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SMRT and Illumina sequencing provide insights into mechanisms of lignin and terpenoids biosynthesis in Pinus massoniana Lamb. Int J Biol Macromol 2023; 232:123267. [PMID: 36657535 DOI: 10.1016/j.ijbiomac.2023.123267] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/28/2022] [Accepted: 01/10/2023] [Indexed: 01/18/2023]
Abstract
Wood and oleoresin are important industrial raw materials with high economic value; however, their molecular formation and biosynthesis mechanisms in different tissues of Pinus massoniana remain unexplored. Therefore, we used single-molecule real-time sequencing technology (SMRT) and Illumina RNA sequencing to establish a transcriptome dataset and explore the expression pattern of genes related to secondary metabolites involved in wood formation and oleoresin biosynthesis in six different P. massoniana tissues. In total, 63.58 Gb of polymerase reads were obtained, including 41,407 isoforms with an average length of 1822 bp. We identified 3939 and 8785 isoforms and 161 and 481 transcription factors with tissue expression specificity and in the reproductive and vegetative organs, respectively. Eighty isoforms were annotated as cellulose synthases and 224 isoforms involved in lignin biosynthesis were enriched. Additionally, we identified 217 isoforms involved in the terpenoid biosynthesis pathway, with needles having the most tissue-specific genes for terpenoid biosynthesis. Some isoforms related to lignin biosynthesis were highly expressed in the xylem, according to the results of transcriptome sequencing and real-time quantitative reverse-transcription polymerase chain reaction. Our research confirmed the advantages of SMRT sequencing and provided valuable information for the transcriptional annotation of P. massoniana, which will be beneficial for producing better raw wood and oleoresin materials.
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Genome-Wide Identification and Characterization of Auxin Response Factor (ARF) Gene Family Involved in Wood Formation and Response to Exogenous Hormone Treatment in Populus trichocarpa. Int J Mol Sci 2023; 24:ijms24010740. [PMID: 36614182 PMCID: PMC9820880 DOI: 10.3390/ijms24010740] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/22/2022] [Accepted: 12/30/2022] [Indexed: 01/03/2023] Open
Abstract
Auxin is a key regulator that virtually controls almost every aspect of plant growth and development throughout its life cycle. As the major components of auxin signaling, auxin response factors (ARFs) play crucial roles in various processes of plant growth and development. In this study, a total of 35 PtrARF genes were identified, and their phylogenetic relationships, chromosomal locations, synteny relationships, exon/intron structures, cis-elements, conserved motifs, and protein characteristics were systemically investigated. We also analyzed the expression patterns of these PtrARF genes and revealed that 16 of them, including PtrARF1, 3, 7, 11, 13-17, 21, 23, 26, 27, 29, 31, and 33, were preferentially expressed in primary stems, while 15 of them, including PtrARF2, 4, 6, 9, 10, 12, 18-20, 22, 24, 25, 28, 32, and 35, participated in different phases of wood formation. In addition, some PtrARF genes, with at least one cis-element related to indole-3-acetic acid (IAA) or abscisic acid (ABA) response, responded differently to exogenous IAA and ABA treatment, respectively. Three PtrARF proteins, namely PtrARF18, PtrARF23, and PtrARF29, selected from three classes, were characterized, and only PtrARF18 was a transcriptional self-activator localized in the nucleus. Moreover, Y2H and bimolecular fluorescence complementation (BiFC) assay demonstrated that PtrARF23 interacted with PtrIAA10 and PtrIAA28 in the nucleus, while PtrARF29 interacted with PtrIAA28 in the nucleus. Our results provided comprehensive information regarding the PtrARF gene family, which will lay some foundation for future research about PtrARF genes in tree development and growth, especially the wood formation, in response to cellular signaling and environmental cues.
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Qi J, Yu X, Wang X, Zhang F, Ma C. Differentially expressed genes related to plant height and yield in two alfalfa cultivars based on RNA-seq. PeerJ 2022; 10:e14096. [PMID: 36248707 PMCID: PMC9558622 DOI: 10.7717/peerj.14096] [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: 04/08/2022] [Accepted: 08/30/2022] [Indexed: 01/21/2023] Open
Abstract
Background Alfalfa (Medicago sativa L.) is a kind of forage with high relative feeding value in farming and livestock breeding, and is of great significance to the development of animal husbandry. The growth of the aboveground part of alfalfa is an important factor that limits crop yield. Clarifying the molecular mechanisms that maintain vigorous growth in alfalfa may contribute to the development of molecular breeding for this crop. Methods Here, we evaluated the growth phenotypes of five cultivars of alfalfa (WL 712, WL 525HQ, Victoria, Knight 2, and Aohan). Then RNA-seq was performed on the stems of WL 712, chosen as a fast growing cultivar, and Aohan, chosen as a slow growing cultivar. GO enrichment analysis was conducted on all differentially expressed genes (DEGs). Result Among the differentially expressed genes that were up-regulated in the fast growing cultivar, GO analysis revealed enrichment in the following seven categories: formation of water-conducting tissue in vascular plants, biosynthesis and degradation of lignin, formation of the primary or secondary cell wall, cell enlargement and plant growth, cell division and shoot initiation, stem growth and induced germination, and cell elongation. KEGG analysis showed that differentially expressed genes were annotated as being involved in plant hormone signal transduction, photosynthesis, and phenylpropanoid biosynthesis. KEGG analysis also showed that up-regulated in the fast growing cultivar were members of the WRKY family of transcription factors related to plant growth and development, members of the NAC and MYB gene families related to the synthesis of cellulose and hemicellulose, and the development of secondary cell wall fibres, and finally, MYB family members that are involved in plant growth regulation. Our research results not only enrich the transcriptome database of alfalfa, but also provide valuable information for explaining the molecular mechanism of fast growth, and can provide reference for the production of alfalfa.
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Affiliation(s)
- Jiangjiao Qi
- College of Animal Science & Technology, Shihezi University, Shihezi, Xinjiang, China
| | - Xue Yu
- College of Animal Science & Technology, Shihezi University, Shihezi, Xinjiang, China
| | - Xuzhe Wang
- College of Animal Science & Technology, Shihezi University, Shihezi, Xinjiang, China
| | - Fanfan Zhang
- College of Animal Science & Technology, Shihezi University, Shihezi, Xinjiang, China
| | - Chunhui Ma
- College of Animal Science & Technology, Shihezi University, Shihezi, Xinjiang, China
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Payyavula RS, Badmi R, Jawdy SS, Rodriguez M, Gunter L, Sykes RW, Winkeler KA, Collins CM, Rottmann WH, Chen J, Yang X, Tuskan GA, Kalluri UC. Biomass formation and sugar release efficiency of Populus modified by altered expression of a NAC transcription factor. PLANT DIRECT 2022; 6:e419. [PMID: 35979037 PMCID: PMC9373907 DOI: 10.1002/pld3.419] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 05/15/2022] [Accepted: 06/10/2022] [Indexed: 06/15/2023]
Abstract
Woody biomass is an important feedstock for biofuel production. Manipulation of wood properties that enable efficient conversion of biomass to biofuel reduces cost of biofuel production. Wood cell wall composition is regulated at several levels that involve expression of transcription factors such as wood-/secondary cell wall-associated NAC domains (WND or SND). In Arabidopsis thaliana, SND1 regulates cell wall composition through activation of its down-stream targets such as MYBs. The functional aspects of SND1 homologs in the woody Populus have been studied through transgenic manipulation. In this study, we investigated the role of PdWND1B, Populus SND1 sequence ortholog, in wood formation using transgenic manipulation through over-expression or silencing under the control of a vascular-specific 4-coumarate-CoA ligase (4CL) promoter. As compared with control plants, PdWND1B-RNAi plants were shorter in height, with significantly reduced stem diameter and dry biomass, whereas there were no significant differences in growth and productivity of PdWND1B over-expression plants. Conversely, PdWND1B over-expression lines showed a significant reduction in cellulose and increase in lignin content, whereas there was no significant impact on lignin content of downregulated lines. Stem carbohydrate composition analysis revealed a decrease in glucose, mannose, arabinose, and galactose, but an increase in xylose in the over-expression lines. Transcriptome analysis revealed upregulation of several downstream transcription factors and secondary cell wall related structural genes in the PdWND1B over-expression lines, partly explaining the observed phenotypic changes in cell wall chemistry. Relative to the control, glucose release efficiency and ethanol production from stem biomass was significantly reduced in over-expression lines. Our results show that PdWND1B is an important factor determining biomass productivity, cell wall chemistry and its conversion to biofuels in Populus.
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Affiliation(s)
- Raja S. Payyavula
- BioEnergy Science Centre, Center for Bioenergy Innovation and Biosciences DivisionOak Ridge National LaboratoryOak RidgeTennesseeUSA
| | - Raghuram Badmi
- BioEnergy Science Centre, Center for Bioenergy Innovation and Biosciences DivisionOak Ridge National LaboratoryOak RidgeTennesseeUSA
| | - Sara S. Jawdy
- BioEnergy Science Centre, Center for Bioenergy Innovation and Biosciences DivisionOak Ridge National LaboratoryOak RidgeTennesseeUSA
| | - Miguel Rodriguez
- BioEnergy Science Centre, Center for Bioenergy Innovation and Biosciences DivisionOak Ridge National LaboratoryOak RidgeTennesseeUSA
| | - Lee Gunter
- BioEnergy Science Centre, Center for Bioenergy Innovation and Biosciences DivisionOak Ridge National LaboratoryOak RidgeTennesseeUSA
| | - Robert W. Sykes
- The Biosciences CenterNational Renewable Energy LaboratoryGoldenColoradoUSA
| | | | | | | | - Jin‐Gui Chen
- BioEnergy Science Centre, Center for Bioenergy Innovation and Biosciences DivisionOak Ridge National LaboratoryOak RidgeTennesseeUSA
| | - Xiaohan Yang
- BioEnergy Science Centre, Center for Bioenergy Innovation and Biosciences DivisionOak Ridge National LaboratoryOak RidgeTennesseeUSA
| | - Gerald A Tuskan
- BioEnergy Science Centre, Center for Bioenergy Innovation and Biosciences DivisionOak Ridge National LaboratoryOak RidgeTennesseeUSA
| | - Udaya C. Kalluri
- BioEnergy Science Centre, Center for Bioenergy Innovation and Biosciences DivisionOak Ridge National LaboratoryOak RidgeTennesseeUSA
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Zhang L, Xie S, Yang C, Cao D, Fan S, Zhang X. Comparative Transcriptome Analysis Reveals Candidate Genes and Pathways for Potential Branch Growth in Elm ( Ulmus pumila) Cultivars. BIOLOGY 2022; 11:711. [PMID: 35625439 PMCID: PMC9139171 DOI: 10.3390/biology11050711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 04/29/2022] [Accepted: 05/02/2022] [Indexed: 11/16/2022]
Abstract
Wood plays a vital role in human life. It is important to study the thickening mechanism of tree branches and explore the mechanism of wood formation. Elm (Ulmus pumila) is a strong essential wood, and it is widely used in cabinets, sculptures, and ship making. In the present study, phenotypic and comparative transcriptomic analyses were performed in U. pumila fast- (UGu17 and UZuantian) and slow-growing cultivars (U81-07 and U82-39). Phenotypic observation showed that the thickness of secondary xylem of 2-year-old fast-growing branches was greater compared with slow-growing cultivars. A total of 9367 (up = 4363, down = 5004), 7159 (3413/3746), 7436 (3566/3870), and 5707 (2719/2988) differentially expressed genes (DEGs) were identified between fast- and slow-growing cultivars. Moreover, GO and KEGG enrichment analyses predicted that many pathways were involved in vascular development and transcriptional regulation in elm, such as "plant-type secondary cell wall biogenesis", "cell wall thickening", and "phenylpropanoid biosynthesis". NAC domain transcriptional factors (TFs) and their master regulators (VND1/MYB26), cellulose synthase catalytic subunits (CESAs) (such as IRX5/IRX3/IRX1), xylan synthesis, and secondary wall thickness (such as IRX9/IRX10/IRX8) were supposed to function in the thickening mechanism of elm branches. Our results indicated that the general phenylpropanoid pathway (such as PAL/C4H/4CL) and lignin metabolism (such as HCL/CSE/CCoAOMT/CCR/F5H) had vital functions in the growth of elm branches. Our transcriptome data were consistent with molecular results for branch thickening in elm cultivars.
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Affiliation(s)
| | | | | | | | - Shoujin Fan
- Key Lab of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan 250014, China; (L.Z.); (S.X.); (C.Y.); (D.C.)
| | - Xuejie Zhang
- Key Lab of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan 250014, China; (L.Z.); (S.X.); (C.Y.); (D.C.)
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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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Wang X, Chao N, Zhang A, Kang J, Jiang X, Gai Y. Systematic Analysis and Biochemical Characterization of the Caffeoyl Shikimate Esterase Gene Family in Poplar. Int J Mol Sci 2021; 22:ijms222413366. [PMID: 34948162 PMCID: PMC8704367 DOI: 10.3390/ijms222413366] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/09/2021] [Accepted: 12/10/2021] [Indexed: 02/07/2023] Open
Abstract
Caffeoyl shikimate esterase (CSE) hydrolyzes caffeoyl shikimate into caffeate and shikimate in the phenylpropanoid pathway. In this study, we performed a systematic analysis of the CSE gene family and investigated the possible roles of CSE and CSE-like genes in Populus. We conducted a genome-wide analysis of the CSE gene family, including functional and phylogenetic analyses of CSE and CSE-like genes, using the poplar (Populus trichocarpa) genome. Eighteen CSE and CSE-like genes were identified in the Populus genome, and five phylogenetic groups were identified from phylogenetic analysis. CSEs in Group Ia, which were proposed as bona fide CSEs, have probably been lost in most monocots except Oryza sativa. Primary functional classification showed that PoptrCSE1 and PoptrCSE2 had putative function in lignin biosynthesis. In addition, PoptrCSE2, along with PoptrCSE12, might also respond to stress with a function in cell wall biosynthesis. Enzymatic assay of PoptoCSE1 (Populus tomentosa), -2 and -12 showed that PoptoCSE1 and -2 maintained CSE activity. PoptoCSE1 and 2 had similar biochemical properties, tissue expression patterns and subcellular localization. Most of the PoptrCSE-like genes are homologs of AtMAGL (monoacylglycerol lipase) genes in Arabidopsis and may function as MAG lipase in poplar. Our study provides a systematic understanding of this novel gene family and suggests the function of CSE in monolignol biosynthesis in Populus.
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Affiliation(s)
- Xuechun Wang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (X.W.); (N.C.); (A.Z.); (J.K.); (X.J.)
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory, National Forestry and Grassland Administration, Beijing 100083, China
- National Engineering Laboratory for Tree Breeding, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing 100083, China
| | - Nan Chao
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (X.W.); (N.C.); (A.Z.); (J.K.); (X.J.)
- Jiangsu Key Laboratory of Sericutural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212018, China
| | - Aijing Zhang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (X.W.); (N.C.); (A.Z.); (J.K.); (X.J.)
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory, National Forestry and Grassland Administration, Beijing 100083, China
- National Engineering Laboratory for Tree Breeding, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing 100083, China
| | - Jiaqi Kang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (X.W.); (N.C.); (A.Z.); (J.K.); (X.J.)
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory, National Forestry and Grassland Administration, Beijing 100083, China
- National Engineering Laboratory for Tree Breeding, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing 100083, China
| | - Xiangning Jiang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (X.W.); (N.C.); (A.Z.); (J.K.); (X.J.)
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory, National Forestry and Grassland Administration, Beijing 100083, China
- National Engineering Laboratory for Tree Breeding, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing 100083, China
| | - Ying Gai
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (X.W.); (N.C.); (A.Z.); (J.K.); (X.J.)
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory, National Forestry and Grassland Administration, Beijing 100083, China
- National Engineering Laboratory for Tree Breeding, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing 100083, China
- Correspondence: ; Tel.: +86-10-6233-8063
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De Meester B, Vanholme R, de Vries L, Wouters M, Van Doorsselaere J, Boerjan W. Vessel- and ray-specific monolignol biosynthesis as an approach to engineer fiber-hypolignification and enhanced saccharification in poplar. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:752-765. [PMID: 34403547 DOI: 10.1111/tpj.15468] [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: 06/24/2021] [Revised: 08/06/2021] [Accepted: 08/12/2021] [Indexed: 06/13/2023]
Abstract
Lignin is one of the main factors determining recalcitrance to processing of lignocellulosic biomass towards bio-based materials and fuels. Consequently, wood of plants engineered for low lignin content is typically more amenable to processing. However, lignin-modified plants often exhibit collapsed vessels and associated growth defects. Vessel-specific reintroduction of lignin biosynthesis in dwarfed low-lignin cinnamoyl-CoA reductase1 (ccr1) Arabidopsis mutants using the ProSNBE:AtCCR1 construct overcame the yield penalty while maintaining high saccharification yields, and showed that monolignols can be transported between the different xylem cells acting as 'good neighbors' in Arabidopsis. Here, we translated this research into the bio-energy crop poplar. By expressing ProSNBE:AtCCR1 into CRISPR/Cas9-generated ccr2 poplars, we aimed for vessel-specific lignin biosynthesis to: (i) achieve growth restoration while maintaining high saccharification yields; and (ii) study the existence of 'good neighbors' in poplar wood. Analyzing the resulting ccr2 ProSNBE:AtCCR1 poplars showed that vessels and rays act as good neighbors for lignification in poplar. If sufficient monolignols are produced by these cells, monolignols migrate over multiple cell layers, resulting in a restoration of the lignin amount to wild-type levels. If the supply of monolignols is limited, the monolignols are incorporated into the cell walls of the vessels and rays producing them and their adjoining cells resulting in fiber hypolignification. One such fiber-hypolignified line had 18% less lignin and, despite its small yield penalty, had an increase of up to 71% in sugar release on a plant base upon saccharification.
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Affiliation(s)
- Barbara De Meester
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, 9052, Belgium
| | - Ruben Vanholme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, 9052, Belgium
| | - Lisanne de Vries
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, 9052, Belgium
| | - Marlies Wouters
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, 9052, Belgium
| | - Jan Van Doorsselaere
- Higher Institute for Nursing and Biotechnology, VIVES University College, Wilgenstraat 32, Roeselare, 8800, Belgium
| | - Wout Boerjan
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, 9052, Belgium
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Yu H, Liu C, Dixon RA. A gene-editing/complementation strategy for tissue-specific lignin reduction while preserving biomass yield. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:175. [PMID: 34479620 PMCID: PMC8417962 DOI: 10.1186/s13068-021-02026-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Accepted: 08/25/2021] [Indexed: 05/08/2023]
Abstract
BACKGROUND Lignification of secondary cell walls is a major factor conferring recalcitrance of lignocellulosic biomass to deconstruction for fuels and chemicals. Genetic modification can reduce lignin content and enhance saccharification efficiency, but usually at the cost of moderate-to-severe growth penalties. We have developed a method, using a single DNA construct that uses CRISPR-Cas9 gene editing to knock-out expression of an endogenous gene of lignin monomer biosynthesis while at the same time expressing a modified version of the gene's open reading frame that escapes cutting by the Cas9 system and complements the introduced mutation in a tissue-specific manner. RESULTS Expressing the complementing open reading frame in vessels allows for the regeneration of Arabidopsis plants with reduced lignin, wild-type biomass yield, and up to fourfold enhancement of cell wall sugar yield per plant. The above phenotypes are seen in both homozygous and bi-allelic heterozygous T1 lines, and are stable over at least four generations. CONCLUSIONS The method provides a rapid approach for generating reduced lignin trees or crops with one single transformation event, and, paired with a range of tissue-specific promoters, provides a general strategy for optimizing loss-of-function traits that are associated with growth penalties. This method should be applicable to any plant species in which transformation and gene editing are feasible and validated vessel-specific promoters are available.
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Affiliation(s)
- Hasi Yu
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, 1155 Union Circle #311428, Denton, TX, 76203, USA
- Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Chang Liu
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, 1155 Union Circle #311428, Denton, TX, 76203, USA
| | - Richard A Dixon
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, 1155 Union Circle #311428, Denton, TX, 76203, USA.
- Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
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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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11
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Forlani S, Mizzotti C, Masiero S. The NAC side of the fruit: tuning of fruit development and maturation. BMC PLANT BIOLOGY 2021; 21:238. [PMID: 34044765 PMCID: PMC8157701 DOI: 10.1186/s12870-021-03029-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 05/10/2021] [Indexed: 05/16/2023]
Abstract
Fruits and seeds resulting from fertilization of flowers, represent an incredible evolutionary advantage in angiosperms and have seen them become a critical element in our food supply.Many studies have been conducted to reveal how fruit matures while protecting growing seeds and ensuring their dispersal. As result, several transcription factors involved in fruit maturation and senescence have been isolated both in model and crop plants. These regulators modulate several cellular processes that occur during fruit ripening such as chlorophyll breakdown, tissue softening, carbohydrates and pigments accumulation.The NAC superfamily of transcription factors is known to be involved in almost all these aspects of fruit development and maturation. In this review, we summarise the current knowledge regarding NACs that modulate fruit ripening in model species (Arabidopsis thaliana and Solanum lycopersicum) and in crops of commercial interest (Oryza sativa, Malus domestica, Fragaria genus, Citrus sinensis and Musa acuminata).
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Affiliation(s)
- Sara Forlani
- Department of Biosciences, Università Degli Studi Di Milano, Via Celoria 26, 20133, Milan, Italy
| | - Chiara Mizzotti
- Department of Biosciences, Università Degli Studi Di Milano, Via Celoria 26, 20133, Milan, Italy
| | - Simona Masiero
- Department of Biosciences, Università Degli Studi Di Milano, Via Celoria 26, 20133, Milan, Italy.
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12
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Soni N, Altartouri B, Hegde N, Duggavathi R, Nazarian-Firouzabadi F, Kushalappa AC. TaNAC032 transcription factor regulates lignin-biosynthetic genes to combat Fusarium head blight in wheat. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 304:110820. [PMID: 33568310 DOI: 10.1016/j.plantsci.2021.110820] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 12/31/2020] [Accepted: 01/04/2021] [Indexed: 06/12/2023]
Abstract
Fusarium head blight (FHB) is a destructive disease affecting cereal crops globally due to mycotoxin contamination of grains that reduce yield and quality. Among hundreds of QTLs identified for resistance, the QTL-Fhb1 is of significant interest even today, for its major contribution to FHB resistance. Previously, QTL-Fhb1 dissection based on a combined metabolo-genomics approach, identified a few potential resistance genes, including a NAC like transcription factor for FHB resistance. Sequencing and phylogenetic analysis confirmed NAC to be the wheat TaNAC032. Also, the quantitative RT-PCR studies revealed a greater induced expression of TaNAC032 in resistant NIL in comparison to susceptible NIL upon Fusarium graminearum (Fg) infection. The virus-induced gene silencing (VIGS) based functional validation of TaNAC032 in resistant NIL confirmed increased disease severity and fungal biomass. Metabolic profiling revealed low abundances of resistance-related (RR) metabolites in TaNAC032 silenced NIL-R compared to non-silenced. Silenced plants showed decreased transcript abundances of RR metabolite biosynthetic genes associated with a reduction in total lignin content in rachis, confirming the regulatory role of TaNAC032 in wheat in response to Fg infection. If TaNA032 is mutated in an FHB susceptible cultivar, it can be edited to enhance FHB resistance.
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Affiliation(s)
- Nancy Soni
- Plant Science Department, McGill University, Quebec, Canada
| | - Bara Altartouri
- Department of Biological Sciences, Université de Montréal, Quebec, Canada
| | - Niranjan Hegde
- Plant Science Department, McGill University, Quebec, Canada
| | - Raj Duggavathi
- Animal Science Department, McGill University, Quebec, Canada
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13
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Sakeh NM, Abdullah SNA, Bahari MNA, Azzeme AM, Shaharuddin NA, Idris AS. EgJUB1 and EgERF113 transcription factors as potential master regulators of defense response in Elaeis guineensis against the hemibiotrophic Ganoderma boninense. BMC PLANT BIOLOGY 2021; 21:59. [PMID: 33482731 PMCID: PMC7825162 DOI: 10.1186/s12870-020-02812-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 12/22/2020] [Indexed: 06/12/2023]
Abstract
BACKGROUND Hemibiotrophic pathogen such as the fungal pathogen Ganoderma boninense that is destructive to oil palm, manipulates host defense mechanism by strategically switching from biotrophic to necrotrophic phase. Our previous study revealed two distinguishable expression profiles of oil palm genes that formed the basis in deducing biotrophic phase at early interaction which switched to necrotrophic phase at a later stage of infection. RESULTS The present report is a continuing study from our previous published transcriptomic profiling of oil palm seedlings against G. boninense. We focused on identifying differentially expressed genes (DEGs) encoding transcription factors (TFs) from the same RNA-seq data; resulting in 106 upregulated and 108 downregulated TFs being identified. The DEGs are involved in four established defense-related pathways responsible for cell wall modification, reactive oxygen species (ROS)-mediated signaling, programmed cell death (PCD) and plant innate immunity. We discovered upregulation of JUNGBRUNNEN 1 (EgJUB1) during the fungal biotrophic phase while Ethylene Responsive Factor 113 (EgERF113) demonstrated prominent upregulation when the palm switches to defense against necrotrophic phase. EgJUB1 was shown to have a binding activity to a 19 bp palindromic SNBE1 element, WNNYBTNNNNNNNAMGNHW found in the promoter region of co-expressing EgHSFC-2b. Further in silico analysis of promoter regions revealed co-expression of EgJUB1 with TFs containing SNBE1 element with single nucleotide change at either the 5th or 18th position. Meanwhile, EgERF113 binds to both GCC and DRE/CRT elements promoting plasticity in upregulating the downstream defense-related genes. Both TFs were proven to be nuclear-localized based on subcellular localization experiment using onion epidermal cells. CONCLUSION Our findings demonstrated unprecedented transcriptional reprogramming of specific TFs potentially to enable regulation of a specific set of genes during different infection phases of this hemibiotrophic fungal pathogen. The results propose the intricacy of oil palm defense response in orchestrating EgJUB1 during biotrophic and EgERF113 during the subsequent transition to the necrotrophic phase. Binding of EgJUB1 to SNBE motif instead of NACBS while EgERF113 to GCC-box and DRE/CRT motifs is unconventional and not normally associated with pathogen infection. Identification of these phase-specific oil palm TFs is important in designing strategies to tackle or attenuate the progress of infection.
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Affiliation(s)
- Nurshafika Mohd Sakeh
- Institute of Plantation Studies, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia
| | - Siti Nor Akmar Abdullah
- Institute of Plantation Studies, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia.
- Department of Agriculture Technology, Faculty of Agriculture, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia.
| | | | - Azzreena Mohamad Azzeme
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia
| | - Noor Azmi Shaharuddin
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia
| | - Abu Seman Idris
- Ganoderma and Diseases Research for Oil Palm Unit, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
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14
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Ren M, Zhang Y, Liu C, Liu Y, Tian S, Cheng H, Zhang H, Wei H, Wei Z. Characterization of a High Hierarchical Regulator, PtrGATA12, Functioning in Differentially Regulating Secondary Wall Component Biosynthesis in Populus trichocarpa. FRONTIERS IN PLANT SCIENCE 2021; 12:657787. [PMID: 33968111 PMCID: PMC8096934 DOI: 10.3389/fpls.2021.657787] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 04/01/2021] [Indexed: 05/16/2023]
Abstract
In plants, GATA transcription factors (TFs) have been reported to play vital roles in to a wide range of biological processes. To date, there is still no report about the involvement and functions of woody plant GATA TFs in wood formation. In this study, we described the functional characterization of a Populus trichocarpa GATA TF, PtrGATA12, which encodes a nuclear-localized transcriptional activator predominantly expressing in developing xylem tissues. Overexpression of PtrGATA12 not only inhibited growths of most phenotypic traits and biomass accumulation, but also altered the expressions of some master TFs and pathway genes involved in secondary cell wall (SCW) and programmed cell death, leading to alternated SCW components and breaking forces of stems of transgenic lines. The significant changes occurred in the contents of hemicellulose and lignin and SCW thicknesses of fiber and vessel that increased by 13.5 and 10.8%, and 20.83 and 11.83%, respectively. Furthermore, PtrGATA12 bound directly to the promoters of a battery of TFs and pathway genes and activated them; the binding sites include two cis-acting elements that were specifically enriched in their promoter regions. Taken together, our results suggest PtrGATA12, as a higher hierarchical TF on the top of PtrWND6A, PtrWND6B, PtrMYB152, and PtrMYB21, exert a coordinated regulation of SCW components biosynthesis pathways through directly and indirectly controlling master TFs, middle-level TFs, and further downstream pathway genes of the currently known hierarchical transcription network that governs SCW formation.
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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, China
| | - Yang Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Cong Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Yingying Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Shuanghui Tian
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - He Cheng
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Huaxin Zhang
- Research Center of Saline and Alkali Land of State Forestry and Grassland Administration, Chinese Academy of Forestry, Beijing, China
| | - Hairong Wei
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, United States
| | - Zhigang Wei
- Research Center of Saline and Alkali Land of State Forestry and Grassland Administration, Chinese Academy of Forestry, Beijing, China
- *Correspondence: Zhigang Wei,
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15
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Characterization of the UDP-glycosyltransferase UGT72 Family in Poplar and Identification of Genes Involved in the Glycosylation of Monolignols. Int J Mol Sci 2020; 21:ijms21145018. [PMID: 32708651 PMCID: PMC7404001 DOI: 10.3390/ijms21145018] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 07/11/2020] [Accepted: 07/13/2020] [Indexed: 12/28/2022] Open
Abstract
Monolignols are the building blocks for lignin polymerization in the apoplastic domain. Monolignol biosynthesis, transport, storage, glycosylation, and deglycosylation are the main biological processes partaking in their homeostasis. In Arabidopsis thaliana, members of the uridine diphosphate-dependent glucosyltransferases UGT72E and UGT72B subfamilies have been demonstrated to glycosylate monolignols. Here, the poplar UGT72 family, which is clustered into four groups, was characterized: Group 1 UGT72AZ1 and UGT72AZ2, homologs of Arabidopsis UGT72E1-3, as well as group 4 UGT72B37 and UGT72B39, homologs of Arabidopsis UGT72B1-3, glycosylate monolignols. In addition, promoter-GUS analyses indicated that poplar UGT72 members are expressed within vascular tissues. At the subcellular level, poplar UGT72s belonging to group 1 and group 4 were found to be associated with the nucleus and the endoplasmic reticulum. However, UGT72A2, belonging to group 2, was localized in bodies associated with chloroplasts, as well as possibly in chloroplasts. These results show a partial conservation of substrate recognition between Arabidopsis and poplar homologs, as well as divergent functions between different groups of the UGT72 family, for which the substrates remain unknown.
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16
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Ribeiro CL, Conde D, Balmant KM, Dervinis C, Johnson MG, McGrath AP, Szewczyk P, Unda F, Finegan CA, Schmidt HW, Miles B, Drost DR, Novaes E, Gonzalez-Benecke CA, Peter GF, Burleigh JG, Martin TA, Mansfield SD, Chang G, Wickett NJ, Kirst M. The uncharacterized gene EVE contributes to vessel element dimensions in Populus. Proc Natl Acad Sci U S A 2020; 117:5059-5066. [PMID: 32041869 PMCID: PMC7060721 DOI: 10.1073/pnas.1912434117] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The radiation of angiosperms led to the emergence of the vast majority of today's plant species and all our major food crops. Their extraordinary diversification occurred in conjunction with the evolution of a more efficient vascular system for the transport of water, composed of vessel elements. The physical dimensions of these water-conducting specialized cells have played a critical role in angiosperm evolution; they determine resistance to water flow, influence photosynthesis rate, and contribute to plant stature. However, the genetic factors that determine their dimensions are unclear. Here we show that a previously uncharacterized gene, ENLARGED VESSEL ELEMENT (EVE), contributes to the dimensions of vessel elements in Populus, impacting hydraulic conductivity. Our data suggest that EVE is localized in the plasma membrane and is involved in potassium uptake of differentiating xylem cells during vessel development. In plants, EVE first emerged in streptophyte algae, but expanded dramatically among vessel-containing angiosperms. The phylogeny, structure and composition of EVE indicates that it may have been involved in an ancient horizontal gene-transfer event.
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Affiliation(s)
- Cíntia L Ribeiro
- Plant Molecular and Cellular Biology Graduate Program, University of Florida, Gainesville, FL 32611
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL 32611
| | - Daniel Conde
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL 32611
| | - Kelly M Balmant
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL 32611
| | - Christopher Dervinis
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL 32611
| | | | - Aaron P McGrath
- Skaggs School of Pharmacy and Pharmaceutical Science, University of California San Diego, La Jolla, CA 92093
| | - Paul Szewczyk
- Skaggs School of Pharmacy and Pharmaceutical Science, University of California San Diego, La Jolla, CA 92093
| | - Faride Unda
- Department of Wood Science, Faculty of Forestry, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Christina A Finegan
- Plant Molecular and Cellular Biology Graduate Program, University of Florida, Gainesville, FL 32611
| | - Henry W Schmidt
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL 32611
| | - Brianna Miles
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL 32611
| | - Derek R Drost
- Plant Molecular and Cellular Biology Graduate Program, University of Florida, Gainesville, FL 32611
| | - Evandro Novaes
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL 32611
| | | | - Gary F Peter
- Plant Molecular and Cellular Biology Graduate Program, University of Florida, Gainesville, FL 32611
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL 32611
- Genetics Institute, University of Florida, Gainesville, FL 32611
| | - J Gordon Burleigh
- Plant Molecular and Cellular Biology Graduate Program, University of Florida, Gainesville, FL 32611
- Department of Biology, University of Florida, Gainesville, FL 32611
| | - Timothy A Martin
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL 32611
| | - Shawn D Mansfield
- Department of Wood Science, Faculty of Forestry, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Geoffrey Chang
- Skaggs School of Pharmacy and Pharmaceutical Science, University of California San Diego, La Jolla, CA 92093
- Department of Pharmacology, School of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Norman J Wickett
- Plant Science and Conservation, Chicago Botanic Garden, Glencoe, IL 60622
- Plant Biology and Conservation, Northwestern University, Evanston, IL 60208
| | - Matias Kirst
- Plant Molecular and Cellular Biology Graduate Program, University of Florida, Gainesville, FL 32611;
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL 32611
- Genetics Institute, University of Florida, Gainesville, FL 32611
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17
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Zhang Y, Showalter AM. CRISPR/Cas9 Genome Editing Technology: A Valuable Tool for Understanding Plant Cell Wall Biosynthesis and Function. FRONTIERS IN PLANT SCIENCE 2020; 11:589517. [PMID: 33329650 PMCID: PMC7714752 DOI: 10.3389/fpls.2020.589517] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 10/23/2020] [Indexed: 05/05/2023]
Abstract
For the past 5 years, clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) technology has appeared in the molecular biology research spotlight. As a game-changing player in genome editing, CRISPR/Cas9 technology has revolutionized animal research, including medical research and human gene therapy as well as plant science research, particularly for crop improvement. One of the most common applications of CRISPR/Cas9 is to generate genetic knock-out mutants. Recently, several multiplex genome editing approaches utilizing CRISPR/Cas9 were developed and applied in various aspects of plant research. Here we summarize these approaches as they relate to plants, particularly with respect to understanding the biosynthesis and function of the plant cell wall. The plant cell wall is a polysaccharide-rich cell structure that is vital to plant cell formation, growth, and development. Humans are heavily dependent on the byproducts of the plant cell wall such as shelter, food, clothes, and fuel. Genes involved in the assembly of the plant cell wall are often highly redundant. To identify these redundant genes, higher-order knock-out mutants need to be generated, which is conventionally done by genetic crossing. Compared with genetic crossing, CRISPR/Cas9 multi-gene targeting can greatly shorten the process of higher-order mutant generation and screening, which is especially useful to characterize cell wall related genes in plant species that require longer growth time. Moreover, CRISPR/Cas9 makes it possible to knock out genes when null T-DNA mutants are not available or are genetically linked. Because of these advantages, CRISPR/Cas9 is becoming an ideal and indispensable tool to perform functional studies in plant cell wall research. In this review, we provide perspectives on how to design CRISPR/Cas9 to achieve efficient gene editing and multi-gene targeting in plants. We also discuss the recent development of the virus-based CRISPR/Cas9 system and the application of CRISPR/Cas9 to knock in genes. Lastly, we summarized current progress on using CRISPR/Cas9 for the characterization of plant cell wall-related genes.
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Affiliation(s)
- Yuan Zhang
- Molecular and Cellular Biology Program, Ohio University, Athens, OH, United States
- Department of Environmental & Plant Biology, Ohio University, Athens, OH, United States
| | - Allan M. Showalter
- Molecular and Cellular Biology Program, Ohio University, Athens, OH, United States
- Department of Environmental & Plant Biology, Ohio University, Athens, OH, United States
- *Correspondence: Allan M. Showalter,
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18
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Tamura T, Endo H, Suzuki A, Sato Y, Kato K, Ohtani M, Yamaguchi M, Demura T. Affinity-based high-resolution analysis of DNA binding by VASCULAR-RELATED NAC-DOMAIN7 via fluorescence correlation spectroscopy. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:298-313. [PMID: 31313414 DOI: 10.1111/tpj.14443] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 05/30/2019] [Accepted: 06/11/2019] [Indexed: 06/10/2023]
Abstract
VASCULAR-RELATED NAC-DOMAIN7 (VND7) is the master transcription factor for vessel element differentiation in Arabidopsis thaliana. To identify the cis-acting sequence(s) bound by VND7, we employed fluorescence correlation spectroscopy (FCS) to find VND7-DNA interactions quantitatively. This identified an 18-bp sequence from the promoter of XYLEM CYSTEINE PEPTIDASE1 (XCP1), a direct target of VND7. A quantitative assay for binding affinity between VND7 and the 18-bp sequence revealed the core nucleotides contributing to specific binding between VND7 and the 18-bp sequence. Moreover, by combining the systematic evolution of ligands by exponential enrichment (SELEX) technique with known consensus sequences, we defined a motif termed the Ideal Core Structure for binding by VND7 (ICSV). We also used FCS to search for VND7 binding sequences in the promoter regions of other direct targets. Taking these data together, we proposed that VND7 preferentially binds to the ICSV sequence. Additionally, we found that substitutions among the core nucleotides affected transcriptional regulation by VND7 in vivo, indicating that the core nucleotides contribute to vessel-element-specific gene expression. Furthermore, our results demonstrate that FCS is a powerful tool for unveiling the DNA-binding properties of transcription factors.
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Affiliation(s)
- Taizo Tamura
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Hitoshi Endo
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, Aichi, 464-8602, Japan
| | - Atsunobu Suzuki
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Yutaka Sato
- Genetic Strains Research Center, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Ko Kato
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Misato Ohtani
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan
| | - Masatoshi Yamaguchi
- Graduate School of Science and Engineering, Saitama University, Saitama, Saitama, 338-8570, Japan
| | - Taku Demura
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
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19
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Carrasco-Orellana C, Stappung Y, Mendez-Yañez A, Allan AC, Espley RV, Plunkett BJ, Moya-Leon MA, Herrera R. Characterization of a ripening-related transcription factor FcNAC1 from Fragaria chiloensis fruit. Sci Rep 2018; 8:10524. [PMID: 30002382 PMCID: PMC6043618 DOI: 10.1038/s41598-018-28226-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 06/19/2018] [Indexed: 11/15/2022] Open
Abstract
Fragaria chiloensis is a strawberry endemic from Chile with attractive white-pink fruit, pleasant aroma and taste. However, this fruit has a limited post-harvest period due to fast softening. Several transcription factors (TFs) are involved in the regulation of fruit ripening, and members of the NAC family have been implicated in cell wall remodeling. FcNAC1 was isolated from F. chiloensis fruit, coding a protein of 332 amino acid residues and displaying a characteristic NAC domain at the N terminus. FcNAC1 protein showed nuclear localization. An increase in transcript level was observed during ripening. A sequence of 1488 bp of FcNAC1 promoter was obtained. In silico analysis identified cis elements able to respond to some hormones and Secondary wall NAC binding elements (SNBE), and responding to auxin and ABA. A structural model of FcNAC1 provided evidence for interaction with DNA sequences containing SNBE, while a dual luciferase assay confirmed the transcriptional activation by FcNAC1 of the promoter of FcPL, a gene involved in cell wall remodeling in F. chiloensis fruit. The results suggest the participation of FcNAC1 during ripening development of strawberry fruit, by regulating pectin metabolism during softening.
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Affiliation(s)
- C Carrasco-Orellana
- Instituto de Ciencias Biológicas, Universidad de Talca, 2 Norte 685, Talca, Chile
| | - Y Stappung
- Instituto de Ciencias Biológicas, Universidad de Talca, 2 Norte 685, Talca, Chile
| | - A Mendez-Yañez
- Instituto de Ciencias Biológicas, Universidad de Talca, 2 Norte 685, Talca, Chile
| | - A C Allan
- New Zealand Institute for Plant and Food Research Limited, Mt. Albert Research Centre, Auckland, 1025, New Zealand
- School of Biological Sciences, University of Auckland, Private Bag, 92019, Auckland, New Zealand
| | - R V Espley
- New Zealand Institute for Plant and Food Research Limited, Mt. Albert Research Centre, Auckland, 1025, New Zealand
| | - B J Plunkett
- New Zealand Institute for Plant and Food Research Limited, Mt. Albert Research Centre, Auckland, 1025, New Zealand
| | - M A Moya-Leon
- Instituto de Ciencias Biológicas, Universidad de Talca, 2 Norte 685, Talca, Chile
| | - R Herrera
- Instituto de Ciencias Biológicas, Universidad de Talca, 2 Norte 685, Talca, Chile.
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20
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Mathew IE, Agarwal P. May the Fittest Protein Evolve: Favoring the Plant-Specific Origin and Expansion of NAC Transcription Factors. Bioessays 2018; 40:e1800018. [PMID: 29938806 DOI: 10.1002/bies.201800018] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 05/26/2018] [Indexed: 12/12/2022]
Abstract
Plant-specific NAC transcription factors (TFs) evolve during the transition from aquatic to terrestrial plant life and are amplified to become one of the biggest TF families. This is because they regulate genes involved in water conductance and cell support. They also control flower and fruit formation. The review presented here focuses on various properties, regulatory intricacies, and developmental roles of NAC family members. Processes controlled by NACs depend majorly on their transcriptional properties. NACs can function as both activators and/or repressors. Additionally, their homo/hetero dimerization abilities can also affect DNA binding and activation properties. The active protein levels are dependent on the regulatory cascades. Because NACs regulate both development and stress responses in plants, in-depth knowledge about them has the potential to help guide future crop improvement studies.
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Affiliation(s)
- Iny Elizebeth Mathew
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Pinky Agarwal
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
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Ye Y, Wu K, Chen J, Liu Q, Wu Y, Liu B, Fu X. OsSND2, a NAC family transcription factor, is involved in secondary cell wall biosynthesis through regulating MYBs expression in rice. RICE (NEW YORK, N.Y.) 2018; 11:36. [PMID: 29855737 PMCID: PMC5981155 DOI: 10.1186/s12284-018-0228-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 05/23/2018] [Indexed: 05/03/2023]
Abstract
BACKGROUND As one of the most important staple food crops, rice produces huge agronomic biomass residues that contain lots of secondary cell walls (SCWs) comprising cellulose, hemicelluloses and lignin. The transcriptional regulation mechanism underlying SCWs biosynthesis remains elusive. RESULTS In this study, we isolated a NAC family transcription factor (TF), OsSND2 through yeast one-hybrid screening using the secondary wall NAC-binding element (SNBE) on the promoter region of OsMYB61 which is known transcription factor for regulation of SCWs biosynthesis as bait. We used an electrophoretic mobility shift assay (EMSA) and chromatin immunoprecipitation analysis (ChIP) to further confirm that OsSND2 can directly bind to the promoter of OsMYB61 both in vitro and in vivo. OsSND2, a close homolog of AtSND2, is localized in the nucleus and has transcriptional activation activity. Expression pattern analysis indicated that OsSND2 was mainly expressed in internodes and panicles. Overexpression of OsSND2 resulted in rolled leaf, increased cellulose content and up-regulated expression of SCWs related genes. The knockout of OsSND2 using CRISPR/Cas9 system decreased cellulose content and down-regulated the expression of SCWs related genes. Furthermore, OsSND2 can also directly bind to the promoters of other MYB family TFs by transactivation analysis in yeast cells and rice protoplasts. Altogether, our findings suggest that OsSND2 may function as a master regulator to mediate SCWs biosynthesis. CONCLUSION OsSND2 was identified as a positive regulator of cellulose biosynthesis in rice. An increase in the expression level of this gene can improve the SCWs cellulose content. Therefore, the study of the function of OsSND2 can provide a strategy for manipulating plant biomass production.
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Affiliation(s)
- Yafeng Ye
- Institute of Technical Biology and Agricultural Engineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, 230031, People's Republic of China
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, 230031, People's Republic of China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Kun Wu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jianfeng Chen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qian Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yuejin Wu
- Institute of Technical Biology and Agricultural Engineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, 230031, People's Republic of China
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, 230031, People's Republic of China
| | - Binmei Liu
- Institute of Technical Biology and Agricultural Engineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, 230031, People's Republic of China.
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, 230031, People's Republic of China.
| | - Xiangdong Fu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
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De Meester B, de Vries L, Özparpucu M, Gierlinger N, Corneillie S, Pallidis A, Goeminne G, Morreel K, De Bruyne M, De Rycke R, Vanholme R, Boerjan W. Vessel-Specific Reintroduction of CINNAMOYL-COA REDUCTASE1 (CCR1) in Dwarfed ccr1 Mutants Restores Vessel and Xylary Fiber Integrity and Increases Biomass. PLANT PHYSIOLOGY 2018; 176:611-633. [PMID: 29158331 PMCID: PMC5761799 DOI: 10.1104/pp.17.01462] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 11/14/2017] [Indexed: 05/19/2023]
Abstract
Lignocellulosic biomass is recalcitrant toward deconstruction into simple sugars due to the presence of lignin. To render lignocellulosic biomass a suitable feedstock for the bio-based economy, plants can be engineered to have decreased amounts of lignin. However, engineered plants with the lowest amounts of lignin exhibit collapsed vessels and yield penalties. Previous efforts were not able to fully overcome this phenotype without settling in sugar yield upon saccharification. Here, we reintroduced CINNAMOYL-COENZYME A REDUCTASE1 (CCR1) expression specifically in the protoxylem and metaxylem vessel cells of Arabidopsis (Arabidopsis thaliana) ccr1 mutants. The resulting ccr1 ProSNBE:CCR1 lines had overcome the vascular collapse and had a total stem biomass yield that was increased up to 59% as compared with the wild type. Raman analysis showed that monolignols synthesized in the vessels also contribute to the lignification of neighboring xylary fibers. The cell wall composition and metabolome of ccr1 ProSNBE:CCR1 still exhibited many similarities to those of ccr1 mutants, regardless of their yield increase. In contrast to a recent report, the yield penalty of ccr1 mutants was not caused by ferulic acid accumulation but was (largely) the consequence of collapsed vessels. Finally, ccr1 ProSNBE:CCR1 plants had a 4-fold increase in total sugar yield when compared with wild-type plants.
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Affiliation(s)
- Barbara De Meester
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium
| | - Lisanne de Vries
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium
| | - Merve Özparpucu
- Institute for Building Materials, Swiss Federal Institute of Technology Zürich, 8093 Zuerich, Switzerland
- Applied Wood Materials, Swiss Federal Laboratories of Materials Science and Technology, 8600 Duebendorf, Switzerland
| | - Notburga Gierlinger
- Institute for Biophysics, University of Natural Resources and Life Sciences Vienna, 1190 Vienna, Austria
| | - Sander Corneillie
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium
| | - Andreas Pallidis
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium
| | - Geert Goeminne
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium
- VIB Metabolomics Core, B-9052 Ghent, Belgium
| | - Kris Morreel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium
- VIB Metabolomics Core, B-9052 Ghent, Belgium
| | - Michiel De Bruyne
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium
| | - Riet De Rycke
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium
| | - Ruben Vanholme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- VIB Metabolomics Core, B-9052 Ghent, Belgium
| | - Wout Boerjan
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium
- VIB Metabolomics Core, B-9052 Ghent, Belgium
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23
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Liu Y, Wei M, Hou C, Lu T, Liu L, Wei H, Cheng Y, Wei Z. Functional Characterization of Populus PsnSHN2 in Coordinated Regulation of Secondary Wall Components in Tobacco. Sci Rep 2017; 7:42. [PMID: 28246387 PMCID: PMC5428377 DOI: 10.1038/s41598-017-00093-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 02/03/2017] [Indexed: 11/13/2022] Open
Abstract
Wood formation is a biological process during which the most abundant lignocellulosic biomass on earth is produced. Although a number of transcription factors have been linked to the regulation of wood formation process, none of them has been demonstrated to be a higher hierarchical regulator that coordinately regulates secondary wall biosynthesis genes. Here, we identified a Populus gene, PsnSHN2, a counterpart of the Arabidopsis AP2/ERF type transcription factor, SHINE2. PsnSHN2 is predominantly expressed in xylem tissues and acted evidently as a high hierarchical transcriptional activator. Overexpression of PsnSHN2 in tobacco significantly altered the expression of both transcription factors and biosynthesis genes involved in secondary wall formation, leading to the thickened secondary walls and the changed cell wall composition. The most significant changes occurred in the contents of cellulose and hemicellulose that increased 37% and 28%, respectively, whereas the content of lignin that decreased 34%. Furthermore, PsnSHN2 activated or repressed the promoter activities of transcription factors involved in secondary wall biosynthesis and bound to five cis-acting elements enriched in the promoter regions of these transcription factors. Taken together, our results suggest PsnSHN2 coordinately regulate secondary wall formation through selective up/down-regulation of its downstream transcription factors that control secondary wall formation.
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Affiliation(s)
- Yingying Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Heilongjiang Harbin, 150040, P.R. China
| | - Minjing Wei
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Heilongjiang Harbin, 150040, P.R. China
| | - Cong Hou
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Heilongjiang Harbin, 150040, P.R. China
| | - Tingting Lu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Heilongjiang Harbin, 150040, P.R. China
| | | | - Hairong Wei
- School of Forest Resource and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA
| | - Yuxiang Cheng
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Heilongjiang Harbin, 150040, P.R. China.
| | - Zhigang Wei
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Heilongjiang Harbin, 150040, P.R. China.
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Zhang J, Zhang S, Li H, Du H, Huang H, Li Y, Hu Y, Liu H, Liu Y, Yu G, Huang Y. Identification of Transcription Factors ZmMYB111 and ZmMYB148 Involved in Phenylpropanoid Metabolism. FRONTIERS IN PLANT SCIENCE 2016; 7:148. [PMID: 26913047 PMCID: PMC4753300 DOI: 10.3389/fpls.2016.00148] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 01/28/2016] [Indexed: 05/07/2023]
Abstract
Maize is the leading crop worldwide in terms of both planting area and total yields, but environmental stresses cause significant losses in productivity. Phenylpropanoid compounds play an important role in plant stress resistance; however, the mechanism of their synthesis is not fully understood, especially in regard to the expression and regulation of key genes. Phenylalanine ammonia-lyase (PAL) is the first key enzyme involved in phenylpropanoid metabolism, and it has a significant effect on the synthesis of important phenylpropanoid compounds. According to the results of sequence alignments and functional prediction, we selected two conserved R2R3-MYB transcription factors as candidate genes for the regulation of phenylpropanoid metabolism. The two candidate R2R3-MYB genes, which we named ZmMYB111 and ZmMYB148, were cloned, and then their structural characteristics and phylogenetic placement were predicted and analyzed. In addition, a series of evaluations were performed, including expression profiles, subcellular localization, transcription activation, protein-DNA interaction, and transient expression in maize endosperm. Our results indicated that both ZmMYB111 and ZmMYB148 are indeed R2R3-MYB transcription factors and that they may play a regulatory role in PAL gene expression.
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Affiliation(s)
- Junjie Zhang
- College of Life Science, Sichuan Agricultural UniversityChengdu, China
| | | | - Hui Li
- College of Agronomy, Sichuan Agricultural UniversityChengdu, China
| | - Hai Du
- College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
| | - Huanhuan Huang
- College of Agronomy, Sichuan Agricultural UniversityChengdu, China
| | - Yangping Li
- College of Agronomy, Sichuan Agricultural UniversityChengdu, China
| | - Yufeng Hu
- College of Agronomy, Sichuan Agricultural UniversityChengdu, China
| | - Hanmei Liu
- College of Life Science, Sichuan Agricultural UniversityChengdu, China
| | - Yinghong Liu
- Maize Research Institute, Sichuan Agricultural UniversityChengdu, China
| | - Guowu Yu
- College of Life Science, Sichuan Agricultural UniversityChengdu, China
| | - Yubi Huang
- College of Agronomy, Sichuan Agricultural UniversityChengdu, China
- *Correspondence: Yubi Huang,
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25
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Didi V, Jackson P, Hejátko J. Hormonal regulation of secondary cell wall formation. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:5015-27. [PMID: 26002972 DOI: 10.1093/jxb/erv222] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Secondary cell walls (SCWs) have critical functional importance but also constitute a high proportion of the plant biomass and have high application potential. This is true mainly for the lignocellulosic constituents of the SCWs in xylem vessels and fibres, which form a structured layer between the plasma membrane and the primary cell wall (PCW). Specific patterning of the SCW thickenings contributes to the mechanical properties of the different xylem cell types, providing the plant with mechanical support and facilitating the transport of solutes via vessels. In the last decade, our knowledge of the basic molecular mechanisms controlling SCW formation has increased substantially. Several members of the multi-layered regulatory cascade participating in the initiation and transcriptional regulation of SCW formation have been described, and the first cellular components determining the pattern of SCW at the subcellular resolution are being uncovered. The essential regulatory role of phytohormones in xylem development is well known and the molecular mechanisms that link hormonal signals to SCW formation are emerging. Here, we review recent knowledge about the role of individual plant hormones and hormonal crosstalk in the control over the regulatory cascades guiding SCW formation and patterning. Based on the analogy between many of the mechanisms operating during PCW and SCW formation, recently identified mechanisms underlying the hormonal control of PCW remodelling are discussed as potentially novel mechanisms mediating hormonal regulatory inputs in SCW formation.
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Affiliation(s)
- Vojtěch Didi
- Functional Genomics and Proteomics of Plants, Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Phil Jackson
- Functional Genomics and Proteomics of Plants, Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Jan Hejátko
- Functional Genomics and Proteomics of Plants, Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
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26
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Wang H, Tang R, Wang C, Qi Q, Gai Y, Jiang X, Zhang H. Functional repression of PtSND2 represses growth and development by disturbing auxin biosynthesis, transport and signaling in transgenic poplar. TREE PHYSIOLOGY 2015; 35:95-105. [PMID: 25516528 DOI: 10.1093/treephys/tpu100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Using chimeric repressor silencing technology, we previously reported that functional repression of PtSND2 severely arrested wood formation in transgenic poplar (Populus). Here, we provide further evidence that auxin biosynthesis, transport and signaling were disturbed in these transgenic plants, leading to pleiotropic defects in their growth patterns, including inhibited leaf enlargement and vascular tissue development in the leaf central vein, suppressed cambial growth and fiber elongation in the stem, and arrested growth in the root system. Two transgenic lines, which displayed the most remarkable phenotypic deviation from the wild-type, were selected for detailed studies. In both transgenic lines, expression of genes for auxin biosynthesis, transport and signaling was down-regulated, and indole-3-acetic acid distribution was severely disturbed in the apical buds, leaves, stems and roots of field-grown transgenic plants. Transient transcription dual-luciferase assays of ProPtTYDC2::LUC, ProPttLAX2::LUC and ProPoptrIAA20.2::LUC in poplar protoplasts revealed that expression of auxin-related genes might be regulated by PtSND2 at the transcriptional level. All these results indicate that functional repression of PtSND2 altered auxin biosynthesis, transport and signaling, and thereby disturbed the normal growth and development of transgenic plants.
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Affiliation(s)
- Haihai Wang
- National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
| | - Renjie Tang
- National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China Present address: Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Cuiting Wang
- National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
| | - Qi Qi
- College of Life Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, P. R. China
| | - Ying Gai
- College of Life Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, P. R. China
| | - Xiangning Jiang
- College of Life Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, P. R. China The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of Chinese Forestry Administration, National Engineering Laboratory for Tree Breeding, Beijing 100083, P. R. China
| | - Hongxia Zhang
- National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
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27
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Zhong R, Ye ZH. Complexity of the transcriptional network controlling secondary wall biosynthesis. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2014; 229:193-207. [PMID: 25443846 DOI: 10.1016/j.plantsci.2014.09.009] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 09/14/2014] [Accepted: 09/15/2014] [Indexed: 05/02/2023]
Abstract
Secondary walls in the form of wood and fibers are the most abundant biomass produced by vascular plants, and are important raw materials for many industrial uses. Understanding how secondary walls are constructed is of significance in basic plant biology and also has far-reaching implications in genetic engineering of plant biomass better suited for various end uses, such as biofuel production. Secondary walls are composed of three major biopolymers, i.e., cellulose, hemicelluloses and lignin, the biosynthesis of which requires the coordinated transcriptional regulation of all their biosynthesis genes. Genomic and molecular studies have identified a number of transcription factors, whose expression is associated with secondary wall biosynthesis. We comprehensively review how these secondary wall-associated transcription factors function together to turn on the secondary wall biosynthetic program, which leads to secondary wall deposition in vascular plants. The transcriptional network regulating secondary wall biosynthesis employs a multi-leveled feed-forward loop regulatory structure, in which the top-level secondary wall NAC (NAM, ATAF1/2 and CUC2) master switches activate the second-level MYB master switches and they together induce the expression of downstream transcription factors and secondary wall biosynthesis genes. Secondary wall NAC master switches and secondary wall MYB master switches bind to and activate the SNBE (secondary wall NAC binding element) and SMRE (secondary wall MYB-responsive element) sites, respectively, in their target gene promoters. Further investigation of what and how developmental signals trigger the transcriptional network to regulate secondary wall biosynthesis and how different secondary wall-associated transcription factors function cooperatively in activating secondary wall biosynthetic pathways will lead to a better understanding of the molecular mechanisms underlying the transcriptional control of secondary wall biosynthesis.
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Affiliation(s)
- Ruiqin Zhong
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Zheng-Hua Ye
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA.
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28
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Herrero J, Esteban Carrasco A, Zapata JM. Arabidopsis thaliana peroxidases involved in lignin biosynthesis: in silico promoter analysis and hormonal regulation. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2014; 80:192-202. [PMID: 24792389 DOI: 10.1016/j.plaphy.2014.03.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 03/26/2014] [Indexed: 05/08/2023]
Abstract
Phytohormones such as auxins, cytokinins, and brassinosteroids, act by means of a signaling cascade of transcription factors of the families NAC, MYB, AP2 (APETALA2), MADS and class III HD (homeodomain) Zip, regulating secondary growth. When the hormonal regulation of Zinnia elegans peroxidase (ZePrx), an enzyme involved in lignin biosynthesis, was studied, it was found that this peroxidase is sensitive to a plethora of hormones which control xylem lignification. In a previous study we sought Arabidopsis thaliana homologues to ZePrx. Peroxidases 4, 52, 49 and 72 are the four peroxidases that fulfill the restrictive conditions that a peroxidase involved in lignification must have. In the present study, we focus our attention on hormonal regulation in order to establish the minimal structural and regulatory elements contained in the promoter region which an AtPrx involved in lignification must have. The results indicate that of the four peroxidases selected in our previous study, the one most likely to be homologous to ZePrx is AtPrx52. The results suggest that hormones such as auxins, cytokinins and BRs directly regulate AtPrx52, and that the AtPrx52 promoter may be the target of the set of transcription factors (NAC, MYB, AP2 and class I and III HD Zip) which are up-regulated by these hormones during secondary growth. In addition, the AtPrx52 promoter contains multiple copies of all the putative cis-elements (the ACGT box, the OCS box, the OPAQ box, the L1BX, the MYCL box and the W box) known to confer regulation by NO and H2O2.
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Affiliation(s)
- Joaquín Herrero
- Department of Life Sciences, University of Alcalá, E-28871 Alcalá de Henares, Madrid, Spain.
| | | | - José Miguel Zapata
- Department of Life Sciences, University of Alcalá, E-28871 Alcalá de Henares, Madrid, Spain.
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29
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Valdivia ER, Herrera MT, Gianzo C, Fidalgo J, Revilla G, Zarra I, Sampedro J. Regulation of secondary wall synthesis and cell death by NAC transcription factors in the monocot Brachypodium distachyon. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:1333-43. [PMID: 23386682 PMCID: PMC3598421 DOI: 10.1093/jxb/ers394] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
In several dicotyledonous species, NAC transcription factors act as master switches capable of turning on programmes of secondary cell-wall synthesis and cell death. This work used an oestradiol-inducible system to overexpress the NAC transcription factor BdSWN5 in the monocot model Brachypodium distachyon. This resulted in ectopic secondary cell-wall formation in both roots and shoots. Some of the genes upregulated in the process were a secondary cell-wall cellulose synthase (BdCESA4), a xylem-specific protease (BdXCP1) and an orthologue of AtMYB46 (BdMYB1). While activation of BdMYB1 may not be direct, this study showed that BdSWN5 is capable of transactivating the BdXCP1 promoter through two conserved binding sites. In the course of Brachypodium development, the BdXCP1 promoter was observed to be active in all types of differentiating tracheary elements. Together, these results suggest that Brachypodium SWNs can act as switches that turn on secondary cell-wall synthesis and programmed cell death.
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Affiliation(s)
- Elene R. Valdivia
- Dpto. Fisiología Vegetal, Facultad de Biología, Universidad de Santiago, Santiago de Compostela, 15782, Spain
| | - María Teresa Herrera
- Dpto. Fisiología Vegetal, Facultad de Biología, Universidad de Santiago, Santiago de Compostela, 15782, Spain
| | - Cristina Gianzo
- Dpto. Fisiología Vegetal, Facultad de Biología, Universidad de Santiago, Santiago de Compostela, 15782, Spain
| | - Javier Fidalgo
- Dpto. Fisiología Vegetal, Facultad de Biología, Universidad de Santiago, Santiago de Compostela, 15782, Spain
| | - Gloria Revilla
- Dpto. Fisiología Vegetal, Facultad de Biología, Universidad de Santiago, Santiago de Compostela, 15782, Spain
| | - Ignacio Zarra
- Dpto. Fisiología Vegetal, Facultad de Biología, Universidad de Santiago, Santiago de Compostela, 15782, Spain
| | - Javier Sampedro
- Dpto. Fisiología Vegetal, Facultad de Biología, Universidad de Santiago, Santiago de Compostela, 15782, Spain
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