis. Among them, MYB, C2H2, and NAC TFs could regulate all the DEGs involved in phenylpropanoid biosynthesis. Overall, this study identified candidate genes and TFs likely involved in phenylpropanoid biosynthesis and provides novel insights into the mechanisms regulating rubber tree lignin biosynthesis.
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Affiliation(s)
- Xiangxu Meng
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, Haikou, China.,Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, Institute of Tropical Agriculture and Forestry, School of Forestry, Hainan University, Haikou, China
| | - Yue Wang
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, Haikou, China.,Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, Institute of Tropical Agriculture and Forestry, School of Forestry, Hainan University, Haikou, China
| | - Jia Li
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, Haikou, China.,Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, Institute of Tropical Agriculture and Forestry, School of Forestry, Hainan University, Haikou, China
| | - Nanbo Jiao
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, Haikou, China.,Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, Institute of Tropical Agriculture and Forestry, School of Forestry, Hainan University, Haikou, China
| | - Xiujie Zhang
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, Haikou, China.,Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, Institute of Tropical Agriculture and Forestry, School of Forestry, Hainan University, Haikou, China
| | - Yuanyuan Zhang
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China.,State Centre for Rubber Breeding, Haikou, China
| | - Jinhui Chen
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, Haikou, China.,Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, Institute of Tropical Agriculture and Forestry, School of Forestry, Hainan University, Haikou, China
| | - Zhihua Tu
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, Haikou, China.,Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, Institute of Tropical Agriculture and Forestry, School of Forestry, Hainan University, Haikou, China
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Hu Y, Cheng H, Zhang Y, Zhang J, Niu S, Wang X, Li W, Zhang J, Yao Y. The MdMYB16/MdMYB1-miR7125-MdCCR module regulates the homeostasis between anthocyanin and lignin biosynthesis during light induction in apple. THE NEW PHYTOLOGIST 2021; 231:1105-1122. [PMID: 33908060 DOI: 10.1111/nph.17431] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 04/19/2021] [Indexed: 05/22/2023]
Abstract
Light induces anthocyanin accumulation and hence decides the coloration of apple fruit. It also plays a key role in regulating the biosynthesis of other secondary metabolites. However, the crosstalk between anthocyanin and lignin metabolism during light induction, which affects the edible quality and visual quality of apple fruit, respectively, have rarely been characterized. In this study, we identified and functionally elucidated the roles of miR7125 and its target, cinnamoyl-coenzyme A reductase gene (CCR), in regulating the homeostasis between anthocyanin and lignin biosynthesis during light induction. Overexpressing miR7125 or inhibiting CCR transiently in apple fruit promoted anthocyanin biosynthesis but reduced lignin production under light-induced conditions. Consistently, opposite results were observed under the background of repressed miR7125 or overexpressed CCR. We found that the repressor MdMYB16 and the activator MdMYB1 bound to the miR7125 promoter. Transient repression of MdMYB16 upregulated miR7125 expression significantly, accompanied by decreased levels of MdCCR transcript, resulting in a reduction in the lignin biosynthesis and an increase in anthocyanin accumulation. However, transient overexpression of MdMYB16 produced the opposite effects to MdMYB16-RNAi. The results reveal a novel mechanism by which the MdMYB16/MdMYB1-miR7125-MdCCR module collaboratively regulates homeostasis between anthocyanin and lignin biosynthesis under light induction in apple.
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Affiliation(s)
- Yujing Hu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, 102206, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing, 102206, China
| | - Hao Cheng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, 102206, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing, 102206, China
| | - Yan Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, 102206, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing, 102206, China
| | - Jie Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, 102206, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing, 102206, China
| | - Shuqing Niu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, 102206, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing, 102206, China
| | - Xingsui Wang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, 102206, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing, 102206, China
| | - Wenjing Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, 102206, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing, 102206, China
| | - Jie Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, 102206, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing, 102206, China
| | - Yuncong Yao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, 102206, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing, 102206, China
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29
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Yaya Lancheros ML, Rai KM, Balasubramanian VK, Dampanaboina L, Mendu V, Terán W. De novo transcriptome analysis of white teak (Gmelina arborea Roxb) wood reveals critical genes involved in xylem development and secondary metabolism. BMC Genomics 2021; 22:494. [PMID: 34215181 PMCID: PMC8252223 DOI: 10.1186/s12864-021-07777-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 06/07/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Gmelina arborea Roxb is a fast-growing tree species of commercial importance for tropical countries due to multiple industrial uses of its wood. Wood is primarily composed of thick secondary cell walls of xylem cells which imparts the strength to the wood. Identification of the genes involved in the secondary cell wall biosynthesis as well as their cognate regulators is crucial to understand how the production of wood occurs and serves as a starting point for developing breeding strategies to produce varieties with improved wood quality, better paper pulping or new potential uses such as biofuel production. In order to gain knowledge on the molecular mechanisms and gene regulation related with wood development in white teak, a de novo sequencing and transcriptome assembly approach was used employing secondary cell wall synthesizing cells from young white teak trees. RESULTS For generation of transcriptome, RNA-seq reads were assembled into 110,992 transcripts and 49,364 genes were functionally annotated using plant databases; 5071 GO terms and 25,460 SSR markers were identified within xylem transcripts and 10,256 unigenes were assigned to KEGG database in 130 pathways. Among transcription factor families, C2H2, C3H, bLHLH and MYB were the most represented in xylem. Differential gene expression analysis using leaves as a reference was carried out and a total of 20,954 differentially expressed genes were identified including monolignol biosynthetic pathway genes. The differential expression of selected genes (4CL, COMT, CCoAOMT, CCR and NST1) was validated using qPCR. CONCLUSIONS We report the very first de novo transcriptome of xylem-related genes in this tropical timber species of commercial importance and constitutes a valuable extension of the publicly available transcriptomic resource aimed at fostering both basic and breeding studies.
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Affiliation(s)
- Mary Luz Yaya Lancheros
- Department of Biology, Pontificia Universidad Javeriana, Carrera 7 N° 43-82, Bogotá, 110231, Colombia
| | - Krishan Mohan Rai
- Department of Plant and Soil Sciences, Fiber and Biopolymer Research Institute, Texas Tech University, Lubbock, TX, 79409, USA
- Department of Plant and Microbial Biology, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
| | - Vimal Kumar Balasubramanian
- Department of Plant and Soil Sciences, Fiber and Biopolymer Research Institute, Texas Tech University, Lubbock, TX, 79409, USA
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Lavanya Dampanaboina
- Department of Plant and Soil Sciences, Fiber and Biopolymer Research Institute, Texas Tech University, Lubbock, TX, 79409, USA
| | - Venugopal Mendu
- Department of Plant and Soil Sciences, Fiber and Biopolymer Research Institute, Texas Tech University, Lubbock, TX, 79409, USA
| | - Wilson Terán
- Department of Biology, Pontificia Universidad Javeriana, Carrera 7 N° 43-82, Bogotá, 110231, Colombia.
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30
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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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31
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Hu Q, Xiao S, Wang X, Ao C, Zhang X, Zhu L. GhWRKY1-like enhances cotton resistance to Verticillium dahliae via an increase in defense-induced lignification and S monolignol content. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 305:110833. [PMID: 33691967 DOI: 10.1016/j.plantsci.2021.110833] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/27/2021] [Accepted: 01/30/2021] [Indexed: 05/08/2023]
Abstract
Cotton is one of the most important economic crops and is cultivated globally. Verticillium wilt, caused by the soil-borne hemibiotrophic fungus Verticillium dahliae, is the most destructive disease in cotton production for its infection strategies and great genetic plasticity. Recent studies have identified the accumulation of lignin is a general and basal defense reaction in plant immunity and cotton resistance to V. dahliae. However, the functions and regulatory mechanisms of transcription factors in cotton defense-induced lignification and lignin composition alteration were less reported. Here, we identified a WRKY transcription factor GhWRKY1-like from upland cotton (Gossypium hirsutum) as a positive regulator in resistance to V. dahliae via directly manipulating lignin biosynthesis. Further analysis revealed that GhWRKY1-like interacts with the promoters of lignin biosynthesis related genes GhPAL6 and GhCOMT1, and activates the expression of GhPAL6 and GhCOMT1, which led to enhanced total lignin especially S monomers biosynthesis. These results demonstrate that GhWRKY1-like enhances Verticillium wilt resistance via an increase in defense-induced lignification and broaden our knowledge of the roles of lignification and the lignin composition in plant defense responses.
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Affiliation(s)
- Qin Hu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China; State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei, 430062, China
| | - Shenghua Xiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Xiaorui Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei, 430062, China
| | - Chuanwei Ao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei, 430062, China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Longfu Zhu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
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32
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Singh V, Zemach H, Shabtai S, Aloni R, Yang J, Zhang P, Sergeeva L, Ligterink W, Firon N. Proximal and Distal Parts of Sweetpotato Adventitious Roots Display Differences in Root Architecture, Lignin, and Starch Metabolism and Their Developmental Fates. FRONTIERS IN PLANT SCIENCE 2021; 11:609923. [PMID: 33552103 PMCID: PMC7855870 DOI: 10.3389/fpls.2020.609923] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 12/10/2020] [Indexed: 06/10/2023]
Abstract
Sweetpotato is an important food crop globally, serving as a rich source of carbohydrates, vitamins, fiber, and micronutrients. Sweetpotato yield depends on the modification of adventitious roots into storage roots. The underlying mechanism of this developmental switch is not fully understood. Interestingly, storage-root formation is manifested by formation of starch-accumulating parenchyma cells and bulking of the distal part of the root, while the proximal part does not show bulking. This system, where two parts of the same adventitious root display different developmental fates, was used by us in order to better characterize the anatomical, physiological, and molecular mechanisms involved in sweetpotato storage-root formation. We show that, as early as 1 and 2 weeks after planting, the proximal part of the root exhibited enhanced xylem development together with increased/massive lignin deposition, while, at the same time, the distal root part exhibited significantly elevated starch accumulation. In accordance with these developmental differences, the proximal root part exhibited up-regulated transcript levels of sweetpotato orthologs of Arabidopsis vascular-development regulators and key genes of lignin biosynthesis, while the distal part showed up-regulation of genes encoding enzymes of starch biosynthesis. All these recorded differences between proximal and distal root parts were further enhanced at 5 weeks after planting, when storage roots were formed at the distal part. Our results point to down-regulation of fiber formation and lignification, together with up-regulation of starch biosynthesis, as the main events underlying storage-root formation, marking/highlighting several genes as potential regulators, providing a valuable database of genes for further research.
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Affiliation(s)
- Vikram Singh
- Department of Vegetable and Field Crops, Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, Rishon Le-Zion, Israel
| | - Hanita Zemach
- Department of Fruit Tree Sciences, Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, Rishon Le-Zion, Israel
| | - Sara Shabtai
- Department of Vegetable and Field Crops, Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, Rishon Le-Zion, Israel
| | - Roni Aloni
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Jun Yang
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Peng Zhang
- CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Lidiya Sergeeva
- Laboratory of Plant Physiology, Department of Plant Sciences, Wageningen University & Research, Wageningen, Netherlands
| | - Wilco Ligterink
- Laboratory of Plant Physiology, Department of Plant Sciences, Wageningen University & Research, Wageningen, Netherlands
| | - Nurit Firon
- Department of Vegetable and Field Crops, Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, Rishon Le-Zion, Israel
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33
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Sun Y, Jiang C, Jiang R, Wang F, Zhang Z, Zeng J. A Novel NAC Transcription Factor From Eucalyptus, EgNAC141, Positively Regulates Lignin Biosynthesis and Increases Lignin Deposition. FRONTIERS IN PLANT SCIENCE 2021; 12:642090. [PMID: 33897732 PMCID: PMC8061705 DOI: 10.3389/fpls.2021.642090] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/05/2021] [Indexed: 05/22/2023]
Abstract
Wood formation is a complicated process under the control of a large set of transcription factors. NAC transcription factors are considered "master switches" in this process. However, few NAC members have been cloned and characterized in Eucalyptus, which is one of the most economically important woody plants. Here, we reported an NAC transcription factor from Eucalyptus grandis, EgNAC141, which has no Arabidopsis orthologs associated with xylogenesis-related processes. EgNAC141 was predominantly expressed in lignin-rich tissues, such as the stem and xylem. Overexpression of EgNAC141 in Arabidopsis resulted in stronger lignification, larger xylem, and higher lignin content. The expression of lignin biosynthetic genes in transgenic plants was significantly higher compared with wild-type plants. The transient expression of EgNAC141 activated the expression of Arabidopsis lignin biosynthetic genes in a dual-luciferase assay. Overall, these results showed that EgNAC141 is a positive regulator of lignin biosynthesis and may help us understand the regulatory mechanism of wood formation.
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Affiliation(s)
- YiMing Sun
- School of Life Sciences, Southwest University, Chongqing, China
| | - Chunxue Jiang
- School of Life Sciences, Southwest University, Chongqing, China
| | - Ruiqi Jiang
- School of Life Sciences, Southwest University, Chongqing, China
| | - Fengying Wang
- Chongqing Three Gorges University College of Public Administration, Chongqing, China
| | - Zhenguo Zhang
- College of Life Sciences, Shandong Normal University (SDNU), Jinan, China
| | - Jianjun Zeng
- School of Life Sciences, Jinggangshan University, Ji’an, China
- *Correspondence: Jianjun Zeng,
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34
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Holt CA, Cottyn B, Baumberger S, Kovacs-Schreiner K, Blacker AJ. High-Throughput Analysis of Lignin by Agarose Gel Electrophoresis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:14297-14306. [PMID: 33200936 DOI: 10.1021/acs.jafc.0c06308] [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] [Indexed: 06/11/2023]
Abstract
A high-throughput agarose gel electrophoresis (AGE) analytical method has been developed to separate lignin fractions according to their molecular weight (Mw), charge, and shape. Operating conditions to effect separation of species have been evaluated along with imaging parameters. Kraft, soda (Protobind), and Organosolv lignins showed distinct differences in migration. Bands were cut, extracted, and cross-analyzed by gel permeation chromatography (GPC), 1H NMR, and pyrolysis GC/MS to confirm their identity as lignin. The band intensity was correlated with lignin concentration by running serially diluted samples and imaging each lane to produce a precise calibration curve. The AGE technique was used to monitor and compare enzymatic, bacterial, chemical, and hydrothermal lignin digestions. Each method showed changes in lignin migration and band intensities over time. Low Mw species were seen in samples collected from the anode buffer tank. Though requiring further development, the AGE method can provide structural information about the lignin and is accessible to biological and chemistry laboratories.
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Affiliation(s)
- Christopher A Holt
- Institute of Process Research and Development, School of Chemistry and School of Chemical and Process Engineering, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, United Kingdom
| | - Betty Cottyn
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles 78000, France
| | - Stephanie Baumberger
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles 78000, France
| | | | - A John Blacker
- Institute of Process Research and Development, School of Chemistry and School of Chemical and Process Engineering, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, United Kingdom
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35
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Chen K, Guo Y, Song M, Liu L, Xue H, Dai H, Zhang Z. Dual role of MdSND1 in the biosynthesis of lignin and in signal transduction in response to salt and osmotic stress in apple. HORTICULTURE RESEARCH 2020; 7:204. [PMID: 33328445 PMCID: PMC7705020 DOI: 10.1038/s41438-020-00433-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 09/08/2020] [Accepted: 10/17/2020] [Indexed: 05/15/2023]
Abstract
Clarifying the stress signal transduction pathway would be helpful for understanding the abiotic stress resistance mechanism in apple (Malus × domestica Borkh.) and could assist in the development of new varieties with high stress tolerance by genetic engineering. The key NAC transcription factor SND1, which is involved in the lignin biosynthesis process in apple, was functionally analyzed. The results of the stress treatments indicated that MdSND1 could be induced by salt, mannitol and ABA. Compared with wild-type GL-3 plants, MdSND1-overexpressing apple plants with greater antioxidant capacity and lignin were more resistant to salt and simulated osmotic stress, while RNAi plants were more vulnerable. Additionally, molecular experiments confirmed that MdSND1 could regulate the biosynthesis of lignin by activating the transcription of MdMYB46/83. Moreover, genes known to be involved in the stress signal transduction pathway (MdAREB1A, MdAREB1B, MdDREB2A, MdRD29A, and MdRD22) were screened for their close correlations with the expression of MdSND1 and the response to salt and osmotic stress. Multiple verification tests further demonstrated that MdSND1 could directly bind to these gene promoters and activate their transcription. The above results revealed that MdSND1 is directly involved in the regulation of lignin biosynthesis and the signal transduction pathway involved in the response to both salt and osmotic stress in apple.
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Affiliation(s)
- Keqin Chen
- Group of Molecular Biology of Fruit Trees, College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenyang, Liaoning, 110866, China
| | - Yunna Guo
- Group of Fruit Germplasm Evaluation & Utilization, College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenyang, Liaoning, 110866, China
| | - Mengru Song
- Group of Fruit Germplasm Evaluation & Utilization, College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenyang, Liaoning, 110866, China
| | - Lifu Liu
- Group of Fruit Germplasm Evaluation & Utilization, College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenyang, Liaoning, 110866, China
| | - Hao Xue
- Group of Molecular Biology of Fruit Trees, College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenyang, Liaoning, 110866, China
| | - Hongyan Dai
- Group of Fruit Germplasm Evaluation & Utilization, College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenyang, Liaoning, 110866, China.
| | - Zhihong Zhang
- Group of Molecular Biology of Fruit Trees, College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenyang, Liaoning, 110866, China.
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Yu M, Wang M, Gyalpo T, Basang Y. Stem lodging resistance in hulless barley: Transcriptome and metabolome analysis of lignin biosynthesis pathways in contrasting genotypes. Genomics 2020; 113:935-943. [PMID: 33127582 DOI: 10.1016/j.ygeno.2020.10.027] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/28/2020] [Accepted: 10/25/2020] [Indexed: 01/15/2023]
Abstract
Hulless barley is an important economic and food crop for local population in the Qinghai-Tibet plateau. However, due to extreme weather conditions, its production suffers from stem lodging stress, inflicting significant yield losses. Herein, we selected five lodging resistant and five non-resistant genotypes to investigate changes in concentration of lignin related metabolites and expression levels of related genes in node samples. The lodging resistant genotypes displayed high content of lignin intermediate metabolites. 57% of the expressed genes were differentially expressed (DEG) between the two groups. 31 DEGs participate in the lignin pathways and we found that 65% of these DEGs were strongly up-regulated in the lodging resistant group, indicating a mechanism towards high lignin synthesis within said group. The candidate structural genes as well as the co-expressed TFs identified in this study represent important molecular tools for functional characterization and exploitation in molecular breeding programmes.
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Affiliation(s)
- Mingzhai Yu
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet, China; Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa, China
| | - Mu Wang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet, China; Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa, China
| | - Thondup Gyalpo
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet, China; Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa, China
| | - Yuzhen Basang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet, China; Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa, China.
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Zhang Z, Li C, Zhang H, Ying Y, Hu Y, Song L. Comparative Analysis of the Lignification Process of Two Bamboo Shoots Stored at Room Temperature. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1399. [PMID: 33096642 PMCID: PMC7589782 DOI: 10.3390/plants9101399] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 10/13/2020] [Accepted: 10/14/2020] [Indexed: 11/18/2022]
Abstract
Two types of bamboo shoots, high bamboo (Phyllostachys prominens) shoots (HBSes) and moso bamboo (Phyllostachys edulis) shoots (MBSes), underwent a fast post-harvest lignification process under room temperature storage. To explore the mechanism of lignification in two types of bamboo shoots after post-harvest during room temperature storage, the measurement of cell wall polymers (lignin and cellulose) and enzyme activities of phenylalanine ammonialyase (PAL) and peroxidase (POD), and relative expression of related transcription networks factors (TFs) were performed. The results suggested that the lignification process in HBSes is faster than that in MBSes because of incremental increase in lignin and cellulose contents within 6 days and the shorter shelf-life. Additionally, compared with the expression pattern of lignification-related TFs and correlation analysis of lignin and cellulose contents, MYB20, MYB43, MYB85 could function positively in the lignification process of two types of bamboo shoots. A negative regulator, KNAT7, could negatively regulate the lignin biosynthesis in two types of bamboo shoots. In addition, MYB63 could function positively in HBSes, and NST1 could function negatively in MBSes. Notably, MYB42 may function differently in the two types of bamboo shoots, that is, a positive regulator in HBSes, but a negative regulator in MBSes. Transcription networks provide a comprehensive analysis to explore the mechanism of lignification in two types of bamboo shoots after post-harvest during room temperature storage. These results suggest that the lignification of bamboo shoots was mainly due to the increased activity of POD, higher expression levels of MYB20, MYB43, MYB63, and MYB85 genes, and lower expression levels of KNAT7 and NST1 genes, and the lignification process of HBSes and MBSes had significant differences.
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Affiliation(s)
| | | | | | | | - Yuanyuan Hu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin’an 311300, China; (Z.Z.); (C.L.); (H.Z.); (Y.Y.)
| | - Lili Song
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin’an 311300, China; (Z.Z.); (C.L.); (H.Z.); (Y.Y.)
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Hori C, Yu X, Mortimer JC, Sano R, Matsumoto T, Kikuchi J, Demura T, Ohtani M. Impact of abiotic stress on the regulation of cell wall biosynthesis in Populus trichocarpa. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2020; 37:273-283. [PMID: 33088190 PMCID: PMC7557660 DOI: 10.5511/plantbiotechnology.20.0326a] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 03/26/2020] [Indexed: 05/22/2023]
Abstract
Growth of biomass for lignocellulosic biofuels and biomaterials may take place on land unsuitable for foods, meaning the biomass plants are exposed to increased abiotic stresses. Thus, the understanding how this affects biomass composition and quality is important for downstream bioprocessing. Here, we analyzed the effect of drought and salt stress on cell wall biosynthesis in young shoots and xylem tissues of Populus trichocarpa using transcriptomic and biochemical methods. Following exposure to abiotic stress, stem tissues reduced vessel sizes, and young shoots increased xylem formation. Compositional analyses revealed a reduction in the total amount of cell wall polysaccharides. In contrast, the total lignin amount was unchanged, while the ratio of S/G lignin was significantly decreased in young shoots. Consistent with these observations, transcriptome analyses show that the expression of a subset of cell wall-related genes is tightly regulated by drought and salt stresses. In particular, the expression of a part of genes encoding key enzymes for S-lignin biosynthesis, caffeic acid O-methyltransferase and ferulate 5-hydroxylase, was decreased, suggesting the lower S/G ratio could be partly attributed to the down-regulation of these genes. Together, our data identifies a transcriptional abiotic stress response strategy in poplar, which results in adaptive changes to the plant cell wall.
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Affiliation(s)
- Chiaki Hori
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Research Faculty of Engineering, Hokkaido University, North 13, West 8, Sapporo, Hokkaido 060-8628, Japan
| | - Xiang Yu
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Jenny C. Mortimer
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Joint BioEnergy Institute, Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ryosuke Sano
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
| | - Tomoko Matsumoto
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Jun Kikuchi
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Taku Demura
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
- E-mail: Tel: +81-743-72-5460 Fax: +81-743-72-5469
| | - Misato Ohtani
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
- E-mail: Tel: +81-4-7136-3673 Fax: +81-4-7136-3674
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Petit J, Salentijn EMJ, Paulo MJ, Denneboom C, van Loo EN, Trindade LM. Elucidating the Genetic Architecture of Fiber Quality in Hemp ( Cannabis sativa L.) Using a Genome-Wide Association Study. Front Genet 2020; 11:566314. [PMID: 33093845 PMCID: PMC7527631 DOI: 10.3389/fgene.2020.566314] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 08/25/2020] [Indexed: 01/12/2023] Open
Abstract
Hemp (Cannabis sativa L.) is a bast-fiber crop with a great potential in the emerging bio-based economy. Yet, hemp breeding for fiber quality is restricted and that is mainly due to the limited knowledge of the genetic architecture of its fiber quality. A panel of 123 hemp accessions, with large phenotypic variability, was used to study the genetic basis of seven cell wall and bast fiber traits relevant to fiber quality. These traits showed large genetic variance components and high values of broad sense heritability in this hemp panel, as concluded from the phenotypic evaluation across three test locations with contrasting environments. The hemp panel was genotyped using restriction site associated DNA sequencing (RAD-seq). Subsequently, a large set (> 600,000) of selected genome-wide single nucleotide polymorphism (SNP) markers was used for a genome-wide association study (GWAS) approach to get insights into quantitative trait loci (QTLs) controlling fiber quality traits. In absence of a complete hemp genome sequence, identification of QTLs was based on the following characteristics: (i) association level to traits, (ii) fraction of explained trait variance, (iii) collinearity between QTLs, and (iv) detection across different environments. Using this approach, 16 QTLs were identified across locations for different fiber quality traits, including contents of glucose, glucuronic acid, mannose, xylose, lignin, and bast fiber content. Among them, six were found across the three environments. The genetic markers composing the QTLs that are common across locations are valuable tools to develop novel genotypes of hemp with improved fiber quality. Underneath the QTLs, 12 candidate genes were identified which are likely to be involved in the biosynthesis and modification of monosaccharides, polysaccharides, and lignin. These candidate genes were suggested to play an important role in determining fiber quality in hemp. This study provides new insights into the genetic architecture of fiber traits, identifies QTLs and candidate genes that form the basis for molecular breeding for high fiber quality hemp cultivars.
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Affiliation(s)
- Jordi Petit
- Wageningen UR Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
| | - Elma M J Salentijn
- Wageningen UR Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
| | - Maria-João Paulo
- Biometris, Wageningen University & Research, Wageningen, Netherlands
| | - Christel Denneboom
- Wageningen UR Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
| | - Eibertus N van Loo
- Wageningen UR Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
| | - Luisa M Trindade
- Wageningen UR Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
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Transcriptomic Profiling of Cryptomeria fortunei Hooibrenk Vascular Cambium Identifies Candidate Genes Involved in Phenylpropanoid Metabolism. FORESTS 2020. [DOI: 10.3390/f11070766] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Cryptomeria fortunei Hooibrenk (Chinese cedar) is a coniferous tree from southern China that has an important function in landscaping and timber production. Lignin is one of the key components of secondary cell walls, which have a crucial role in conducting water and providing mechanical support for the upward growth of plants. It is mainly biosynthesized via the phenylpropanoid metabolic pathway, of which the molecular mechanism remains so far unresolved in C. fortunei. In order to obtain further insight into this pathway, we performed transcriptome sequencing of the C. fortunei cambial zone at 5 successive growth stages. We generated 78,673 unigenes from transcriptome data, of which 45,214 (57.47%) were successfully annotated in the non-redundant protein database (NR). A total of 8975 unigenes were identified to be significantly differentially expressed between Sample_B and Sample_A after analyzing their expression profiles. Of the differentially expressed genes (DEGs), 6817 (75.96%) and 2158 (24.04%) were up- and down-regulated, respectively. 83 DEGs were involved in phenylpropanoid metabolism, 37 DEGs that encoded v-Myb avian myeloblastosis viral oncogene homolog (MYB) transcription factor (TF), and many candidates that encoded lignin synthesizing enzymes. These findings contribute to understanding the expression pattern of C. fortunei cambial zone transcriptome. Furthermore, our results provide additional insight towards understanding the molecular mechanisms of wood formation in C. fortunei.
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Singh V, Kumar N, Dwivedi AK, Sharma R, Sharma MK. Phylogenomic Analysis of R2R3 MYB Transcription Factors in Sorghum and their Role in Conditioning Biofuel Syndrome. Curr Genomics 2020; 21:138-154. [PMID: 32655308 PMCID: PMC7324873 DOI: 10.2174/1389202921666200326152119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 03/17/2020] [Accepted: 03/19/2020] [Indexed: 11/30/2022] Open
Abstract
Background Large scale cultivation of sorghum for food, feed, and biofuel requires concerted efforts for engineering multipurpose cultivars with optimised agronomic traits. Due to their vital role in regulating the biosynthesis of phenylpropanoid-derived compounds, biomass composition, biotic, and abiotic stress response, R2R3-MYB family transcription factors are ideal targets for improving environmental resilience and economic value of sorghum. Methods We used diverse computational biology tools to survey the sorghum genome to identify R2R3-MYB transcription factors followed by their structural and phylogenomic analysis. We used in-house generated as well as publicly available high throughput expression data to analyse the R2R3 expression patterns in various sorghum tissue types. Results We have identified a total of 134 R2R3-MYB genes from sorghum and developed a framework to predict gene functions. Collating information from the physical location, duplication, structural analysis, orthologous sequences, phylogeny, and expression patterns revealed the role of duplications in clade-wise expansion of the R2R3-MYB family as well as intra-clade functional diversification. Using publicly available and in-house generated RNA sequencing data, we provide MYB candidates for conditioning biofuel syndrome by engineering phenylpropanoid biosynthesis and sugar signalling pathways in sorghum. Conclusion The results presented here are pivotal to prioritize MYB genes for functional validation and optimize agronomic traits in sorghum.
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Affiliation(s)
- Vinay Singh
- 1Crop Genetics & Informatics Group, School of Biotechnology, Jawaharlal Nehru University, New Mehrauli Road, New Delhi-110067, India; 2Crop Genetics & Informatics Group, School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Mehrauli Road, New Delhi-110067, India
| | - Neeraj Kumar
- 1Crop Genetics & Informatics Group, School of Biotechnology, Jawaharlal Nehru University, New Mehrauli Road, New Delhi-110067, India; 2Crop Genetics & Informatics Group, School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Mehrauli Road, New Delhi-110067, India
| | - Anuj K Dwivedi
- 1Crop Genetics & Informatics Group, School of Biotechnology, Jawaharlal Nehru University, New Mehrauli Road, New Delhi-110067, India; 2Crop Genetics & Informatics Group, School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Mehrauli Road, New Delhi-110067, India
| | - Rita Sharma
- 1Crop Genetics & Informatics Group, School of Biotechnology, Jawaharlal Nehru University, New Mehrauli Road, New Delhi-110067, India; 2Crop Genetics & Informatics Group, School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Mehrauli Road, New Delhi-110067, India
| | - Manoj K Sharma
- 1Crop Genetics & Informatics Group, School of Biotechnology, Jawaharlal Nehru University, New Mehrauli Road, New Delhi-110067, India; 2Crop Genetics & Informatics Group, School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Mehrauli Road, New Delhi-110067, India
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Sun Y, Ren S, Ye S, Tian Q, Luo K. Identification and Functional Characterization of PtoMYB055 Involved in the Regulation of the Lignin Biosynthesis Pathway in Populus tomentosa. Int J Mol Sci 2020; 21:ijms21144857. [PMID: 32659969 PMCID: PMC7402297 DOI: 10.3390/ijms21144857] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/04/2020] [Accepted: 07/06/2020] [Indexed: 01/23/2023] Open
Abstract
Wood, which is mainly composed of lignified secondary cell wall, is the most abundant biomass in woody plants. Previous studies have revealed that R2R3-type MYB transcription factors are important regulators of the formation of the secondary cell wall in vascular plants. In this study, we isolated the R2R3-type MYB transcription factor gene PtoMYB055, which is mainly expressed in xylem and phloem tissue, from Populus tomentosa and demonstrate that PtoMYB055 is a key regulator of lignin biosynthesis. PtoMYB055 as a transcriptional activator is localized to the nucleus. Overexpression of PtoMYB055 upregulates expression of lignin biosynthetic genes in transgenic poplar plants, resulting in ectopic deposition of lignin in phloem tissue and an increase in thickness of the secondary cell wall. In sum, PtoMYB055 is a transcriptional activator that is involved in regulating lignin biosynthesis during the formation of the secondary cell wall in poplar.
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El-Azaz J, de la Torre F, Pascual MB, Debille S, Canlet F, Harvengt L, Trontin JF, Ávila C, Cánovas FM. Transcriptional analysis of arogenate dehydratase genes identifies a link between phenylalanine biosynthesis and lignin biosynthesis. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:3080-3093. [PMID: 32090267 PMCID: PMC7260716 DOI: 10.1093/jxb/eraa099] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 02/17/2020] [Indexed: 05/29/2023]
Abstract
Biogenesis of the secondary cell wall in trees involves the massive biosynthesis of the phenylalanine-derived polymer lignin. Arogenate dehydratase (ADT) catalyzes the last, and rate-limiting, step of the main pathway for phenylalanine biosynthesis. In this study, we found that transcript levels for several members of the large ADT gene family, including ADT-A and ADT-D, were enhanced in compression wood of maritime pine, a xylem tissue enriched in lignin. Transcriptomic analysis of maritime pine silenced for PpMYB8 revealed that this gene plays a critical role in coordinating the deposition of lignin with the biosynthesis of phenylalanine. Specifically, it was found that ADT-A and ADT-D were strongly down-regulated in PpMYB8-silenced plants and that they were transcriptionally regulated through direct interaction of this transcription factor with regulatory elements present in their promoters. Another transcription factor, PpHY5, exhibited an expression profile opposite to that of PpMYB8 and also interacted with specific regulatory elements of ADT-A and ADT-D genes, suggesting that it is involved in transcriptional regulation of phenylalanine biosynthesis. Taken together, our results reveal that PpMYB8 and PpHY5 are involved in the control of phenylalanine formation and its metabolic channeling for lignin biosynthesis and deposition during wood formation in maritime pine.
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Affiliation(s)
- Jorge El-Azaz
- Grupo de Biología Molecular y Biotecnología de Plantas (BIO-114), Universidad de Málaga, Málaga, Spain
| | - Fernando de la Torre
- Grupo de Biología Molecular y Biotecnología de Plantas (BIO-114), Universidad de Málaga, Málaga, Spain
| | - María Belén Pascual
- Grupo de Biología Molecular y Biotecnología de Plantas (BIO-114), Universidad de Málaga, Málaga, Spain
| | - Sandrine Debille
- Institut Technologique FCBA, Pôle Biotechnologies et Sylviculture Avancée (BSA), Pierroton, Cestas, France
| | - Francis Canlet
- Institut Technologique FCBA, Pôle Biotechnologies et Sylviculture Avancée (BSA), Pierroton, Cestas, France
| | - Luc Harvengt
- Institut Technologique FCBA, Pôle Biotechnologies et Sylviculture Avancée (BSA), Pierroton, Cestas, France
| | - Jean-François Trontin
- Institut Technologique FCBA, Pôle Biotechnologies et Sylviculture Avancée (BSA), Pierroton, Cestas, France
| | - Concepción Ávila
- Grupo de Biología Molecular y Biotecnología de Plantas (BIO-114), Universidad de Málaga, Málaga, Spain
| | - Francisco M Cánovas
- Grupo de Biología Molecular y Biotecnología de Plantas (BIO-114), Universidad de Málaga, Málaga, Spain
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Yadav V, Wang Z, Wei C, Amo A, Ahmed B, Yang X, Zhang X. Phenylpropanoid Pathway Engineering: An Emerging Approach towards Plant Defense. Pathogens 2020; 9:pathogens9040312. [PMID: 32340374 PMCID: PMC7238016 DOI: 10.3390/pathogens9040312] [Citation(s) in RCA: 146] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/11/2020] [Accepted: 04/17/2020] [Indexed: 11/23/2022] Open
Abstract
Pathogens hitting the plant cell wall is the first impetus that triggers the phenylpropanoid pathway for plant defense. The phenylpropanoid pathway bifurcates into the production of an enormous array of compounds based on the few intermediates of the shikimate pathway in response to cell wall breaches by pathogens. The whole metabolomic pathway is a complex network regulated by multiple gene families and it exhibits refined regulatory mechanisms at the transcriptional, post-transcriptional, and post-translational levels. The pathway genes are involved in the production of anti-microbial compounds as well as signaling molecules. The engineering in the metabolic pathway has led to a new plant defense system of which various mechanisms have been proposed including salicylic acid and antimicrobial mediated compounds. In recent years, some key players like phenylalanine ammonia lyases (PALs) from the phenylpropanoid pathway are proposed to have broad spectrum disease resistance (BSR) without yield penalties. Now we have more evidence than ever, yet little understanding about the pathway-based genes that orchestrate rapid, coordinated induction of phenylpropanoid defenses in response to microbial attack. It is not astonishing that mutants of pathway regulator genes can show conflicting results. Therefore, precise engineering of the pathway is an interesting strategy to aim at profitably tailored plants. Here, this review portrays the current progress and challenges for phenylpropanoid pathway-based resistance from the current prospective to provide a deeper understanding.
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Affiliation(s)
- Vivek Yadav
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of horticulture, Northwest A&F University, Xianyang 712100, China; (V.Y.); (Z.W.); (C.W.); (B.A.); (X.Y.)
| | - Zhongyuan Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of horticulture, Northwest A&F University, Xianyang 712100, China; (V.Y.); (Z.W.); (C.W.); (B.A.); (X.Y.)
| | - Chunhua Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of horticulture, Northwest A&F University, Xianyang 712100, China; (V.Y.); (Z.W.); (C.W.); (B.A.); (X.Y.)
| | - Aduragbemi Amo
- College of Agronomy, Northwest A&F University, Xianyang 712100, China;
| | - Bilal Ahmed
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of horticulture, Northwest A&F University, Xianyang 712100, China; (V.Y.); (Z.W.); (C.W.); (B.A.); (X.Y.)
| | - Xiaozhen Yang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of horticulture, Northwest A&F University, Xianyang 712100, China; (V.Y.); (Z.W.); (C.W.); (B.A.); (X.Y.)
| | - Xian Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of horticulture, Northwest A&F University, Xianyang 712100, China; (V.Y.); (Z.W.); (C.W.); (B.A.); (X.Y.)
- Correspondence: ; Tel.: +86-029-8708-2613
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Zhu L, Guan Y, Zhang Z, Song A, Chen S, Jiang J, Chen F. CmMYB8 encodes an R2R3 MYB transcription factor which represses lignin and flavonoid synthesis in chrysanthemum. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 149:217-224. [PMID: 32078899 DOI: 10.1016/j.plaphy.2020.02.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 01/16/2020] [Accepted: 02/11/2020] [Indexed: 05/24/2023]
Abstract
R2R3-MYB transcription factors are important regulators of the growth and development of plants. Here, CmMYB8 a chrysanthemum gene encoding an R2R3-MYB transcription factor, was isolated and functionally characterized. The gene was transcribed throughout the plant, but most strongly in the stem. When CmMYB8 was over-expressed, a number of genes encoding components of lignin synthesis were down-regulated, and the plants' lignin content was reduced. The composition of the lignin in the transgenic plants was also altered, and its S/G ratio was reduced. A further consequence of the over-expression of CmMYB8 was to lessen the transcript abundance of key genes involved in flavonoid synthesis, resulting in a reduced accumulation of flavonoids. The indication is that the CmMYB8 protein participates in the negative regulation of both lignin and flavonoid synthesis.
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Affiliation(s)
- Lu Zhu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, China.
| | - Yunxiao Guan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, China.
| | - Zhaohe Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, China.
| | - Aiping Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, China.
| | - Sumei Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, China.
| | - Jiafu Jiang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, China.
| | - Fadi Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, China.
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Wei X, Yang Z, Han G, Zhao X, Yin S, Yuan F, Wang B. The developmental dynamics of the sweet sorghum root transcriptome elucidate the differentiation of apoplastic barriers. PLANT SIGNALING & BEHAVIOR 2020; 15:1724465. [PMID: 32024414 PMCID: PMC7194387 DOI: 10.1080/15592324.2020.1724465] [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: 08/29/2019] [Revised: 10/12/2019] [Accepted: 10/14/2019] [Indexed: 06/01/2023]
Abstract
Apoplastic barriers in the endodermis, such as Casparian strips and suberin lamellae, control the passage of water and minerals into the stele. Apoplastic barriers are thus thought to contribute to salt exclusion in salt-excluding plants such as sweet sorghum (Sorghum bicolor). However, little is known about the genes involved in the development of the apoplastic barrier. Here, we identified candidate genes involved in Casparian strip and suberin lamella development in the roots of a sweet sorghum line (M-81E). Three distinct developmental regions (no differentiation, developing, and mature) were identified based on Casparian strip and suberin lamella staining in root cross sections. Sequencing of RNA extracted from these distinct sections identified key genes participating in the differentiation of the apoplastic barrier. The different sections were structurally distinct, presumably due to differences in gene expression. Genes controlling the phenylpropanoid pathway, fatty acid elongation, and fatty acid ω-hydroxylation appeared to be directly responsible for the formation of the apoplastic barrier. Our dataset elucidates the molecular processes underpinning apoplastic barrier development and provides a basis for future research on molecular mechanisms of apoplastic barrier formation and salt exclusion.Abbreviations: SHR, SHORTROOT; MYB, MYB DOMAIN PROTEIN; CIFs, Casparian strip integrity factors; CASP, Casparian strip domain proteins; PER, peroxidase; ESB1, ENHANCED SUBERIN1; CS, Casparian strip; RPKM, reads per kilobase per million reads; DEGs, differentially expressed genes; FDR, false discovery rate; GO, Gene Ontology; KEGG, Kyoto Encyclopedia of Genes and Genomes; RNA-seq, RNA sequencing; PAL, phenylalanine ammonia-lyase; CYP, cytochrome P450 monooxygenases; 4CL, 4-coumarate-CoA ligase; AAE5, ACYL-ACTIVATING ENZYME5; CCR, cinnamoyl CoA reductase; TKPR, TETRAKETIDE ALPHA-PYRONE REDUCTASE1; CAD, cinnamyl alcohol dehydrogenase; HST, shikimate O-hydroxycinnamoyltransferase; PMAT2, PHENOLIC GLUCOSIDE MALONYLTRANSFERASE2; CCOAOMT, caffeoyl-CoA O-methyltransferase; KCS, β-ketoacyl-CoA synthase; CUT1, CUTICULAR PROTEIN1; DET2, 5-alpha-reductase; TAX, 3'-N-debenzoyl-2'-deoxytaxol N-benzoyltransferase; CER1, ECERIFERUM1; FAR, fatty acyl reductase; AF-CoA, alcohol-forming fatty acyl-CoA reductase; ABCG, ATP-binding cassette, subfamily G; ERF, ethylene-responsive transcription factor; HSF, heat stress transcription factor; NTF, NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT B-5; GPAT, glycerol 3-phosphate acyltransferase.
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Affiliation(s)
- Xiaocen Wei
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Ji’nan, Shandong, P.R. China
| | - Zhen Yang
- Shandong Provincial Key Laboratory of Microbial Engineering, School of Biologic Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, China
| | - Guoliang Han
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Ji’nan, Shandong, P.R. China
| | - Xin Zhao
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Ji’nan, Shandong, P.R. China
| | - Shanshan Yin
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Ji’nan, Shandong, P.R. China
| | - Fang Yuan
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Ji’nan, Shandong, P.R. China
| | - Baoshan Wang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Ji’nan, Shandong, P.R. China
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He F, Machemer-Noonan K, Golfier P, Unda F, Dechert J, Zhang W, Hoffmann N, Samuels L, Mansfield SD, Rausch T, Wolf S. The in vivo impact of MsLAC1, a Miscanthus laccase isoform, on lignification and lignin composition contrasts with its in vitro substrate preference. BMC PLANT BIOLOGY 2019; 19:552. [PMID: 31830911 PMCID: PMC6909574 DOI: 10.1186/s12870-019-2174-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 11/28/2019] [Indexed: 05/18/2023]
Abstract
BACKGROUND Understanding lignin biosynthesis and composition is of central importance for sustainable bioenergy and biomaterials production. Species of the genus Miscanthus have emerged as promising bioenergy crop due to their rapid growth and modest nutrient requirements. However, lignin polymerization in Miscanthus is poorly understood. It was previously shown that plant laccases are phenol oxidases that have multiple functions in plant, one of which is the polymerization of monolignols. Herein, we link a newly discovered Miscanthus laccase, MsLAC1, to cell wall lignification. Characterization of recombinant MsLAC1 and Arabidopsis transgenic plants expressing MsLAC1 were carried out to understand the function of MsLAC1 both in vitro and in vivo. RESULTS Using a comprehensive suite of molecular, biochemical and histochemical analyses, we show that MsLAC1 localizes to cell walls and identify Miscanthus transcription factors capable of regulating MsLAC1 expression. In addition, MsLAC1 complements the Arabidopsis lac4-2 lac17 mutant and recombinant MsLAC1 is able to oxidize monolignol in vitro. Transgenic Arabidopsis plants over-expressing MsLAC1 show higher G-lignin content, although recombinant MsLAC1 seemed to prefer sinapyl alcohol as substrate. CONCLUSIONS In summary, our results suggest that MsLAC1 is regulated by secondary cell wall MYB transcription factors and is involved in lignification of xylem fibers. This report identifies MsLAC1 as a promising breeding target in Miscanthus for biofuel and biomaterial applications.
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Affiliation(s)
- Feng He
- Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Katja Machemer-Noonan
- Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Philippe Golfier
- Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Faride Unda
- Department of Wood Science, University of British Columbia, Vancouver, Canada
| | - Johanna Dechert
- Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Wan Zhang
- Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Natalie Hoffmann
- Department of Botany, University of British Columbia, Vancouver, Canada
| | - Lacey Samuels
- Department of Botany, University of British Columbia, Vancouver, Canada
| | - Shawn D Mansfield
- Department of Wood Science, University of British Columbia, Vancouver, Canada
| | - Thomas Rausch
- Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Heidelberg, Germany.
| | - Sebastian Wolf
- Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Heidelberg, Germany.
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Induction of PrMADS10 on the lower side of bent pine tree stems: potential role in modifying plant cell wall properties and wood anatomy. Sci Rep 2019; 9:18981. [PMID: 31831838 PMCID: PMC6908731 DOI: 10.1038/s41598-019-55276-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 11/07/2019] [Indexed: 12/20/2022] Open
Abstract
The molecular mechanisms underlying inclination responses in trees are unclear. In this study, we identified a MADS-box transcription factor differentially expressed early after inclination in the stems of Pinus radiata D. Don. PrMADS10 has a CDS of 582 bp and encodes a group II MADS-box transcription factor. We measured highest accumulation of this transcript on the lower side of inclined pine stems. In an effort to identify putative targets, we stably transformed Arabidopsis thaliana with a 35S::PrMADS10 construct. Transcriptome analysis revealed 1,219 genes differentially-expressed, with 690 and 529 genes up- and down-regulated respectively, when comparing the transgenic and wild-type. Differentially-expressed genes belong to different biological processes, but were enriched in cell wall remodeling and phenylpropanoid metabolic functions. Interestingly, lignin content was 30% higher in transgenic as compared to wild-type plants consistent with observed changes in gene expression. Differentially expressed transcription factors and phenylpropanoid genes were analyzed using STRING. Several MYB and NAC transcription factors showed interactions with genes of the phenylpropanoid pathway. Together, these results implicate PrMADS10 as a regulatory factor, triggering the expression of other transcription factors and genes involved in the synthesis of lignin.
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Li M, Cheng C, Zhang X, Zhou S, Wang C, Ma C, Yang S. PpNAC187 Enhances Lignin Synthesis in 'Whangkeumbae' Pear ( Pyrus pyrifolia) 'Hard-End' Fruit. Molecules 2019; 24:E4338. [PMID: 31783586 PMCID: PMC6930614 DOI: 10.3390/molecules24234338] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 11/23/2019] [Accepted: 11/25/2019] [Indexed: 11/16/2022] Open
Abstract
A disorder in pears that is known as 'hard-end' fruit affects the appearance, edible quality, and market value of pear fruit. RNA-Seq was carried out on the calyx end of 'Whangkeumbae' pear fruit with and without the hard-end symptom to explore the mechanism underlying the formation of hard-end. The results indicated that the genes in the phenylpropanoid pathway affecting lignification were up-regulated in hard-end fruit. An analysis of differentially expressed genes (DEGs) identified three NAC transcription factors, and RT-qPCR analysis of PpNAC138, PpNAC186, and PpNAC187 confirmed that PpNAC187 gene expression was correlated with the hard-end disorder in pear fruit. A transient increase in PpNAC187 was observed in the calyx end of 'Whangkeumbae' fruit when they began to exhibit hard-end symptom. Concomitantly, the higher level of PpCCR and PpCOMT transcripts was observed, which are the key genes in lignin biosynthesis. Notably, lignin content in the stem and leaf tissues of transgenic tobacco overexpressing PpNAC187 was significantly higher than in the control plants that were transformed with an empty vector. Furthermore, transgenic tobacco overexpressing PpNAC187 had a larger number of xylem vessel elements. The results of this study confirmed that PpNAC187 functions in inducing lignification in pear fruit during the development of the hard-end disorder.
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Affiliation(s)
- Mingtong Li
- College of Horticulture, Qingdao Agricultural University, No. 700 Changcheng Road, Chengyang, Qingdao 266109, China; (M.L.); (C.C.); (X.Z.); (C.W.); (C.M.)
| | - Chenxia Cheng
- College of Horticulture, Qingdao Agricultural University, No. 700 Changcheng Road, Chengyang, Qingdao 266109, China; (M.L.); (C.C.); (X.Z.); (C.W.); (C.M.)
| | - Xinfu Zhang
- College of Horticulture, Qingdao Agricultural University, No. 700 Changcheng Road, Chengyang, Qingdao 266109, China; (M.L.); (C.C.); (X.Z.); (C.W.); (C.M.)
| | - Suping Zhou
- Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, 3500 John Merritt Blvd, Nashville, TN 37209, USA;
| | - Caihong Wang
- College of Horticulture, Qingdao Agricultural University, No. 700 Changcheng Road, Chengyang, Qingdao 266109, China; (M.L.); (C.C.); (X.Z.); (C.W.); (C.M.)
| | - Chunhui Ma
- College of Horticulture, Qingdao Agricultural University, No. 700 Changcheng Road, Chengyang, Qingdao 266109, China; (M.L.); (C.C.); (X.Z.); (C.W.); (C.M.)
| | - Shaolan Yang
- College of Horticulture, Qingdao Agricultural University, No. 700 Changcheng Road, Chengyang, Qingdao 266109, China; (M.L.); (C.C.); (X.Z.); (C.W.); (C.M.)
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Li M, Sui N, Lin L, Yang Z, Zhang Y. Transcriptomic profiling revealed genes involved in response to cold stress in maize. FUNCTIONAL PLANT BIOLOGY : FPB 2019; 46:830-844. [PMID: 31217070 DOI: 10.1071/fp19065] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 05/06/2019] [Indexed: 05/18/2023]
Abstract
Maize is an important food crop. Chilling stress can decrease maize production by affecting seed germination and seedling growth, especially in early spring. We analysed chlorophyll fluorescence, membrane lipids, secondary metabolites and the transcriptome of two maize inbred lines (chilling-tolerant M54 and chilling-sensitive 753F) after 0, 4 and 24 h cold stress. M54 showed better ability to protect PSII and accumulate secondary metabolites. From RNA sequencing data, we determined that the majority of cold-affected genes were involved in photosynthesis, secondary metabolism, and signal transduction. Genes important for maintaining photosystem structure and for regulating electron transport were less affected by cold stress in M54 than in 753F. Expression of genes related to secondary metabolism and unsaturated fatty acid synthesis were upregulated more strongly in M54 than in 753F and M54 accumulated more unsaturated fatty acids and secondary metabolites. As a result, M54 achieved relatively high cold tolerance by protecting the photosystems and maintaining the stability of cell membranes.
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Affiliation(s)
- Meng Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, China; and Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
| | - Na Sui
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, Shandong, China
| | - Lin Lin
- Water Research Institute of Shandong Province, No. 125 Lishan Road, Jinan City, Shandong Province, China
| | - Zhen Yang
- Shandong Provincial Key Laboratory of Microbial Engineering, School of Biologic Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, China; and Corresponding authors. ;
| | - Yuanhu Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, China; and Corresponding authors. ;
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