1
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Huang X, Wang W, Gong T, Wickell D, Kuo LY, Zhang X, Wen J, Kim H, Lu F, Zhao H, Chen S, Li H, Wu W, Yu C, Chen S, Fan W, Chen S, Bao X, Li L, Zhang D, Jiang L, Khadka D, Yan X, Liao Z, Zhou G, Guo Y, Ralph J, Sederoff RR, Wei H, Zhu P, Li FW, Ming R, Li Q. Author Correction: The flying spider-monkey tree fern genome provides insights into fern evolution and arborescence. Nat Plants 2024; 10:344. [PMID: 38307950 PMCID: PMC10881380 DOI: 10.1038/s41477-024-01631-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2024]
Affiliation(s)
- Xiong Huang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
| | - Wenling Wang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Ting Gong
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; NHC Key Laboratory of Biosynthesis of Natural Products; CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - David Wickell
- Thompson Institute, Ithaca, NY, USA
- Plant Biology Section, Cornell University, Ithaca, NY, USA
| | - Li-Yaung Kuo
- Institute of Molecular & Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Xingtan Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Jialong Wen
- Beijing Key Laboratory of Lignocellulosic Chemistry, Beijing Forestry University, Beijing, China
| | - Hoon Kim
- Department of Biochemistry and DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, WI, USA
| | - Fachuang Lu
- Department of Biochemistry and DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, WI, USA
| | - Hansheng Zhao
- State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing, China
| | - Song Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Hui Li
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
| | - Wenqi Wu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
| | - Changjiang Yu
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, China
| | - Su Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Wei Fan
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
| | - Shuai Chen
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xiuqi Bao
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; NHC Key Laboratory of Biosynthesis of Natural Products; CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Li Li
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; NHC Key Laboratory of Biosynthesis of Natural Products; CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Dan Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; NHC Key Laboratory of Biosynthesis of Natural Products; CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Longyu Jiang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; NHC Key Laboratory of Biosynthesis of Natural Products; CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Dipak Khadka
- GoldenGate International College, Tribhuvan University, Battisputali, Kathmandu, Nepal
| | - Xiaojing Yan
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
| | - Zhenyang Liao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Gongke Zhou
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, China
| | - Yalong Guo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Science, Beijing, China
| | - John Ralph
- Department of Biochemistry and DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, WI, USA
| | - Ronald R Sederoff
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, USA
| | - Hairong Wei
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, USA.
| | - Ping Zhu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; NHC Key Laboratory of Biosynthesis of Natural Products; CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
| | - Fay-Wei Li
- Thompson Institute, Ithaca, NY, USA.
- Plant Biology Section, Cornell University, Ithaca, NY, USA.
| | - Ray Ming
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Quanzi Li
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China.
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2
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Peng X, Tong B, Lee J, Wang K, Yu X, Huang X, Wen J, Makarem M, Pang H, Hinjan S, Yan X, Yao S, Lu F, Wang B, Peng F, Ralph J, Kim SH, Sederoff RR, Li Q. Overexpression of a gibberellin 20-oxidase gene in poplar xylem led to an increase in the size of nanocellulose fibrils and improved paper properties. Carbohydr Polym 2023; 314:120959. [PMID: 37173053 DOI: 10.1016/j.carbpol.2023.120959] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 04/19/2023] [Accepted: 04/23/2023] [Indexed: 05/15/2023]
Abstract
Cellulose, the major component of secondary cell walls, is the most abundant renewable long-chain polymer on earth. Nanocellulose has become a prominent nano-reinforcement agent for polymer matrices in various industries. We report the generation of transgenic hybrid poplar overexpressing the Arabidopsis gibberellin 20-oxidase1 gene driven by a xylem-specific promoter to increase gibberellin (GA) biosynthesis in wood. X-ray diffraction (XRD) and sum frequency generation spectroscopic (SFG) analyses showed that cellulose in transgenic trees was less crystalline, but the crystal size was larger. The nanocellulose fibrils prepared from transgenic wood had an increased size compared to those from wild type. When such fibrils were used as a reinforcing agent in sheet paper preparation, the mechanical strength of the paper was significantly enhanced. Engineering the GA pathway can therefore affect nanocellulose properties, providing a new strategy for expanding nanocellulose applications.
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Affiliation(s)
- Xiaopeng Peng
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China; Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Botong Tong
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China; State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Jongcheol Lee
- Department of Chemical Engineering and Materials Research Institute, The Pennsylvania State University, University Park, PA 16802, USA
| | - Kun Wang
- College of Materials Science and Technology, Beijing Forestry University, Beijing 100083, China
| | - Xiaojuan Yu
- College of Materials Science and Technology, Beijing Forestry University, Beijing 100083, China
| | - Xiong Huang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China
| | - Jialong Wen
- College of Materials Science and Technology, Beijing Forestry University, Beijing 100083, China
| | - Mohamadamin Makarem
- Department of Chemical Engineering and Materials Research Institute, The Pennsylvania State University, University Park, PA 16802, USA
| | - Hongying Pang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China
| | - Subin Hinjan
- Bangkok Cordyceps Co., Ltd, Thanyaburi, Pathumthani 12130, Thailand
| | - Xiaojing Yan
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China
| | - Shuangquan Yao
- Guangxi Key Laboratory of Clean Pulp & Papermaking and Pollution Control, College of Light Industry and Food Engineering, Guangxi University, Nanning 530004, China
| | - Fachuang Lu
- Department of Biochemistry and DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, WI 53726, USA
| | - Baichen Wang
- Key Laboratory of Photobiology, Photosynthesis Research Center, Institute of Botany, Chinese Academy of Science, Beijing 100093, China
| | - Feng Peng
- College of Materials Science and Technology, Beijing Forestry University, Beijing 100083, China
| | - John Ralph
- Department of Biochemistry and DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, WI 53726, USA
| | - Seong H Kim
- Department of Chemical Engineering and Materials Research Institute, The Pennsylvania State University, University Park, PA 16802, USA
| | - Ronald R Sederoff
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, USA
| | - Quanzi Li
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China.
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3
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Sulis D, Jiang X, Yang C, Matthews ML, Marques B, Miller Z, Lan K, Cofre-Vega C, Liu B, Sun R, Sederoff H, Bing R, Sun X, Williams CM, Jameel H, Phillips R, Chang HM, Peszlen I, Huang YY, Li W, Kelly RM, Sederoff RR, Chiang VL, Barrangou R, Wang JP. Multiplex CRISPR editing of wood for sustainable fiber production. Science 2023; 381:216-221. [PMID: 37440632 PMCID: PMC10542590 DOI: 10.1126/science.add4514] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 05/16/2023] [Indexed: 07/15/2023]
Abstract
The domestication of forest trees for a more sustainable fiber bioeconomy has long been hindered by the complexity and plasticity of lignin, a biopolymer in wood that is recalcitrant to chemical and enzymatic degradation. Here, we show that multiplex CRISPR editing enables precise woody feedstock design for combinatorial improvement of lignin composition and wood properties. By assessing every possible combination of 69,123 multigenic editing strategies for 21 lignin biosynthesis genes, we deduced seven different genome editing strategies targeting the concurrent alteration of up to six genes and produced 174 edited poplar variants. CRISPR editing increased the wood carbohydrate-to-lignin ratio up to 228% that of wild type, leading to more-efficient fiber pulping. The edited wood alleviates a major fiber-production bottleneck regardless of changes in tree growth rate and could bring unprecedented operational efficiencies, bioeconomic opportunities, and environmental benefits.
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Affiliation(s)
- Daniel Sulis
- TreeCo, Raleigh, NC 27695
- Forest Biotechnology Group, North Carolina State University, Raleigh, NC 27695
| | - Xiao Jiang
- Department of Forest Biomaterials, North Carolina State University, Raleigh, NC 27695
| | - Chenmin Yang
- TreeCo, Raleigh, NC 27695
- Forest Biotechnology Group, North Carolina State University, Raleigh, NC 27695
| | - Megan L. Matthews
- Department of Electrical and Computer Engineering, North Carolina State University, Raleigh, NC 27695
| | - Barbara Marques
- Forest Biotechnology Group, North Carolina State University, Raleigh, NC 27695
| | - Zachary Miller
- Department of Forest Biomaterials, North Carolina State University, Raleigh, NC 27695
| | - Kai Lan
- Department of Forest Biomaterials, North Carolina State University, Raleigh, NC 27695
| | - Carlos Cofre-Vega
- Forest Biotechnology Group, North Carolina State University, Raleigh, NC 27695
| | - Baoguang Liu
- TreeCo, Raleigh, NC 27695
- Forest Biotechnology Group, North Carolina State University, Raleigh, NC 27695
| | - Runkun Sun
- Department of Forest Biomaterials, North Carolina State University, Raleigh, NC 27695
| | - Henry Sederoff
- Forest Biotechnology Group, North Carolina State University, Raleigh, NC 27695
| | - Ryan Bing
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695
| | - Xiaoyan Sun
- Molecular Education, Technology and Research Innovation Center (METRIC), North Carolina State University, Raleigh, NC 27695
| | - Cranos M. Williams
- Department of Electrical and Computer Engineering, North Carolina State University, Raleigh, NC 27695
| | - Hasan Jameel
- Department of Forest Biomaterials, North Carolina State University, Raleigh, NC 27695
| | - Richard Phillips
- Department of Forest Biomaterials, North Carolina State University, Raleigh, NC 27695
| | - Hou-min Chang
- Department of Forest Biomaterials, North Carolina State University, Raleigh, NC 27695
| | - Ilona Peszlen
- Department of Forest Biomaterials, North Carolina State University, Raleigh, NC 27695
| | - Yung-Yun Huang
- Department of Operations Research, North Carolina State University, Raleigh, NC 27695
| | - Wei Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China 10040
| | - Robert M. Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695
| | - Ronald R. Sederoff
- TreeCo, Raleigh, NC 27695
- Forest Biotechnology Group, North Carolina State University, Raleigh, NC 27695
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China 10040
| | - Vincent L. Chiang
- TreeCo, Raleigh, NC 27695
- Forest Biotechnology Group, North Carolina State University, Raleigh, NC 27695
- Department of Forest Biomaterials, North Carolina State University, Raleigh, NC 27695
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China 10040
| | - Rodolphe Barrangou
- TreeCo, Raleigh, NC 27695
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC 27695
| | - Jack P. Wang
- TreeCo, Raleigh, NC 27695
- Forest Biotechnology Group, North Carolina State University, Raleigh, NC 27695
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China 10040
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4
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Chen S, Yu Y, Wang X, Wang S, Zhang T, Zhou Y, He R, Meng N, Wang Y, Liu W, Liu Z, Liu J, Guo Q, Huang H, Sederoff RR, Wang G, Qu G, Chen S. Chromosome-level genome assembly of a triploid poplar Populus alba 'Berolinensis'. Mol Ecol Resour 2023. [PMID: 36789493 DOI: 10.1111/1755-0998.13770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/16/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023]
Abstract
Many recent studies have provided significant insights into polyploid breeding, but limited research has been carried out on trees. The genomic information needed to understand growth and response to abiotic stress in polyploidy trees is largely unknown, but has become critical due to the threats to forests imposed by climate change. Populus alba 'Berolinensis,' also known "Yinzhong poplar," is a triploid poplar from northeast China. This hybrid triploid poplar is widely used as a landscape ornamental and in urban forestry owing to its adaptation to adverse environments and faster growth than its parental diploid. It is an artificially synthesized male allotriploid hybrid, with three haploid genomes of P. alba 'Berolinensis' originating from different poplar species, so it is attractive for studying polyploidy genomic mechanisms in heterosis. In this study, we focused on the allelic genomic interactions in P. alba 'Berolinensis,' and generated a high-quality chromosome-level genome assembly consisting of 19 allelic chromosomes. Its three haploid chromosome sets are polymorphic with an average of 25.73 nucleotide polymorphism sites per kilobase. We found that some stress-related genes such as RD22 and LEA7 exhibited sequence differences between different haploid genomes. The genome assembly has been deposited in our polyploid genome online analysis website TreeGenomes (https://www.treegenomes.com). These polyploid genome-related resources will provide a critical foundation for the molecular breeding of P. alba 'Berolinensis' and help us uncover the allopolyploidization effects of heterosis and abiotic stress resistance and traits of polyploidy species in the future.
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Affiliation(s)
- Song Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Yue Yu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Xinyu Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Sui Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China.,Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Tianjiao Zhang
- College of Information and Computer Engineering, Northeast Forestry University, Harbin, China
| | - Yan Zhou
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Ruihan He
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Nan Meng
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Yiran Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Wenxuan Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Zhijie Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Jinwen Liu
- Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, Wenzhou University, Wenzhou, China
| | - Qiwen Guo
- Department of Forest and Soil Sciences, Institute of Forest Ecology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Haijiao Huang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Ronald R Sederoff
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China.,Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina, USA
| | - Guohua Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China.,College of Information and Computer Engineering, Northeast Forestry University, Harbin, China
| | - Guanzheng Qu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Su Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
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5
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Wang H, Lu Y, Zhang T, Liu Z, Cao L, Chang Q, Liu Y, Lu X, Yu S, Li H, Jiang J, Liu G, Sederoff HW, Sederoff RR, Zhang Q, Zheng Z. The double flower variant of yellowhorn is due to a LINE1 transposon-mediated insertion. Plant Physiol 2023; 191:1122-1137. [PMID: 36494195 PMCID: PMC9922402 DOI: 10.1093/plphys/kiac571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 11/16/2022] [Indexed: 06/17/2023]
Abstract
As essential organs of reproduction in angiosperms, flowers, and the genetic mechanisms of their development have been well characterized in many plant species but not in the woody tree yellowhorn (Xanthoceras sorbifolium). Here, we focused on the double flower phenotype in yellowhorn, which has high ornamental value. We found a candidate C-class gene, AGAMOUS1 (XsAG1), through bovine serum albumin sequencing and genetics analysis with a Long Interpersed Nuclear Elements 1 (LINE1) transposable element fragment (Xsag1-LINE1-1) inserted into its second intron that caused a loss-of-C-function and therefore the double flower phenotype. In situ hybridization of XsAG1 and analysis of the expression levels of other ABC genes were used to identify differences between single- and double-flower development processes. These findings enrich our understanding of double flower formation in yellowhorn and provide evidence that transposon insertions into genes can reshape plant traits in forest trees.
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6
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Tang X, Wang C, Chai G, Wang D, Xu H, Liu Y, He G, Liu S, Zhang Y, Kong Y, Li S, Lu M, Sederoff RR, Li Q, Zhou G. Ubiquitinated DA1 negatively regulates vascular cambium activity through modulating the stability of WOX4 in Populus. Plant Cell 2022; 34:3364-3382. [PMID: 35703939 PMCID: PMC9421475 DOI: 10.1093/plcell/koac178] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 05/05/2022] [Indexed: 05/15/2023]
Abstract
Activity of the vascular cambium gives rise to secondary xylem for wood formation in trees. The transcription factor WUSCHEL-related HOMEOBOX4 (WOX4) is a central regulator downstream of the hormone and peptide signaling pathways that maintain cambial activity. However, the genetic regulatory network underlying WOX4-mediated wood formation at the post-transcriptional level remains to be elucidated. In this study, we identified the ubiquitin receptor PagDA1 in hybrid poplar (Populus alba × Populus glandulosa clone 84K) as a negative regulator of wood formation, which restricts cambial activity during secondary growth. Overexpression of PagDA1 in poplar resulted in a relatively reduced xylem due to decreased cambial cell division. By contrast, mutation of PagDA1 by CRISPR/Cas9 resulted in an increased cambial cell activity and promoted xylem formation. Genetic analysis demonstrated that PagDA1 functions antagonistically in a common pathway as PagWOX4 to regulate cambial activity. We propose that PagDA1 physically associates with PagWOX4 and modulates the degradation of PagWOX4 by the 26S proteasome. Moreover, genetic analysis revealed that PagDA1 exerts its negative effect on cambial development by modulating the stability of PagWOX4 in a ubiquitin-dependent manner mediated by the E3 ubiquitin ligase PagDA2. In sum, we have identified a cambial regulatory protein complex, PagDA1-PagWOX4, as a potential target for wood biomass improvement.
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Affiliation(s)
- Xianfeng Tang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Shandong Institute of Energy Technology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Congpeng Wang
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, Shandong 266109, China
| | - Guohua Chai
- College of Resources and Environment, Qingdao Agricultural University, Qingdao 266109, China
| | - Dian Wang
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, Shandong 266109, China
| | - Hua Xu
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Shandong Institute of Energy Technology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Yu Liu
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, Shandong 266109, China
| | - Guo He
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Shandong Institute of Energy Technology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Shuqing Liu
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Shandong Institute of Energy Technology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Yiran Zhang
- College of Resources and Environment, Qingdao Agricultural University, Qingdao 266109, China
| | - Yingzhen Kong
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, Shandong 266109, China
| | - Shengjun Li
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Shandong Institute of Energy Technology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Mengzhu Lu
- College of Forestry and Biotechnology, Zhejiang Agriculture & Forestry University, Hangzhou 311300, China
| | - Ronald R Sederoff
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North California 27695, USA
| | - Quanzi Li
- Author for correspondence: (Q.L.), (G.Z.)
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7
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Zhao Y, Yuan Z, Wang S, Wang H, Chao Y, Sederoff RR, Sederoff H, Yan H, Pan J, Peng M, Wu D, Borriss R, Niu B. Gene sdaB Is Involved in the Nematocidal Activity of Enterobacter ludwigii AA4 Against the Pine Wood Nematode Bursaphelenchus xylophilus. Front Microbiol 2022; 13:870519. [PMID: 35602027 PMCID: PMC9121001 DOI: 10.3389/fmicb.2022.870519] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 03/25/2022] [Indexed: 11/13/2022] Open
Abstract
Bursaphelenchus xylophilus, a plant parasitic nematode, is the causal agent of pine wilt, a devastating forest tree disease. Essentially, no efficient methods for controlling B. xylophilus and pine wilt disease have yet been developed. Enterobacter ludwigii AA4, isolated from the root of maize, has powerful nematocidal activity against B. xylophilus in a new in vitro dye exclusion test. The corrected mortality of the B. xylophilus treated by E. ludwigii AA4 or its cell extract reached 98.3 and 98.6%, respectively. Morphological changes in B. xylophilus treated with a cell extract from strain AA4 suggested that the death of B. xylophilus might be caused by an increased number of vacuoles in non-apoptotic cell death and the damage to tissues of the nematodes. In a greenhouse test, the disease index of the seedlings of Scots pine (Pinus sylvestris) treated with the cells of strain AA4 plus B. xylophilus or those treated by AA4 cell extract plus B. xylophilus was 38.2 and 30.3, respectively, was significantly lower than 92.5 in the control plants treated with distilled water and B. xylophilus. We created a sdaB gene knockout in strain AA4 by deleting the gene that was putatively encoding the beta-subunit of L-serine dehydratase through Red homologous recombination. The nematocidal and disease-suppressing activities of the knockout strain were remarkably impaired. Finally, we revealed a robust colonization of P. sylvestris seedling needles by E. ludwigii AA4, which is supposed to contribute to the disease-controlling efficacy of strain AA4. Therefore, E. ludwigii AA4 has significant potential to serve as an agent for the biological control of pine wilt disease caused by B. xylophilus.
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Affiliation(s)
- Yu Zhao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Zhibo Yuan
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Shuang Wang
- Administrative Office of the Summer Palace, Beijing Municipal Administration Center of Parks, Beijing, China
| | - Haoyu Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Yanjie Chao
- The Center for Microbes, Development and Health (CMDH), Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Ronald R. Sederoff
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
| | - Heike Sederoff
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - He Yan
- Center for Biological Disaster Prevention and Control, National Forestry and Grassland Administration, Shenyang, China
| | - Jialiang Pan
- Center for Biological Disaster Prevention and Control, National Forestry and Grassland Administration, Shenyang, China
| | - Mu Peng
- College of Biological Science and Technology, Hubei Minzu University, Enshi, China
| | - Di Wu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Rainer Borriss
- Nord Reet UG, Greifswald, Germany
- Institute of Marine Biotechnology e.V. (IMaB), Greifswald, Germany
- *Correspondence: Rainer Borriss,
| | - Ben Niu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
- Ben Niu,
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8
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Huang X, Wang W, Gong T, Wickell D, Kuo LY, Zhang X, Wen J, Kim H, Lu F, Zhao H, Chen S, Li H, Wu W, Yu C, Chen S, Fan W, Chen S, Bao X, Li L, Zhang D, Jiang L, Khadka D, Yan X, Liao Z, Zhou G, Guo Y, Ralph J, Sederoff RR, Wei H, Zhu P, Li FW, Ming R, Li Q. The flying spider-monkey tree fern genome provides insights into fern evolution and arborescence. Nat Plants 2022; 8:500-512. [PMID: 35534720 PMCID: PMC9122828 DOI: 10.1038/s41477-022-01146-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 03/30/2022] [Indexed: 05/03/2023]
Abstract
To date, little is known about the evolution of fern genomes, with only two small genomes published from the heterosporous Salviniales. Here we assembled the genome of Alsophila spinulosa, known as the flying spider-monkey tree fern, onto 69 pseudochromosomes. The remarkable preservation of synteny, despite resulting from an ancient whole-genome duplication over 100 million years ago, is unprecedented in plants and probably speaks to the uniqueness of tree ferns. Our detailed investigations into stem anatomy and lignin biosynthesis shed new light on the evolution of stem formation in tree ferns. We identified a phenolic compound, alsophilin, that is abundant in xylem, and we provided the molecular basis for its biosynthesis. Finally, analysis of demographic history revealed two genetic bottlenecks, resulting in rapid demographic declines of A. spinulosa. The A. spinulosa genome fills a crucial gap in the plant genomic landscape and helps elucidate many unique aspects of tree fern biology.
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Affiliation(s)
- Xiong Huang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
| | - Wenling Wang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Ting Gong
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; NHC Key Laboratory of Biosynthesis of Natural Products; CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - David Wickell
- Thompson Institute, Ithaca, NY, USA
- Plant Biology Section, Cornell University, Ithaca, NY, USA
| | - Li-Yaung Kuo
- Institute of Molecular & Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Xingtan Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Jialong Wen
- Beijing Key Laboratory of Lignocellulosic Chemistry, Beijing Forestry University, Beijing, China
| | - Hoon Kim
- Department of Biochemistry and DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, WI, USA
| | - Fachuang Lu
- Department of Biochemistry and DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, WI, USA
| | - Hansheng Zhao
- State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing, China
| | - Song Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Hui Li
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
| | - Wenqi Wu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
| | - Changjiang Yu
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, China
| | - Su Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Wei Fan
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
| | - Shuai Chen
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xiuqi Bao
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; NHC Key Laboratory of Biosynthesis of Natural Products; CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Li Li
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; NHC Key Laboratory of Biosynthesis of Natural Products; CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Dan Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; NHC Key Laboratory of Biosynthesis of Natural Products; CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Longyu Jiang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; NHC Key Laboratory of Biosynthesis of Natural Products; CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Dipak Khadka
- GoldenGate International College, Tribhuvan University, Battisputali, Kathmandu, Nepal
| | - Xiaojing Yan
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
| | - Zhenyang Liao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Gongke Zhou
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, China
| | - Yalong Guo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Science, Beijing, China
| | - John Ralph
- Department of Biochemistry and DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, WI, USA
| | - Ronald R Sederoff
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, USA
| | - Hairong Wei
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, USA.
| | - Ping Zhu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; NHC Key Laboratory of Biosynthesis of Natural Products; CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
| | - Fay-Wei Li
- Thompson Institute, Ithaca, NY, USA.
- Plant Biology Section, Cornell University, Ithaca, NY, USA.
| | - Ray Ming
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Quanzi Li
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China.
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9
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Li H, Dai X, Huang X, Xu M, Wang Q, Yan X, Sederoff RR, Li Q. Single-cell RNA sequencing reveals a high-resolution cell atlas of xylem in Populus. J Integr Plant Biol 2021; 63:1906-1921. [PMID: 34347368 DOI: 10.1111/jipb.13159] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 08/02/2021] [Indexed: 05/24/2023]
Abstract
High-throughput single-cell RNA sequencing (scRNA-seq) has advantages over traditional RNA-seq to explore spatiotemporal information on gene dynamic expressions in heterogenous tissues. We performed Drop-seq, a method for the dropwise sequestration of single cells for sequencing, on protoplasts from the differentiating xylem of Populus alba × Populus glandulosa. The scRNA-seq profiled 9,798 cells, which were grouped into 12 clusters. Through characterization of differentially expressed genes in each cluster and RNA in situ hybridizations, we identified vessel cells, fiber cells, ray parenchyma cells and xylem precursor cells. Diffusion pseudotime analyses revealed the differentiating trajectory of vessels, fiber cells and ray parenchyma cells and indicated a different differentiation process between vessels and fiber cells, and a similar differentiation process between fiber cells and ray parenchyma cells. We identified marker genes for each cell type (cluster) and key candidate regulators during developmental stages of xylem cell differentiation. Our study generates a high-resolution expression atlas of wood formation at the single cell level and provides valuable information on wood formation.
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Affiliation(s)
- Hui Li
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
| | - Xinren Dai
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
| | - Xiong Huang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Mengxuan Xu
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
| | - Qiao Wang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Xiaojing Yan
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
| | - Ronald R Sederoff
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, 27695, USA
| | - Quanzi Li
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
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10
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Lin CY, Sun Y, Song J, Chen HC, Shi R, Yang C, Liu J, Tunlaya-Anukit S, Liu B, Loziuk PL, Williams CM, Muddiman DC, Lin YCJ, Sederoff RR, Wang JP, Chiang VL. Enzyme Complexes of Ptr4CL and PtrHCT Modulate Co-enzyme A Ligation of Hydroxycinnamic Acids for Monolignol Biosynthesis in Populus trichocarpa. Front Plant Sci 2021; 12:727932. [PMID: 34691108 PMCID: PMC8527181 DOI: 10.3389/fpls.2021.727932] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 09/13/2021] [Indexed: 06/13/2023]
Abstract
Co-enzyme A (CoA) ligation of hydroxycinnamic acids by 4-coumaric acid:CoA ligase (4CL) is a critical step in the biosynthesis of monolignols. Perturbation of 4CL activity significantly impacts the lignin content of diverse plant species. In Populus trichocarpa, two well-studied xylem-specific Ptr4CLs (Ptr4CL3 and Ptr4CL5) catalyze the CoA ligation of 4-coumaric acid to 4-coumaroyl-CoA and caffeic acid to caffeoyl-CoA. Subsequently, two 4-hydroxycinnamoyl-CoA:shikimic acid hydroxycinnamoyl transferases (PtrHCT1 and PtrHCT6) mediate the conversion of 4-coumaroyl-CoA to caffeoyl-CoA. Here, we show that the CoA ligation of 4-coumaric and caffeic acids is modulated by Ptr4CL/PtrHCT protein complexes. Downregulation of PtrHCTs reduced Ptr4CL activities in the stem-differentiating xylem (SDX) of transgenic P. trichocarpa. The Ptr4CL/PtrHCT interactions were then validated in vivo using biomolecular fluorescence complementation (BiFC) and protein pull-down assays in P. trichocarpa SDX extracts. Enzyme activity assays using recombinant proteins of Ptr4CL and PtrHCT showed elevated CoA ligation activity for Ptr4CL when supplemented with PtrHCT. Numerical analyses based on an evolutionary computation of the CoA ligation activity estimated the stoichiometry of the protein complex to consist of one Ptr4CL and two PtrHCTs, which was experimentally confirmed by chemical cross-linking using SDX plant protein extracts and recombinant proteins. Based on these results, we propose that Ptr4CL/PtrHCT complexes modulate the metabolic flux of CoA ligation for monolignol biosynthesis during wood formation in P. trichocarpa.
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Affiliation(s)
- Chien-Yuan Lin
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Yi Sun
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Jina Song
- Department of Electrical and Computer Engineering, North Carolina State University, Raleigh, NC, United States
| | - Hsi-Chuan Chen
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
| | - Rui Shi
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
| | - Chenmin Yang
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
| | - Jie Liu
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
| | - Sermsawat Tunlaya-Anukit
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
| | - Baoguang Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- Department of Forestry, Beihua University, Jilin, China
| | - Philip L. Loziuk
- W.M. Keck FTMS Laboratory, Department of Chemistry, North Carolina State University, Raleigh, NC, United States
| | - Cranos M. Williams
- Department of Electrical and Computer Engineering, North Carolina State University, Raleigh, NC, United States
| | - David C. Muddiman
- W.M. Keck FTMS Laboratory, Department of Chemistry, North Carolina State University, Raleigh, NC, United States
| | - Ying-Chung Jimmy Lin
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Ronald R. Sederoff
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
| | - Jack P. Wang
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Vincent L. Chiang
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
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11
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Wang Q, Dai X, Pang H, Cheng Y, Huang X, Li H, Yan X, Lu F, Wei H, Sederoff RR, Li Q. Corrigendum: BEL1-like Homeodomain Protein BLH6a Is a Negative Regulator of CAld5H2 in Sinapyl Alcohol Monolignol Biosynthesis in Poplar. Front Plant Sci 2021; 12:761291. [PMID: 34567055 PMCID: PMC8459769 DOI: 10.3389/fpls.2021.761291] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 08/20/2021] [Indexed: 06/13/2023]
Abstract
[This corrects the article DOI: 10.3389/fpls.2021.695223.].
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Affiliation(s)
- Qiao Wang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Xinren Dai
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
| | - Hongying Pang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
| | - Yanxia Cheng
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
| | - Xiong Huang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Hui Li
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
| | - Xiaojing Yan
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
| | - Fachuang Lu
- Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, Madison, WI, United States
| | - Hairong Wei
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, United States
| | - Ronald R. Sederoff
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
| | - Quanzi Li
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
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12
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Wang Q, Dai X, Pang H, Cheng Y, Huang X, Li H, Yan X, Lu F, Wei H, Sederoff RR, Li Q. BEL1-like Homeodomain Protein BLH6a Is a Negative Regulator of CAl5H2 in Sinapyl Alcohol Monolignol Biosynthesis in Poplar. Front Plant Sci 2021; 12:695223. [PMID: 34249068 PMCID: PMC8269948 DOI: 10.3389/fpls.2021.695223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 06/02/2021] [Indexed: 06/13/2023]
Abstract
Lignin is one of the major components of xylem cell walls in tree stems. The lignin in the wood of most flowering plants (dicotyledonous angiosperms) is typically polymerized from three monolignol precursors, coniferyl alcohol, sinapyl alcohol, and p-coumaroyl alcohol, resulting in guaiacyl (G), syringyl (S), and hydroxyphenyl (H) subunits, respectively. In this study, we focus on the transcriptional regulation of a coniferaldehyde 5-hydroxylase (CAld5H2) gene, which encodes a key enzyme for sinapyl alcohol biosynthesis. We carried out a yeast one-hybrid (Y1H) screen to identify candidate upstream transcription factors (TFs) regulating CAld5H2. We obtained 12 upstream TFs as potential regulators of CAld5H2. One of these TF genes, BLH6a, encodes a BEL1-like homeodomain (BLH) protein and negatively regulated the CAld5H2 promoter activity. The direct regulation of CAld5H2 promoter by BLH6a was supported by chromatin immunoprecipitation-quantitative polymerase chain reaction (ChIP-qPCR) and dominant repression of BLH6a in transgenic plants. Luciferase complementation imaging analyses showed extensive protein-protein interactions among these 12 TFs. We propose that BLH6a is a negative regulator of CAld5H2, which acts through combinatorial regulation of multiple TFs for sinapyl alcohol (S monolignol) biosynthesis in poplar.
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Affiliation(s)
- Qiao Wang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Xinren Dai
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
| | - Hongying Pang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
| | - Yanxia Cheng
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
| | - Xiong Huang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Hui Li
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
| | - Xiaojing Yan
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
| | - Fachuang Lu
- Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, Madison, WI, United States
| | - Hairong Wei
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, United States
| | - Ronald R. Sederoff
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
| | - Quanzi Li
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
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13
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Niu B, Wang W, Yuan Z, Sederoff RR, Sederoff H, Chiang VL, Borriss R. Microbial Interactions Within Multiple-Strain Biological Control Agents Impact Soil-Borne Plant Disease. Front Microbiol 2020; 11:585404. [PMID: 33162962 PMCID: PMC7581727 DOI: 10.3389/fmicb.2020.585404] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 09/14/2020] [Indexed: 12/16/2022] Open
Abstract
Major losses of crop yield and quality caused by soil-borne plant diseases have long threatened the ecology and economy of agriculture and forestry. Biological control using beneficial microorganisms has become more popular for management of soil-borne pathogens as an environmentally friendly method for protecting plants. Two major barriers limiting the disease-suppressive functions of biocontrol microbes are inadequate colonization of hosts and inefficient inhibition of soil-borne pathogen growth, due to biotic and abiotic factors acting in complex rhizosphere environments. Use of a consortium of microbial strains with disease inhibitory activity may improve the biocontrol efficacy of the disease-inhibiting microbes. The mechanisms of biological control are not fully understood. In this review, we focus on bacterial and fungal biocontrol agents to summarize the current state of the use of single strain and multi-strain biological control consortia in the management of soil-borne diseases. We discuss potential mechanisms used by microbial components to improve the disease suppressing efficacy. We emphasize the interaction-related factors to be considered when constructing multiple-strain biological control consortia and propose a workflow for assembling them by applying a reductionist synthetic community approach.
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Affiliation(s)
- Ben Niu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Weixiong Wang
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Zhibo Yuan
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Ronald R. Sederoff
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
| | - Heike Sederoff
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - Vincent L. Chiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
| | - Rainer Borriss
- Institute of Biology, Humboldt University of Berlin, Berlin, Germany
- Institute of Marine Biotechnology e.V. (IMaB), Greifswald, Germany
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14
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Abbas M, Peszlen I, Shi R, Kim H, Katahira R, Kafle K, Xiang Z, Huang X, Min D, Mohamadamin M, Yang C, Dai X, Yan X, Park S, Li Y, Kim SH, Davis M, Ralph J, Sederoff RR, Chiang VL, Li Q. Involvement of CesA4, CesA7-A/B and CesA8-A/B in secondary wall formation in Populus trichocarpa wood. Tree Physiol 2020; 40:73-89. [PMID: 31211386 DOI: 10.1093/treephys/tpz020] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 02/10/2019] [Accepted: 02/18/2019] [Indexed: 05/13/2023]
Abstract
Cellulose synthase A genes (CesAs) are responsible for cellulose biosynthesis in plant cell walls. In this study, functions of secondary wall cellulose synthases PtrCesA4, PtrCesA7-A/B and PtrCesA8-A/B were characterized during wood formation in Populus trichocarpa (Torr. & Gray). CesA RNAi knockdown transgenic plants exhibited stunted growth, narrow leaves, early necrosis, reduced stature, collapsed vessels, thinner fiber cell walls and extended fiber lumen diameters. In the RNAi knockdown transgenics, stems exhibited reduced mechanical strength, with reduced modulus of rupture (MOR) and modulus of elasticity (MOE). The reduced mechanical strength may be due to thinner fiber cell walls. Vessels in the xylem of the transgenics were collapsed, indicating that water transport in xylem may be affected and thus causing early necrosis in leaves. A dramatic decrease in cellulose content was observed in the RNAi knockdown transgenics. Compared with wildtype, the cellulose content was significantly decreased in the PtrCesA4, PtrCesA7 and PtrCesA8 RNAi knockdown transgenics. As a result, lignin and xylem contents were proportionally increased. The wood composition changes were confirmed by solid-state NMR, two-dimensional solution-state NMR and sum-frequency-generation vibration (SFG) analyses. Both solid-state nuclear magnetic resonance (NMR) and SFG analyses demonstrated that knockdown of PtrCesAs did not affect cellulose crystallinity index. Our results provided the evidence for the involvement of PtrCesA4, PtrCesA7-A/B and PtrCesA8-A/B in secondary cell wall formation in wood and demonstrated the pleiotropic effects of their perturbations on wood formation.
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Affiliation(s)
- Manzar Abbas
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
| | - Ilona Peszlen
- Department of Forest Biomaterials, North Carolina State University, Raleigh, NC, USA
| | - Rui Shi
- Department of Crop and Soil Science, North Carolina State University, Raleigh, NC, USA
| | - Hoon Kim
- Department of Biochemistry and DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin, WI, USA
| | - Rui Katahira
- National Bioenergy Center, NREL, Golden, Co, USA
| | - Kabindra Kafle
- Department of Chemical Engineering and Materials Research Institute, The Pennsylvania State University, University Park, PA, USA
| | - Zhouyang Xiang
- State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou, China
| | - Xiong Huang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
| | - Douyong Min
- Light Industry and Food Engineering College, Guangxi University, Nanning, China
| | - Makarem Mohamadamin
- Department of Chemical Engineering and Materials Research Institute, The Pennsylvania State University, University Park, PA, USA
| | - Chenmin Yang
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, USA
| | - Xinren Dai
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
| | - Xiaojing Yan
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
| | - Sunkyu Park
- Department of Forest Biomaterials, North Carolina State University, Raleigh, NC, USA
| | - Yun Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Seong H Kim
- Department of Chemical Engineering and Materials Research Institute, The Pennsylvania State University, University Park, PA, USA
| | - Mark Davis
- National Bioenergy Center, NREL, Golden, Co, USA
| | - John Ralph
- Department of Biochemistry and DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin, WI, USA
| | - Ronald R Sederoff
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, USA
| | - Vincent L Chiang
- Department of Forest Biomaterials, North Carolina State University, Raleigh, NC, USA
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, USA
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Quanzi Li
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
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15
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Yan X, Liu J, Kim H, Liu B, Huang X, Yang Z, Lin YCJ, Chen H, Yang C, Wang JP, Muddiman DC, Ralph J, Sederoff RR, Li Q, Chiang VL. CAD1 and CCR2 protein complex formation in monolignol biosynthesis in Populus trichocarpa. New Phytol 2019; 222:244-260. [PMID: 30276825 DOI: 10.1111/nph.15505] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 09/20/2018] [Indexed: 05/18/2023]
Abstract
Lignin is the major phenolic polymer in plant secondary cell walls and is polymerized from monomeric subunits, the monolignols. Eleven enzyme families are implicated in monolignol biosynthesis. Here, we studied the functions of members of the cinnamyl alcohol dehydrogenase (CAD) and cinnamoyl-CoA reductase (CCR) families in wood formation in Populus trichocarpa, including the regulatory effects of their transcripts and protein activities on monolignol biosynthesis. Enzyme activity assays from stem-differentiating xylem (SDX) proteins showed that RNAi suppression of PtrCAD1 in P. trichocarpa transgenics caused a reduction in SDX CCR activity. RNAi suppression of PtrCCR2, the only CCR member highly expressed in SDX, caused a reciprocal reduction in SDX protein CAD activities. The enzyme assays of mixed and coexpressed recombinant proteins supported physical interactions between PtrCAD1 and PtrCCR2. Biomolecular fluorescence complementation and pull-down/co-immunoprecipitation experiments supported a hypothesis of PtrCAD1/PtrCCR2 heterodimer formation. These results provide evidence for the formation of PtrCAD1/PtrCCR2 protein complexes in monolignol biosynthesis in planta.
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Affiliation(s)
- Xiaojing Yan
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Jie Liu
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, 27695, USA
| | - Hoon Kim
- Department of Biochemistry and DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, WI, 53726, USA
| | - Baoguang Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
- Department of Forestry, Beihua University, Jilin, 132013, China
| | - Xiong Huang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
| | - Zhichang Yang
- W.M. Keck FT-ICR Mass Spectrometry Laboratory, Department of Chemistry, North Carolina State University, Raleigh, NC, 27695, USA
| | - Ying-Chung Jimmy Lin
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
- Department of Life Sciences, Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, 10617, Taiwan
| | - Hao Chen
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, 27695, USA
| | - Chenmin Yang
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, 27695, USA
| | - Jack P Wang
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, 27695, USA
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - David C Muddiman
- W.M. Keck FT-ICR Mass Spectrometry Laboratory, Department of Chemistry, North Carolina State University, Raleigh, NC, 27695, USA
| | - John Ralph
- Department of Biochemistry and DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, WI, 53726, USA
| | - Ronald R Sederoff
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, 27695, USA
| | - Quanzi Li
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Vincent L Chiang
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, 27695, USA
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
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16
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Wang JP, Matthews ML, Naik PP, Williams CM, Ducoste JJ, Sederoff RR, Chiang VL. Flux modeling for monolignol biosynthesis. Curr Opin Biotechnol 2019; 56:187-192. [DOI: 10.1016/j.copbio.2018.12.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 10/30/2018] [Accepted: 12/02/2018] [Indexed: 10/27/2022]
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17
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Chen H, Wang JP, Liu H, Li H, Lin YCJ, Shi R, Yang C, Gao J, Zhou C, Li Q, Sederoff RR, Li W, Chiang VL. Hierarchical Transcription Factor and Chromatin Binding Network for Wood Formation in Black Cottonwood ( Populus trichocarpa). Plant Cell 2019; 31:602-626. [PMID: 30755461 PMCID: PMC6482634 DOI: 10.1105/tpc.18.00620] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 01/15/2019] [Accepted: 02/07/2019] [Indexed: 05/18/2023]
Abstract
Wood remains the world's most abundant and renewable resource for timber and pulp and is an alternative to fossil fuels. Understanding the molecular regulation of wood formation can advance the engineering of wood for more efficient material and energy productions. We integrated a black cottonwood (Populus trichocarpa) wood-forming cell system with quantitative transcriptomics and chromatin binding assays to construct a transcriptional regulatory network (TRN) directed by a key transcription factor (TF), PtrSND1-B1 (secondary wall-associated NAC-domain protein). The network consists of four layers of TF-target gene interactions with quantitative regulatory effects, describing the specificity of how the regulation is transduced through these interactions to activate cell wall genes (effector genes) for wood formation. PtrSND1-B1 directs 57 TF-DNA interactions through 17 TFs transregulating 27 effector genes. Of the 57 interactions, 55 are novel. We tested 42 of these 57 interactions in 30 genotypes of transgenic P. trichocarpa and verified that ∼90% of the tested interactions function in vivo. The TRN reveals common transregulatory targets for distinct TFs, leading to the discovery of nine TF protein complexes (dimers and trimers) implicated in regulating the biosynthesis of specific types of lignin. Our work suggests that wood formation may involve regulatory homeostasis determined by combinations of TF-DNA and TF-TF (protein-protein) regulations.
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Affiliation(s)
- Hao Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina 27695
- Department of Genetics, North Carolina State University, Raleigh, North Carolina 27695
| | - Jack P. Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina 27695
| | - Huizi Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Huiyu Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Ying-Chung Jimmy Lin
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
- Department of Life Sciences, College of Life Science, National Taiwan University, Taipei, 10617, Taiwan
- Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Rui Shi
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina 27695
| | - Chenmin Yang
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina 27695
| | - Jinghui Gao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Chenguang Zhou
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Quanzi Li
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China
| | - Ronald R. Sederoff
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina 27695
| | - Wei Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina 27695
| | - Vincent L. Chiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina 27695
- Department of Forest Biomaterials, North Carolina State University, Raleigh, North Carolina 27695
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18
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Wang JP, Liu B, Sun Y, Chiang VL, Sederoff RR. Enzyme-Enzyme Interactions in Monolignol Biosynthesis. Front Plant Sci 2018; 9:1942. [PMID: 30693007 PMCID: PMC6340093 DOI: 10.3389/fpls.2018.01942] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 12/13/2018] [Indexed: 05/18/2023]
Abstract
The enzymes that comprise the monolignol biosynthetic pathway have been studied intensively for more than half a century. A major interest has been the role of pathway in the biosynthesis of lignin and the role of lignin in the formation of wood. The pathway has been typically conceived as linear steps that convert phenylalanine into three major monolignols or as a network of enzymes in a metabolic grid. Potential interactions of enzymes have been investigated to test models of metabolic channeling or for higher order interactions. Evidence for enzymatic or physical interactions has been fragmentary and limited to a few enzymes studied in different species. Only recently the entire pathway has been studied comprehensively in any single plant species. Support for interactions comes from new studies of enzyme activity, co-immunoprecipitation, chemical crosslinking, bimolecular fluorescence complementation, yeast 2-hybrid functional screening, and cell type-specific gene expression based on light amplification by stimulated emission of radiation capture microdissection. The most extensive experiments have been done on differentiating xylem of Populus trichocarpa, where genomic, biochemical, chemical, and cellular experiments have been carried out. Interactions affect the rate, direction, and specificity of both 3 and 4-hydroxylation in the monolignol biosynthetic pathway. Three monolignol P450 mono-oxygenases form heterodimeric and heterotetrameric protein complexes that activate specific hydroxylation of cinnamic acid derivatives. Other interactions include regulatory kinetic control of 4-coumarate CoA ligases through subunit specificity and interactions between a cinnamyl alcohol dehydrogenase and a cinnamoyl-CoA reductase. Monolignol enzyme interactions with other pathway proteins have been associated with biotic and abiotic stress response. Evidence challenging or supporting metabolic channeling in this pathway will be discussed.
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Affiliation(s)
- Jack P. Wang
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Baoguang Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- Department of Forestry, Beihua University, Jilin, China
| | - Yi Sun
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Vincent L. Chiang
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Ronald R. Sederoff
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
- *Correspondence: Ronald R. Sederoff,
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19
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Shi R, Wang JP, Lin YC, Li Q, Sun YH, Chen H, Sederoff RR, Chiang VL. Tissue and cell-type co-expression networks of transcription factors and wood component genes in Populus trichocarpa. Planta 2017; 245:927-938. [PMID: 28083709 DOI: 10.1007/s00425-016-2640-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 12/09/2016] [Indexed: 05/21/2023]
Abstract
Co-expression networks based on transcriptomes of Populus trichocarpa major tissues and specific cell types suggest redundant control of cell wall component biosynthetic genes by transcription factors in wood formation. We analyzed the transcriptomes of five tissues (xylem, phloem, shoot, leaf, and root) and two wood forming cell types (fiber and vessel) of Populus trichocarpa to assemble gene co-expression subnetworks associated with wood formation. We identified 165 transcription factors (TFs) that showed xylem-, fiber-, and vessel-specific expression. Of these 165 TFs, 101 co-expressed (correlation coefficient, r > 0.7) with the 45 secondary cell wall cellulose, hemicellulose, and lignin biosynthetic genes. Each cell wall component gene co-expressed on average with 34 TFs, suggesting redundant control of the cell wall component gene expression. Co-expression analysis showed that the 101 TFs and the 45 cell wall component genes each has two distinct groups (groups 1 and 2), based on their co-expression patterns. The group 1 TFs (44 members) are predominantly xylem and fiber specific, and are all highly positively co-expressed with the group 1 cell wall component genes (30 members), suggesting their roles as major wood formation regulators. Group 1 TFs include a lateral organ boundary domain gene (LBD) that has the highest number of positively correlated cell wall component genes (36) and TFs (47). The group 2 TFs have 57 members, including 14 vessel-specific TFs, and are generally less correlated with the cell wall component genes. An exception is a vessel-specific basic helix-loop-helix (bHLH) gene that negatively correlates with 20 cell wall component genes, and may function as a key transcriptional suppressor. The co-expression networks revealed here suggest a well-structured transcriptional homeostasis for cell wall component biosynthesis during wood formation.
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Affiliation(s)
- Rui Shi
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, 27695, USA
- Mountain Horticultural Crops Research and Extension Center, Department of Horticulture, North Carolina State University, Mills River, NC, 28759, USA
| | - Jack P Wang
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, 27695, USA
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Ying-Chung Lin
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, 27695, USA
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
- Department of Life Sciences, College of Life Science, National Taiwan University, Taipei, 10617, Taiwan
| | - Quanzi Li
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
| | - Ying-Hsuan Sun
- Department of Forestry, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Hao Chen
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, 27695, USA
| | - Ronald R Sederoff
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, 27695, USA.
| | - Vincent L Chiang
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, 27695, USA.
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China.
- Department of Forest Biomaterials, North Carolina State University, Raleigh, NC, 27695, USA.
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20
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Loziuk PL, Parker J, Li W, Lin CY, Wang JP, Li Q, Sederoff RR, Chiang VL, Muddiman DC. Elucidation of Xylem-Specific Transcription Factors and Absolute Quantification of Enzymes Regulating Cellulose Biosynthesis in Populus trichocarpa. J Proteome Res 2015; 14:4158-68. [PMID: 26325666 DOI: 10.1021/acs.jproteome.5b00233] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cellulose, the main chemical polymer of wood, is the most abundant polysaccharide in nature.1 The ability to perturb the abundance and structure of cellulose microfibrils is of critical importance to the pulp and paper industry as well as for the textile, wood products, and liquid biofuels industries. Although much has been learned at the transcript level about the biosynthesis of cellulose, a quantitative understanding at the proteome level has yet to be established. The study described herein sought to identify the proteins directly involved in cellulose biosynthesis during wood formation in Populus trichocarpa along with known xylem-specific transcription factors involved in regulating these key proteins. Development of an effective discovery proteomic strategy through a combination of subcellular fractionation of stem differentiating xylem tissue (SDX) with recently optimized FASP digestion protocols, StageTip fractionation, as well as optimized instrument parameters for global proteomic analysis using the quadrupole-orbitrap mass spectrometer resulted in the deepest proteomic coverage of SDX protein from P. trichocarpa with 9,146 protein groups being identified (1% FDR). Of these, 20 cellulosic/hemicellulosic enzymes and 43 xylem-specific transcription factor groups were identified. Finally, selection of surrogate peptides led to an assay for absolute quantification of 14 cellulosic proteins in SDX of P. trichocarpa.
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Affiliation(s)
- Philip L Loziuk
- W.M. Keck FTMS Laboratory, Department of Chemistry, North Carolina State University , Raleigh, North Carolina 27695, United States
| | - Jennifer Parker
- W.M. Keck FTMS Laboratory, Department of Chemistry, North Carolina State University , Raleigh, North Carolina 27695, United States
| | - Wei Li
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University , Raleigh, North Carolina 27695, United States
| | - Chien-Yuan Lin
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University , Raleigh, North Carolina 27695, United States
| | - Jack P Wang
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University , Raleigh, North Carolina 27695, United States
| | - Quanzi Li
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry , Beijing 100091, China
| | - Ronald R Sederoff
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University , Raleigh, North Carolina 27695, United States
| | - Vincent L Chiang
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University , Raleigh, North Carolina 27695, United States
| | - David C Muddiman
- W.M. Keck FTMS Laboratory, Department of Chemistry, North Carolina State University , Raleigh, North Carolina 27695, United States
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21
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Loziuk PL, Sederoff RR, Chiang VL, Muddiman DC. Establishing ion ratio thresholds based on absolute peak area for absolute protein quantification using protein cleavage isotope dilution mass spectrometry. Analyst 2015; 139:5439-50. [PMID: 25154770 DOI: 10.1039/c4an00567h] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Quantitative mass spectrometry has become central to the field of proteomics and metabolomics. Selected reaction monitoring is a widely used method for the absolute quantification of proteins and metabolites. This method renders high specificity using several product ions measured simultaneously. With growing interest in quantification of molecular species in complex biological samples, confident identification and quantitation has been of particular concern. A method to confirm purity or contamination of product ion spectra has become necessary for achieving accurate and precise quantification. Ion abundance ratio assessments were introduced to alleviate some of these issues. Ion abundance ratios are based on the consistent relative abundance (RA) of specific product ions with respect to the total abundance of all product ions. To date, no standardized method of implementing ion abundance ratios has been established. Thresholds by which product ion contamination is confirmed vary widely and are often arbitrary. This study sought to establish criteria by which the relative abundance of product ions can be evaluated in an absolute quantification experiment. These findings suggest that evaluation of the absolute ion abundance for any given transition is necessary in order to effectively implement RA thresholds. Overall, the variation of the RA value was observed to be relatively constant beyond an absolute threshold ion abundance. Finally, these RA values were observed to fluctuate significantly over a 3 year period, suggesting that these values should be assessed as close as possible to the time at which data is collected for quantification.
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Affiliation(s)
- Philip L Loziuk
- W. M. Keck Fourier Transform Mass Spectrometry Laboratory, Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, USA.
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22
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Lin CY, Wang JP, Li Q, Chen HC, Liu J, Loziuk P, Song J, Williams C, Muddiman DC, Sederoff RR, Chiang VL. 4-Coumaroyl and caffeoyl shikimic acids inhibit 4-coumaric acid:coenzyme A ligases and modulate metabolic flux for 3-hydroxylation in monolignol biosynthesis of Populus trichocarpa. Mol Plant 2015; 8:176-87. [PMID: 25578281 DOI: 10.1016/j.molp.2014.12.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 10/07/2014] [Indexed: 05/06/2023]
Abstract
Downregulation of 4-coumaric acid:coenzyme A ligase (4CL) can reduce lignin content in a number of plant species. In lignin precursor (monolignol) biosynthesis during stem wood formation in Populus trichocarpa, two enzymes, Ptr4CL3 and Ptr4CL5, catalyze the coenzyme A (CoA) ligation of 4-coumaric acid to 4-coumaroyl-CoA and caffeic acid to caffeoyl-CoA. CoA ligation of 4-coumaric acid is essential for the 3-hydroxylation of 4-coumaroyl shikimic acid. This hydroxylation results from sequential reactions of 4-hydroxycinnamoyl-CoA:shikimic acid hydroxycinnamoyl transferases (PtrHCT1 and PtrHCT6) and 4-coumaric acid 3-hydroxylase 3 (PtrC3H3). Alternatively, 3-hydroxylation of 4-coumaric acid to caffeic acid may occur through an enzyme complex of cinnamic acid 4-hydroxylase 1 and 2 (PtrC4H1 and PtrC4H2) and PtrC3H3. We found that 4-coumaroyl and caffeoyl shikimic acids are inhibitors of Ptr4CL3 and Ptr4CL5. 4-Coumaroyl shikimic acid strongly inhibits the formation of 4-coumaroyl-CoA and caffeoyl-CoA. Caffeoyl shikimic acid inhibits only the formation of 4-coumaroyl-CoA. 4-Coumaroyl and caffeoyl shikimic acids both act as competitive and uncompetitive inhibitors. Metabolic flux in wild-type and PtrC3H3 downregulated P. trichocarpa transgenics has been estimated by absolute protein and metabolite quantification based on liquid chromatography-tandem mass spectrometry, mass action kinetics, and inhibition equations. Inhibition by 4-coumaroyl and caffeoyl shikimic acids may play significant regulatory roles when these inhibitors accumulate.
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Affiliation(s)
- Chien-Yuan Lin
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, USA
| | - Jack P Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, USA
| | - Quanzi Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China
| | - Hsi-Chuan Chen
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, USA
| | - Jie Liu
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, USA
| | - Philip Loziuk
- W.M. Keck FT-ICR Mass Spectrometry Laboratory, Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Jina Song
- Department of Electrical and Computer Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Cranos Williams
- Department of Electrical and Computer Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - David C Muddiman
- W.M. Keck FT-ICR Mass Spectrometry Laboratory, Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Ronald R Sederoff
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, USA.
| | - Vincent L Chiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, USA.
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23
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Li Q, Song J, Peng S, Wang JP, Qu GZ, Sederoff RR, Chiang VL. Plant biotechnology for lignocellulosic biofuel production. Plant Biotechnol J 2014; 12:1174-92. [PMID: 25330253 DOI: 10.1111/pbi.12273] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2014] [Revised: 08/11/2014] [Accepted: 09/05/2014] [Indexed: 05/18/2023]
Abstract
Lignocelluloses from plant cell walls are attractive resources for sustainable biofuel production. However, conversion of lignocellulose to biofuel is more expensive than other current technologies, due to the costs of chemical pretreatment and enzyme hydrolysis for cell wall deconstruction. Recalcitrance of cell walls to deconstruction has been reduced in many plant species by modifying plant cell walls through biotechnology. These results have been achieved by reducing lignin content and altering its composition and structure. Reduction of recalcitrance has also been achieved by manipulating hemicellulose biosynthesis and by overexpression of bacterial enzymes in plants to disrupt linkages in the lignin-carbohydrate complexes. These modified plants often have improved saccharification yield and higher ethanol production. Cell wall-degrading (CWD) enzymes from bacteria and fungi have been expressed at high levels in plants to increase the efficiency of saccharification compared with exogenous addition of cellulolytic enzymes. In planta expression of heat-stable CWD enzymes from bacterial thermophiles has made autohydrolysis possible. Transgenic plants can be engineered to reduce recalcitrance without any yield penalty, indicating that successful cell wall modification can be achieved without impacting cell wall integrity or plant development. A more complete understanding of cell wall formation and structure should greatly improve lignocellulosic feedstocks and reduce the cost of biofuel production.
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Affiliation(s)
- Quanzi Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China; State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
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24
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Lin CY, Wang JP, Li Q, Chen HC, Liu J, Loziuk P, Song J, Williams C, Muddiman DC, Sederoff RR, Chiang VL. 4-Coumaroyl and Caffeoyl Shikimic Acids Inhibit 4-Coumaric Acid: Coenzyme A Ligases and Modulate Metabolic Flux for 3-Hydroxylation in Monolignol Biosynthesis of Populus trichocarpa. Mol Plant 2014:ssu117. [PMID: 25336570 DOI: 10.1093/mp/ssu117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
In a number of plant species, downregulation of 4-coumaric acid: coenzyme A ligase (4CL) can reduce lignin content. In lignin precursor (monolignol) biosynthesis during stem wood formation in Populus trichocarpa, two enzymes Ptr4CL3 and Ptr4CL5 catalyze the CoA ligation of 4-coumaric acid to 4-coumaroyl-CoA and caffeic acid to caffeoyl-CoA. CoA ligation of 4-coumaric acid is essential for the 3-hydroxylation of 4-coumaroyl shikimic acid. This hydroxylation results from sequential reactions of 4-hydroxycinnamoyl-CoA: shikimic acid hydroxycinnamoyl transferases (PtrHCT1 and PtrHCT6) and 4-coumaric acid 3-hydroxylase 3 (PtrC3H3). Alternatively, 3-hydroxylation of 4-coumaric acid to caffeic acid may occur through an enzyme complex of cinnamic acid 4-hydroxylase 1 and 2 (PtrC4H1 and PtrC4H2) and PtrC3H3. We found that 4-coumaroyl and caffeoyl shikimic acids are inhibitors of Ptr4CL3 and Ptr4CL5. 4-Coumaroyl shikimic acid strongly inhibits formation of 4-coumaroyl-CoA and caffeoyl-CoA. Caffeoyl shikimic acid inhibits only formation of 4-coumaroyl-CoA. 4-coumaroyl and caffeoyl shikimic acids both act as competitive and uncompetitive inhibitors. Estimates of metabolic flux in wildtype and PtrC3H3 downregulated P. trichocarpa transgenics have been made using LC-MS/MS based absolute protein and metabolite quantification, mass action kinetics and inhibition equations. Inhibition by 4-coumaroyl and caffeoyl shikimic acids may play significant regulatory roles when these inhibitors accumulate.
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Affiliation(s)
- Chien-Yuan Lin
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina 27695, U.S.A
| | - Jack P Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina 27695, U.S.A
| | - Quanzi Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
| | - Hsi-Chuan Chen
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina 27695, U.S.A
| | - Jie Liu
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina 27695, U.S.A
| | - Philip Loziuk
- W.M. Keck FT-ICR Mass Spectrometry Laboratory, Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, U.S.A
| | - Jina Song
- Department of Electrical and Computer Engineering, North Carolina State University, Raleigh North Carolina, 27695, U.S.A
| | - Cranos Williams
- Department of Electrical and Computer Engineering, North Carolina State University, Raleigh North Carolina, 27695, U.S.A
| | - David C Muddiman
- W.M. Keck FT-ICR Mass Spectrometry Laboratory, Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, U.S.A
| | - Ronald R Sederoff
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina 27695, U.S.A
| | - Vincent L Chiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina 27695, U.S.A
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25
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Lin YC, Li W, Chen H, Li Q, Sun YH, Shi R, Lin CY, Wang JP, Chen HC, Chuang L, Qu GZ, Sederoff RR, Chiang VL. A simple improved-throughput xylem protoplast system for studying wood formation. Nat Protoc 2014; 9:2194-205. [PMID: 25144270 DOI: 10.1038/nprot.2014.147] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Isolated protoplasts serve as a transient expression system that is highly representative of stable transgenics in terms of transcriptome responses. They can also be used as a cellular system to study gene transactivation and nucleocytoplasmic protein trafficking. They are particularly useful for systems studies in which stable transgenics and mutants are unavailable. We present a protocol for the isolation and transfection of protoplasts from wood-forming tissue, the stem-differentiating xylem (SDX), in the model woody plant Populus trichocarpa. The method involves tissue preparation, digestion of SDX cell walls, protoplast isolation and DNA transfection. Our approach is markedly faster and provides better yields than previous protocols; small (milligrams)- to large (20 g)-scale SDX preparations can be achieved in ~60 s, with isolation of protoplasts and their subsequent transfection taking ~50 min. Up to ten different samples can be processed simultaneously in this time scale. Our protocol gives a high yield (~2.5 × 10(7) protoplasts per g of SDX) of protoplasts sharing 96% transcriptome identity with intact SDX.
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Affiliation(s)
- Ying-Chung Lin
- 1] State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China. [2] Department of Forestry and Environmental Resources, Forest Biotechnology Group, North Carolina State University, Raleigh, North Carolina, USA
| | - Wei Li
- 1] State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China. [2] Department of Forestry and Environmental Resources, Forest Biotechnology Group, North Carolina State University, Raleigh, North Carolina, USA
| | - Hao Chen
- Department of Forestry and Environmental Resources, Forest Biotechnology Group, North Carolina State University, Raleigh, North Carolina, USA
| | - Quanzi Li
- 1] State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China. [2] Department of Forestry and Environmental Resources, Forest Biotechnology Group, North Carolina State University, Raleigh, North Carolina, USA. [3] College of Forestry, Shandong Agricultural University, Taian, Shandong, China
| | - Ying-Hsuan Sun
- Department of Forestry, National Chung Hsing University, Taichung, Taiwan
| | - Rui Shi
- Department of Forestry and Environmental Resources, Forest Biotechnology Group, North Carolina State University, Raleigh, North Carolina, USA
| | - Chien-Yuan Lin
- Department of Forestry and Environmental Resources, Forest Biotechnology Group, North Carolina State University, Raleigh, North Carolina, USA
| | - Jack P Wang
- 1] State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China. [2] Department of Forestry and Environmental Resources, Forest Biotechnology Group, North Carolina State University, Raleigh, North Carolina, USA
| | - Hsi-Chuan Chen
- Department of Forestry and Environmental Resources, Forest Biotechnology Group, North Carolina State University, Raleigh, North Carolina, USA
| | - Ling Chuang
- Department of Forestry and Environmental Resources, Forest Biotechnology Group, North Carolina State University, Raleigh, North Carolina, USA
| | - Guan-Zheng Qu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Ronald R Sederoff
- Department of Forestry and Environmental Resources, Forest Biotechnology Group, North Carolina State University, Raleigh, North Carolina, USA
| | - Vincent L Chiang
- 1] State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China. [2] Department of Forestry and Environmental Resources, Forest Biotechnology Group, North Carolina State University, Raleigh, North Carolina, USA. [3] Department of Forest Biomaterials, North Carolina State University, Raleigh, North Carolina, USA
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26
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Wang JP, Naik PP, Chen HC, Shi R, Lin CY, Liu J, Shuford CM, Li Q, Sun YH, Tunlaya-Anukit S, Williams CM, Muddiman DC, Ducoste JJ, Sederoff RR, Chiang VL. Complete proteomic-based enzyme reaction and inhibition kinetics reveal how monolignol biosynthetic enzyme families affect metabolic flux and lignin in Populus trichocarpa. Plant Cell 2014; 26:894-914. [PMID: 24619611 PMCID: PMC4001400 DOI: 10.1105/tpc.113.120881] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Revised: 01/12/2014] [Accepted: 02/12/2014] [Indexed: 05/17/2023]
Abstract
We established a predictive kinetic metabolic-flux model for the 21 enzymes and 24 metabolites of the monolignol biosynthetic pathway using Populus trichocarpa secondary differentiating xylem. To establish this model, a comprehensive study was performed to obtain the reaction and inhibition kinetic parameters of all 21 enzymes based on functional recombinant proteins. A total of 104 Michaelis-Menten kinetic parameters and 85 inhibition kinetic parameters were derived from these enzymes. Through mass spectrometry, we obtained the absolute quantities of all 21 pathway enzymes in the secondary differentiating xylem. This extensive experimental data set, generated from a single tissue specialized in wood formation, was used to construct the predictive kinetic metabolic-flux model to provide a comprehensive mathematical description of the monolignol biosynthetic pathway. The model was validated using experimental data from transgenic P. trichocarpa plants. The model predicts how pathway enzymes affect lignin content and composition, explains a long-standing paradox regarding the regulation of monolignol subunit ratios in lignin, and reveals novel mechanisms involved in the regulation of lignin biosynthesis. This model provides an explanation of the effects of genetic and transgenic perturbations of the monolignol biosynthetic pathway in flowering plants.
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Affiliation(s)
- Jack P. Wang
- State Key Laboratory of Tree Genetics and Breeding,
Northeast Forestry University, Harbin 150040, China
- Forest Biotechnology Group, Department of Forestry and
Environmental Resources, North Carolina State University, Raleigh, North Carolina
27695
| | - Punith P. Naik
- Civil, Construction, and Environmental Engineering, North
Carolina State University, Raleigh, North Carolina 27695
| | - Hsi-Chuan Chen
- Forest Biotechnology Group, Department of Forestry and
Environmental Resources, North Carolina State University, Raleigh, North Carolina
27695
| | - Rui Shi
- Forest Biotechnology Group, Department of Forestry and
Environmental Resources, North Carolina State University, Raleigh, North Carolina
27695
| | - Chien-Yuan Lin
- Forest Biotechnology Group, Department of Forestry and
Environmental Resources, North Carolina State University, Raleigh, North Carolina
27695
| | - Jie Liu
- Forest Biotechnology Group, Department of Forestry and
Environmental Resources, North Carolina State University, Raleigh, North Carolina
27695
| | - Christopher M. Shuford
- Forest Biotechnology Group, Department of Forestry and
Environmental Resources, North Carolina State University, Raleigh, North Carolina
27695
| | - Quanzi Li
- State Key Laboratory of Tree Genetics and Breeding,
Northeast Forestry University, Harbin 150040, China
- Forest Biotechnology Group, Department of Forestry and
Environmental Resources, North Carolina State University, Raleigh, North Carolina
27695
- College of Forestry, Shandong Agricultural University,
Taian, Shandong 271018, China
| | - Ying-Hsuan Sun
- Department of Forestry, National Chung-Hsing University,
Taichung, 40227, Taiwan
| | - Sermsawat Tunlaya-Anukit
- Forest Biotechnology Group, Department of Forestry and
Environmental Resources, North Carolina State University, Raleigh, North Carolina
27695
| | - Cranos M. Williams
- Electrical and Computer Engineering, North Carolina State
University, Raleigh, North Carolina 27695
| | - David C. Muddiman
- W.M. Keck FT-ICR Mass Spectrometry Laboratory, Department
of Chemistry, North Carolina State University, Raleigh, North Carolina 27695
| | - Joel J. Ducoste
- Civil, Construction, and Environmental Engineering, North
Carolina State University, Raleigh, North Carolina 27695
| | - Ronald R. Sederoff
- Forest Biotechnology Group, Department of Forestry and
Environmental Resources, North Carolina State University, Raleigh, North Carolina
27695
| | - Vincent L. Chiang
- State Key Laboratory of Tree Genetics and Breeding,
Northeast Forestry University, Harbin 150040, China
- Forest Biotechnology Group, Department of Forestry and
Environmental Resources, North Carolina State University, Raleigh, North Carolina
27695
- Department of Forest Biomaterials, North Carolina State
University, Raleigh, North Carolina 27695
- Address correspondence to
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27
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Chen HC, Song J, Wang JP, Lin YC, Ducoste J, Shuford CM, Liu J, Li Q, Shi R, Nepomuceno A, Isik F, Muddiman DC, Williams C, Sederoff RR, Chiang VL. Systems biology of lignin biosynthesis in Populus trichocarpa: heteromeric 4-coumaric acid:coenzyme A ligase protein complex formation, regulation, and numerical modeling. Plant Cell 2014; 26:876-93. [PMID: 24619612 PMCID: PMC4001399 DOI: 10.1105/tpc.113.119685] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Revised: 01/28/2014] [Accepted: 02/12/2014] [Indexed: 05/17/2023]
Abstract
As a step toward predictive modeling of flux through the pathway of monolignol biosynthesis in stem differentiating xylem of Populus trichocarpa, we discovered that the two 4-coumaric acid:CoA ligase (4CL) isoforms, 4CL3 and 4CL5, interact in vivo and in vitro to form a heterotetrameric protein complex. This conclusion is based on laser microdissection, coimmunoprecipitation, chemical cross-linking, bimolecular fluorescence complementation, and mass spectrometry. The tetramer is composed of three subunits of 4CL3 and one of 4CL5. 4CL5 appears to have a regulatory role. This protein-protein interaction affects the direction and rate of metabolic flux for monolignol biosynthesis in P. trichocarpa. A mathematical model was developed for the behavior of 4CL3 and 4CL5 individually and in mixtures that form the enzyme complex. The model incorporates effects of mixtures of multiple hydroxycinnamic acid substrates, competitive inhibition, uncompetitive inhibition, and self-inhibition, along with characteristic of the substrates, the enzyme isoforms, and the tetrameric complex. Kinetic analysis of different ratios of the enzyme isoforms shows both inhibition and activation components, which are explained by the mathematical model and provide insight into the regulation of metabolic flux for monolignol biosynthesis by protein complex formation.
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Affiliation(s)
- Hsi-Chuan Chen
- State Key Laboratory of Tree Genetics and Breeding,
Northeast Forestry University, Harbin 150040, China
- Forest Biotechnology Group, Department of Forestry and
Environmental Resources, North Carolina State University, Raleigh, North Carolina
27695
| | - Jina Song
- Department of Electrical and Computer Engineering, North
Carolina State University, Raleigh, North Carolina 27695
| | - Jack P. Wang
- State Key Laboratory of Tree Genetics and Breeding,
Northeast Forestry University, Harbin 150040, China
- Forest Biotechnology Group, Department of Forestry and
Environmental Resources, North Carolina State University, Raleigh, North Carolina
27695
| | - Ying-Chung Lin
- State Key Laboratory of Tree Genetics and Breeding,
Northeast Forestry University, Harbin 150040, China
- Forest Biotechnology Group, Department of Forestry and
Environmental Resources, North Carolina State University, Raleigh, North Carolina
27695
| | - Joel Ducoste
- Department of Civil, Construction, and Environmental
Engineering, North Carolina State University, Raleigh, North Carolina 27695
| | - Christopher M. Shuford
- Forest Biotechnology Group, Department of Forestry and
Environmental Resources, North Carolina State University, Raleigh, North Carolina
27695
| | - Jie Liu
- Forest Biotechnology Group, Department of Forestry and
Environmental Resources, North Carolina State University, Raleigh, North Carolina
27695
| | - Quanzi Li
- State Key Laboratory of Tree Genetics and Breeding,
Northeast Forestry University, Harbin 150040, China
- Forest Biotechnology Group, Department of Forestry and
Environmental Resources, North Carolina State University, Raleigh, North Carolina
27695
- College of Forestry, Shandong Agricultural University,
Shandong 271018, China
| | - Rui Shi
- Forest Biotechnology Group, Department of Forestry and
Environmental Resources, North Carolina State University, Raleigh, North Carolina
27695
| | - Angelito Nepomuceno
- W.M. Keck Mass Spectrometry Laboratory, Department of
Chemistry, North Carolina State University, Raleigh, North Carolina 27695
| | - Fikret Isik
- NCSU Cooperative Tree Improvement Program, Department of
Forestry and Environmental Resources, North Carolina State University, Raleigh, North
Carolina 27695
| | - David C. Muddiman
- W.M. Keck Mass Spectrometry Laboratory, Department of
Chemistry, North Carolina State University, Raleigh, North Carolina 27695
| | - Cranos Williams
- Department of Electrical and Computer Engineering, North
Carolina State University, Raleigh, North Carolina 27695
- Address correspondence to
| | - Ronald R. Sederoff
- Forest Biotechnology Group, Department of Forestry and
Environmental Resources, North Carolina State University, Raleigh, North Carolina
27695
- Address correspondence to
| | - Vincent L. Chiang
- State Key Laboratory of Tree Genetics and Breeding,
Northeast Forestry University, Harbin 150040, China
- Forest Biotechnology Group, Department of Forestry and
Environmental Resources, North Carolina State University, Raleigh, North Carolina
27695
- Department of Forest Biomaterials, North Carolina State
University, Raleigh, North Carolina 27695
- Address correspondence to
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28
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Loziuk PL, Wang J, Li Q, Sederoff RR, Chiang VL, Muddiman DC. Understanding the Role of Proteolytic Digestion on Discovery and Targeted Proteomic Measurements Using Liquid Chromatography Tandem Mass Spectrometry and Design of Experiments. J Proteome Res 2013; 12:5820-9. [DOI: 10.1021/pr4008442] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Philip L. Loziuk
- W.M. Keck
Fourier Transform Mass Spectrometry Laboratory, Department of Chemistry, North Carolina State University, Raleigh, North Carolina, 27695, United States
| | - Jack Wang
- Forest
Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina, 27695, United States
| | - Quanzi Li
- Forest
Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina, 27695, United States
| | - Ronald R. Sederoff
- Forest
Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina, 27695, United States
| | - Vincent L. Chiang
- Forest
Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina, 27695, United States
| | - David C. Muddiman
- W.M. Keck
Fourier Transform Mass Spectrometry Laboratory, Department of Chemistry, North Carolina State University, Raleigh, North Carolina, 27695, United States
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29
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Lin YC, Li W, Sun YH, Kumari S, Wei H, Li Q, Tunlaya-Anukit S, Sederoff RR, Chiang VL. SND1 transcription factor-directed quantitative functional hierarchical genetic regulatory network in wood formation in Populus trichocarpa. Plant Cell 2013; 25:4324-41. [PMID: 24280390 PMCID: PMC3875721 DOI: 10.1105/tpc.113.117697] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Revised: 10/13/2013] [Accepted: 10/23/2013] [Indexed: 05/18/2023]
Abstract
Wood is an essential renewable raw material for industrial products and energy. However, knowledge of the genetic regulation of wood formation is limited. We developed a genome-wide high-throughput system for the discovery and validation of specific transcription factor (TF)-directed hierarchical gene regulatory networks (hGRNs) in wood formation. This system depends on a new robust procedure for isolation and transfection of Populus trichocarpa stem differentiating xylem protoplasts. We overexpressed Secondary Wall-Associated NAC Domain 1s (Ptr-SND1-B1), a TF gene affecting wood formation, in these protoplasts and identified differentially expressed genes by RNA sequencing. Direct Ptr-SND1-B1-DNA interactions were then inferred by integration of time-course RNA sequencing data and top-down Graphical Gaussian Modeling-based algorithms. These Ptr-SND1-B1-DNA interactions were verified to function in differentiating xylem by anti-PtrSND1-B1 antibody-based chromatin immunoprecipitation (97% accuracy) and in stable transgenic P. trichocarpa (90% accuracy). In this way, we established a Ptr-SND1-B1-directed quantitative hGRN involving 76 direct targets, including eight TF and 61 enzyme-coding genes previously unidentified as targets. The network can be extended to the third layer from the second-layer TFs by computation or by overexpression of a second-layer TF to identify a new group of direct targets (third layer). This approach would allow the sequential establishment, one two-layered hGRN at a time, of all layers involved in a more comprehensive hGRN. Our approach may be particularly useful to study hGRNs in complex processes in plant species resistant to stable genetic transformation and where mutants are unavailable.
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Affiliation(s)
- Ying-Chung Lin
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina 27695
| | - Wei Li
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina 27695
| | - Ying-Hsuan Sun
- Department of Forestry, National Chung Hsing University, Taichung 40227, Taiwan
| | - Sapna Kumari
- School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan 49931
| | - Hairong Wei
- School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan 49931
| | - Quanzi Li
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina 27695
- College of Forestry, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Sermsawat Tunlaya-Anukit
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina 27695
| | - Ronald R. Sederoff
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina 27695
| | - Vincent L. Chiang
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina 27695
- Address correspondence to
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30
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Shi R, Shuford CM, Wang JP, Sun YH, Yang Z, Chen HC, Tunlaya-Anukit S, Li Q, Liu J, Muddiman DC, Sederoff RR, Chiang VL. Regulation of phenylalanine ammonia-lyase (PAL) gene family in wood forming tissue of Populus trichocarpa. Planta 2013; 238:487-97. [PMID: 23765265 DOI: 10.1007/s00425-013-1905-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Accepted: 05/27/2013] [Indexed: 05/12/2023]
Abstract
Phenylalanine ammonia-lyase (PAL) catalyzes the initial step of phenylpropanoid biosynthesis in plants. Five PAL genes (PtrPAL1 to 5) have been identified in Populus trichocarpa. These genes are classified into two subgroups according to their transcript sequence similarity and tissue specificity. However, the regulation of these genes and their protein functions are not well understood. In this study, enzymatic properties of each PtrPALs were characterized based on their recombinant proteins expressed in E.coli. Subcellular localizations of each PtrPALs in stem wood forming tissue were investigated and individual PtrPAL protein abundances in cytosol and membrane protein fractions were measured using protein cleavage-isotope dilution mass spectrometry (PC-IDMS). Protein/mRNA ratios of PtrPALs were further verified using RNA-Seq and gel-enhanced liquid chromatography mass spectrometry (GeLC-MS). All PtrPALs have similar catalytic properties for the deamination of L-phenylalanine, their major substrate. All PtrPALs have similar subcellular locations in stem wood forming tissue, with major amount in the cytosol (93-96 %) and less in the membrane (4-7 %). However, the protein/mRNA ratios of subgroup A (PtrPAL2, 4 and 5) are about five times that of subgroup B (PtrPAL1 and 3) in stem wood forming tissue, while all PtrPALs have similar transcript abundances. These results indicate a greater functional significance of subgroup A PtrPALs for stem wood formation, and highlight the role of gene post-transcriptional regulation.
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Affiliation(s)
- Rui Shi
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, USA.
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31
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Chen HC, Song J, Williams CM, Shuford CM, Liu J, Wang JP, Li Q, Shi R, Gokce E, Ducoste J, Muddiman DC, Sederoff RR, Chiang VL. Monolignol pathway 4-coumaric acid:coenzyme A ligases in Populus trichocarpa: novel specificity, metabolic regulation, and simulation of coenzyme A ligation fluxes. Plant Physiol 2013; 161:1501-16. [PMID: 23344904 PMCID: PMC3585612 DOI: 10.1104/pp.112.210971] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Accepted: 01/21/2013] [Indexed: 05/20/2023]
Abstract
4-Coumaric acid:coenzyme A ligase (4CL) is involved in monolignol biosynthesis for lignification in plant cell walls. It ligates coenzyme A (CoA) with hydroxycinnamic acids, such as 4-coumaric and caffeic acids, into hydroxycinnamoyl-CoA thioesters. The ligation ensures the activated state of the acid for reduction into monolignols. In Populus spp., it has long been thought that one monolignol-specific 4CL is involved. Here, we present evidence of two monolignol 4CLs, Ptr4CL3 and Ptr4CL5, in Populus trichocarpa. Ptr4CL3 is the ortholog of the monolignol 4CL reported for many other species. Ptr4CL5 is novel. The two Ptr4CLs exhibited distinct Michaelis-Menten kinetic properties. Inhibition kinetics demonstrated that hydroxycinnamic acid substrates are also inhibitors of 4CL and suggested that Ptr4CL5 is an allosteric enzyme. Experimentally validated flux simulation, incorporating reaction/inhibition kinetics, suggested two CoA ligation paths in vivo: one through 4-coumaric acid and the other through caffeic acid. We previously showed that a membrane protein complex mediated the 3-hydroxylation of 4-coumaric acid to caffeic acid. The demonstration here of two ligation paths requiring these acids supports this 3-hydroxylation function. Ptr4CL3 regulates both CoA ligation paths with similar efficiencies, whereas Ptr4CL5 regulates primarily the caffeic acid path. Both paths can be inhibited by caffeic acid. The Ptr4CL5-catalyzed caffeic acid metabolism, therefore, may also act to mitigate the inhibition by caffeic acid to maintain a proper ligation flux. A high level of caffeic acid was detected in stem-differentiating xylem of P. trichocarpa. Our results suggest that Ptr4CL5 and caffeic acid coordinately modulate the CoA ligation flux for monolignol biosynthesis.
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32
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Wang JP, Shuford CM, Li Q, Song J, Lin YC, Sun YH, Chen HC, Williams CM, Muddiman DC, Sederoff RR, Chiang VL. Functional redundancy of the two 5-hydroxylases in monolignol biosynthesis of Populus trichocarpa: LC-MS/MS based protein quantification and metabolic flux analysis. Planta 2012; 236:795-808. [PMID: 22628084 DOI: 10.1007/s00425-012-1663-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Accepted: 05/06/2012] [Indexed: 06/01/2023]
Abstract
Flowering plants have syringyl and guaiacyl subunits in lignin in contrast to the guaiacyl lignin in gymnosperms. The biosynthesis of syringyl subunits is initiated by coniferaldehyde 5-hydroxylase (CAld5H). In Populus trichocarpa there are two closely related CAld5H enzymes (PtrCAld5H1 and PtrCAld5H2) associated with lignin biosynthesis during wood formation. We used yeast recombinant PtrCAld5H1 and PtrCAld5H2 proteins to carry out Michaelis-Menten and inhibition kinetics with LC-MS/MS based absolute protein quantification. CAld5H, a monooxygenase, requires a cytochrome P450 reductase (CPR) as an electron donor. We cloned and expressed three P. trichocarpa CPRs in yeast and show that all are active with both CAld5Hs. The kinetic analysis shows both CAld5Hs have essentially the same biochemical functions. When both CAld5Hs are coexpressed in the same yeast membranes, the resulting enzyme activities are additive, suggesting functional redundancy and independence of these two enzymes. Simulated reaction flux based on Michaelis-Menten kinetics and inhibition kinetics confirmed the redundancy and independence. Subcellular localization of both CAld5Hs as sGFP fusion proteins expressed in P. trichocarpa differentiating xylem protoplasts indicate that they are endoplasmic reticulum resident proteins. These results imply that during wood formation, 5-hydroxylation in monolignol biosynthesis of P. trichocarpa requires the combined metabolic flux of these two CAld5Hs to maintain adequate biosynthesis of syringyl lignin. The combination of genetic analysis, absolute protein quantitation-based enzyme kinetics, homologous CPR specificity, SNP characterization, and ER localization provides a more rigorous basis for a comprehensive systems understanding of 5-hydroxylation in lignin biosynthesis.
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Affiliation(s)
- Jack P Wang
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, USA.
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Liu J, Shi R, Li Q, Sederoff RR, Chiang VL. A standard reaction condition and a single HPLC separation system are sufficient for estimation of monolignol biosynthetic pathway enzyme activities. Planta 2012; 236:879-85. [PMID: 22729823 DOI: 10.1007/s00425-012-1688-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Accepted: 06/04/2012] [Indexed: 05/13/2023]
Abstract
Lignin content and composition are largely determined by the composition and quantity of the monolignol precursors. Individual enzymes of the monolignol biosynthetic pathway determine the composition and quantity of monolignols. Monolignol biosynthesis in angiosperms is mediated by ten enzyme families. We developed a method using a total protein extract (soluble and microsomal) for the comprehensive and simultaneous analysis of these ten enzyme activities in a single target tissue, stem differentiating xylem (SDX) of Populus trichocarpa. As little as 300 mg fresh weight of SDX is sufficient for triplicate assays of all ten enzyme activities. To expand the effectiveness of the analysis, we quantified the reaction products directly by HPLC and developed a universal method that can separate the substrates and products of all enzymes. The specific activities measured with this simple approach are similar to those obtained with the optimum conditions previously established for each individual enzyme. This approach is applicable to the enzyme activity analysis for both P. trichocarpa (angiosperm) and Pinus taeda (gymnosperm) and is particularly useful when a large number of samples need to be analyzed for all monolignol biosynthetic enzymes.
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Affiliation(s)
- Jie Liu
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, USA.
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Abstract
MicroRNAs (miRNAs) are 20-24 nucleotide long molecules processed from a specific class of RNA polymerase II transcripts that mainly regulate the stability of mRNAs containing a complementary sequence by targeted degradation in plants. Many features of tree biology are regulated by miRNAs affecting development, metabolism, adaptation and evolution. MiRNAs may be modified and harnessed for controlled suppression of specific genes to learn about gene function, or for practical applications through genetic engineering. Modified (artificial) miRNAs act as dominant suppressors and are particularly useful in tree genetics because they bypass the generations of inbreeding needed for fixation of recessive mutations. The purpose of this review is to summarize the current status of information on miRNAs in trees and to guide future studies on the role of miRNAs in the biology of woody perennials and to illustrate their utility in directed genetic modification of trees.
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Affiliation(s)
- Ying-Hsuan Sun
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, USA
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Shuford CM, Sederoff RR, Chiang VL, Muddiman DC. Peptide production and decay rates affect the quantitative accuracy of protein cleavage isotope dilution mass spectrometry (PC-IDMS). Mol Cell Proteomics 2012; 11:814-23. [PMID: 22595788 DOI: 10.1074/mcp.o112.017145] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
No consensus has been reached on the proper time to add stable-isotope labeled (SIL) peptides in protein cleavage isotope dilution mass spectrometry workflows. While quantifying 24 monolignol pathway enzymes in the xylem tissue of Populus trichocarpa, we compared the protein concentrations obtained when adding the SIL standard peptides concurrently with the enzyme or after quenching of the digestion (i.e. postdigestion) and observed discrepancies for nearly all tryptic peptides investigated. In some cases, greater than 30-fold differences were observed. To explain these differences and potentially correct for them, we developed a mathematical model based on pseudo-first-order kinetics to account for the dynamic production and decay (e.g. degradation and precipitation) of the native peptide targets in conjunction with the decay of the SIL peptide standards. A time course study of the digests confirmed the results predicted by the proposed model and revealed that the discrepancy between concurrent and postdigestion introduction of the SIL standards was related to differential decay experienced by the SIL peptide and the native peptide in each method. Given these results, we propose concurrent introduction of the SIL peptide is most appropriate, though not free from bias. Mathematical modeling of this method reveals that overestimation of protein quantities would still result when rapid peptide decay occurs and that this bias would be further exaggerated by slow proteolysis. We derive a simple equation to estimate the bias for each peptide based on the relative rates of production and decay. According to this equation, nearly half of the peptides evaluated here were estimated to have quantitative errors greater than 10% and in a few cases over 100%. We conclude that the instability of peptides can often significantly bias the protein quantities measured in protein cleavage isotope dilution mass spectrometry-based assays and suggest peptide stability be made a priority when selecting peptides to use for quantification.
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Affiliation(s)
- Christopher M Shuford
- W M Keck FT-ICR Mass Spectrometry Laboratory, Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, USA
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Shuford CM, Li Q, Sun YH, Chen HC, Wang J, Shi R, Sederoff RR, Chiang VL, Muddiman DC. Comprehensive quantification of monolignol-pathway enzymes in Populus trichocarpa by protein cleavage isotope dilution mass spectrometry. J Proteome Res 2012; 11:3390-404. [PMID: 22524869 DOI: 10.1021/pr300205a] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The economic value of wood/pulp from many tree species is largely dictated by the quantity and chemical properties of lignin, which is directly related to the composition and linkages of monolignols comprising the polymer. Although much is known regarding the monolignol biosynthetic pathway, our understanding is still deficient due to the lack of quantitative information at the proteomic level. We developed an assay based on protein cleavage isotope dilution mass spectrometry (PC-IDMS) for the determination of all potential, primary enzymes involved in the biosynthesis of monolignols and the peroxidases responsible for their polymerization to form lignin in the model tree species, Populus trichocarpa. Described is the identification of quantitative surrogate peptides through shotgun analysis of native and recombinant proteins, optimization of trypsin proteolysis using fractional factorial design of experiments, and development of a liquid chromatography-selected reaction monitoring method for specific detection of all targeted peptides. Of the 25 targeted enzymes, three were undetected in the normal xylem tissues, and all but two of the detectable species showed good day-to-day precision (CV < 10%). This represents the most comprehensive assay for quantification of proteins regulating monolignol biosynthesis and will lead to a better understanding of lignin formation at a systems level.
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Affiliation(s)
- Christopher M Shuford
- W.M. Keck FT-ICR Mass Spectrometry Laboratory, Department of Chemistry, and ‡Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University , Raleigh, North Carolina 27695, United States
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Abstract
Peroxidase has been thought to be the only enzyme that oxidizes monolignol precursors to initiate lignin formation in plants. A laccase was purified from cell walls of differentiating xylem of loblolly pine and shown to coincide in time and place with lignin formation and to oxidize monolignols to dehydrogenation products in vitro. These results suggest that laccase participates in lignin biosynthesis and therefore could be an important target for genetic engineering to modify wood properties or to improve the digestibility of forage crops.
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Abstract
Mitochondria from the S male-sterile cytoplasm (cms-S) of maize contain two plasmid-like DNAs, S-1 and S-2, that appear to be prominently involved with the cytoplasmic male sterility trait. The complete nucleotide sequence of the S-2 DNA molecule was determined by the chain termination method. The linear S-2 DNA molecule contains 5,452 base pairs and is terminated by exact 208-base-pair inverted repetitions. Two large open reading frames were identified in the S-2 DNA, suggesting the possibility of protein-encoding genes. The nucleotide sequence of the S-2 termini are discussed with regard to models proposed for the replication of linear DNA molecules.
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Affiliation(s)
- C S Levings
- Department of Genetics, North Carolina State University, Raleigh, North Carolina 27650
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Neale DB, Marshall KA, Sederoff RR. Chloroplast and mitochondrial DNA are paternally inherited in Sequoia sempervirens D. Don Endl. Proc Natl Acad Sci U S A 2010; 86:9347-9. [PMID: 16594091 PMCID: PMC298492 DOI: 10.1073/pnas.86.23.9347] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Restriction fragment length polymorphisms in controlled crosses were used to infer the mode of inheritance of chloroplast DNA and mitochondrial DNA in coast redwood (Sequoia sempervirens D. Don Endl.). Chloroplast DNA was paternally inherited, as is true for all other conifers studied thus far. Surprisingly, a restriction fragment length polymorphism detected by a mitochondrial probe was paternally inherited as well. This polymorphism could not be detected in hybridizations with chloroplast probes covering the entire chloroplast genome, thus providing evidence that the mitochondrial probe had not hybridized to chloroplast DNA on the blot. We conclude that mitochondrial DNA is paternally inherited in coast redwood. To our knowledge, paternal inheritance of mitochondrial DNA in sexual crosses of a multicellular eukaryotic organism has not been previously reported.
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Affiliation(s)
- D B Neale
- Institute of Forest Genetics, Pacific Southwest Forest and Range Experiment Station, Forest Service, U.S. Department of Agriculture, Berkeley, CA 94701
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Abstract
Molecular mechanisms underlying the evolution of mtDNA in maize and three species of teosinte have been investigated. By using DNA transfer techniques and cloned fragments of maize mtDNA, changes in the position of homologous sequences in restriction digests were analyzed in related taxa. The resulting patterns indicate general conservation of sequence homology in all four species. One-third of the cloned fragments showed sequences conserved in homology and position of BamHI restriction fragments. Other fragments produced patterns indicating that extensive rearrangement of DNA sequences has taken place. In two cases, hybridization patterns revealed major changes in relative abundance of specific sequences that we believe are related to the molecular heterogeneity phenomenon of maize mtDNA. The evolution of mtDNA in these plants appears dramatically different from that in animal mtDNA, where base substitutions may account for most of the observed changes in restriction patterns.
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Affiliation(s)
- R R Sederoff
- Department of Genetics, North Carolina State University, Raleigh, North Carolina 27650
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van Zyl L, von Arnold S, Bozhkov P, Chen Y, Egertsdotter U, Mackay J, Sederoff RR, Shen J, Zelena L, Clapham DH. Heterologous array analysis in Pinaceae: hybridization of Pinus taeda cDNA arrays with cDNA from needles and embryogenic cultures of P. Taeda, P. Sylvestris or Picea abies. Comp Funct Genomics 2010; 3:306-18. [PMID: 18629264 PMCID: PMC2448427 DOI: 10.1002/cfg.199] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2002] [Accepted: 06/14/2002] [Indexed: 11/10/2022] Open
Abstract
Hybridization of labelled cDNA from various cell types with high-density arrays of expressed sequence tags is a powerful technique for investigating gene expression. Few
conifer cDNA libraries have been sequenced. Because of the high level of sequence
conservation between Pinus and Picea we have investigated the use of arrays from
one genus for studies of gene expression in the other. The partial cDNAs from 384
identifiable genes expressed in differentiating xylem of Pinus taeda were printed on
nylon membranes in randomized replicates. These were hybridized with labelled
cDNA from needles or embryogenic cultures of Pinus taeda, P. sylvestris and Picea abies, and with labelled cDNA from leaves of Nicotiana tabacum. The Spearman
correlation of gene expression for pairs of conifer species was high for needles
(r2 = 0.78 − 0.86), and somewhat lower for embryogenic cultures (r2 = 0.68 − 0.83).
The correlation of gene expression for tobacco leaves and needles of each of the three
conifer species was lower but sufficiently high (r2 = 0.52 − 0.63) to suggest that many
partial gene sequences are conserved in angiosperms and gymnosperms. Heterologous
probing was further used to identify tissue-specific gene expression over species
boundaries. To evaluate the significance of differences in gene expression, conventional
parametric tests were compared with permutation tests after four methods of
normalization. Permutation tests after Z-normalization provide the highest degree
of discrimination but may enhance the probability of type I errors. It is concluded
that arrays of cDNA from loblolly pine are useful for studies of gene expression in
other pines or spruces.
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Affiliation(s)
- Leonel van Zyl
- Forest Biotechnology Group, Centennial Campus, North Carolina State University, Raleigh, NC 27695, USA
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Heath LS, Ramakrishnan N, Sederoff RR, Whetten RW, Chevone BI, Struble CA, Jouenne VY, Chen D, van Zyl L, Grene R. Studying the functional genomics of stress responses in loblolly pine with the Expresso microarray experiment management system. Comp Funct Genomics 2010; 3:226-43. [PMID: 18628855 PMCID: PMC2447276 DOI: 10.1002/cfg.169] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2001] [Accepted: 04/04/2002] [Indexed: 12/20/2022] Open
Abstract
Conception, design, and implementation of cDNA microarray experiments present a
variety of bioinformatics challenges for biologists and computational scientists. The multiple
stages of data acquisition and analysis have motivated the design of Expresso, a
system for microarray experiment management. Salient aspects of Expresso include
support for clone replication and randomized placement; automatic gridding, extraction of
expression data from each spot, and quality monitoring; flexible methods of combining
data from individual spots into information about clones and functional categories; and the
use of inductive logic programming for higher-level data analysis and mining. The
development of Expresso is occurring in parallel with several generations of microarray
experiments aimed at elucidating genomic responses to drought stress in loblolly pine
seedlings. The current experimental design incorporates 384 pine cDNAs replicated and
randomly placed in two specific microarray layouts. We describe the design of Expresso as
well as results of analysis with Expresso that suggest the importance of molecular
chaperones and membrane transport proteins in mechanisms conferring successful
adaptation to long-term drought stress.
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Affiliation(s)
- Lenwood S Heath
- Department of Computer Science, Virginia Tech, Blacksburg, VA 24061, USA
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Gleick PH, Adams RM, Amasino RM, Anders E, Anderson DJ, Anderson WW, Anselin LE, Arroyo MK, Asfaw B, Ayala FJ, Bax A, Bebbington AJ, Bell G, Bennett MVL, Bennetzen JL, Berenbaum MR, Berlin OB, Bjorkman PJ, Blackburn E, Blamont JE, Botchan MR, Boyer JS, Boyle EA, Branton D, Briggs SP, Briggs WR, Brill WJ, Britten RJ, Broecker WS, Brown JH, Brown PO, Brunger AT, Cairns J, Canfield DE, Carpenter SR, Carrington JC, Cashmore AR, Castilla JC, Cazenave A, Chapin FS, Ciechanover AJ, Clapham DE, Clark WC, Clayton RN, Coe MD, Conwell EM, Cowling EB, Cowling RM, Cox CS, Croteau RB, Crothers DM, Crutzen PJ, Daily GC, Dalrymple GB, Dangl JL, Darst SA, Davies DR, Davis MB, De Camilli PV, Dean C, DeFries RS, Deisenhofer J, Delmer DP, DeLong EF, DeRosier DJ, Diener TO, Dirzo R, Dixon JE, Donoghue MJ, Doolittle RF, Dunne T, Ehrlich PR, Eisenstadt SN, Eisner T, Emanuel KA, Englander SW, Ernst WG, Falkowski PG, Feher G, Ferejohn JA, Fersht A, Fischer EH, Fischer R, Flannery KV, Frank J, Frey PA, Fridovich I, Frieden C, Futuyma DJ, Gardner WR, Garrett CJR, Gilbert W, Goldberg RB, Goodenough WH, Goodman CS, Goodman M, Greengard P, Hake S, Hammel G, Hanson S, Harrison SC, Hart SR, Hartl DL, Haselkorn R, Hawkes K, Hayes JM, Hille B, Hökfelt T, House JS, Hout M, Hunten DM, Izquierdo IA, Jagendorf AT, Janzen DH, Jeanloz R, Jencks CS, Jury WA, Kaback HR, Kailath T, Kay P, Kay SA, Kennedy D, Kerr A, Kessler RC, Khush GS, Kieffer SW, Kirch PV, Kirk K, Kivelson MG, Klinman JP, Klug A, Knopoff L, Kornberg H, Kutzbach JE, Lagarias JC, Lambeck K, Landy A, Langmuir CH, Larkins BA, Le Pichon XT, Lenski RE, Leopold EB, Levin SA, Levitt M, Likens GE, Lippincott-Schwartz J, Lorand L, Lovejoy CO, Lynch M, Mabogunje AL, Malone TF, Manabe S, Marcus J, Massey DS, McWilliams JC, Medina E, Melosh HJ, Meltzer DJ, Michener CD, Miles EL, Mooney HA, Moore PB, Morel FMM, Mosley-Thompson ES, Moss B, Munk WH, Myers N, Nair GB, Nathans J, Nester EW, Nicoll RA, Novick RP, O'Connell JF, Olsen PE, Opdyke ND, Oster GF, Ostrom E, Pace NR, Paine RT, Palmiter RD, Pedlosky J, Petsko GA, Pettengill GH, Philander SG, Piperno DR, Pollard TD, Price PB, Reichard PA, Reskin BF, Ricklefs RE, Rivest RL, Roberts JD, Romney AK, Rossmann MG, Russell DW, Rutter WJ, Sabloff JA, Sagdeev RZ, Sahlins MD, Salmond A, Sanes JR, Schekman R, Schellnhuber J, Schindler DW, Schmitt J, Schneider SH, Schramm VL, Sederoff RR, Shatz CJ, Sherman F, Sidman RL, Sieh K, Simons EL, Singer BH, Singer MF, Skyrms B, Sleep NH, Smith BD, Snyder SH, Sokal RR, Spencer CS, Steitz TA, Strier KB, Südhof TC, Taylor SS, Terborgh J, Thomas DH, Thompson LG, Tjian RT, Turner MG, Uyeda S, Valentine JW, Valentine JS, Van Etten JL, van Holde KE, Vaughan M, Verba S, von Hippel PH, Wake DB, Walker A, Walker JE, Watson EB, Watson PJ, Weigel D, Wessler SR, West-Eberhard MJ, White TD, Wilson WJ, Wolfenden RV, Wood JA, Woodwell GM, Wright HE, Wu C, Wunsch C, Zoback ML. Climate change and the integrity of science. Science 2010; 328:689-90. [PMID: 20448167 DOI: 10.1126/science.328.5979.689] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Grattapaglia D, Plomion C, Kirst M, Sederoff RR. Genomics of growth traits in forest trees. Curr Opin Plant Biol 2009; 12:148-56. [PMID: 19186096 DOI: 10.1016/j.pbi.2008.12.008] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2008] [Revised: 12/08/2008] [Accepted: 12/10/2008] [Indexed: 05/21/2023]
Abstract
Growth traits in trees are fundamental components of adaptation in a forest ecosystem and of productivity in planted forests. A number of processes determine tree growth, which are controlled by genetic and epigenetic factors that respond dynamically to environmental signals throughout centuries. Advances in genomics have allowed an increased comprehension of the complex mechanisms of tree growth and adaptation. Yet, the application of genomics to improving forest productivity and sustainability still entails capturing a large proportion of the total genetic variation controlling the component traits. Nonetheless, genetics and genomics are unifying disciplines that will serve well to dissect the variables and mechanisms of tree growth and development.
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Affiliation(s)
- Dario Grattapaglia
- EMBRAPA Genetic Resources and Biotechnology, CP 2372, Brasília 70770-970 DF, and Graduate Program in Genomic Sciences and Biotechnology, Universidade Católica de Brasília - SGAN 916 módulo B, Brasília 70790-160 DF, Brazil.
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Novaes E, Drost DR, Farmerie WG, Pappas GJ, Grattapaglia D, Sederoff RR, Kirst M. High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome. BMC Genomics 2008; 9:312. [PMID: 18590545 PMCID: PMC2483731 DOI: 10.1186/1471-2164-9-312] [Citation(s) in RCA: 386] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2008] [Accepted: 06/30/2008] [Indexed: 11/13/2022] Open
Abstract
Background Benefits from high-throughput sequencing using 454 pyrosequencing technology may be most apparent for species with high societal or economic value but few genomic resources. Rapid means of gene sequence and SNP discovery using this novel sequencing technology provide a set of baseline tools for genome-level research. However, it is questionable how effective the sequencing of large numbers of short reads for species with essentially no prior gene sequence information will support contig assemblies and sequence annotation. Results With the purpose of generating the first broad survey of gene sequences in Eucalyptus grandis, the most widely planted hardwood tree species, we used 454 technology to sequence and assemble 148 Mbp of expressed sequences (EST). EST sequences were generated from a normalized cDNA pool comprised of multiple tissues and genotypes, promoting discovery of homologues to almost half of Arabidopsis genes, and a comprehensive survey of allelic variation in the transcriptome. By aligning the sequencing reads from multiple genotypes we detected 23,742 SNPs, 83% of which were validated in a sample. Genome-wide nucleotide diversity was estimated for 2,392 contigs using a modified theta (θ) parameter, adapted for measuring genetic diversity from polymorphisms detected by randomly sequencing a multi-genotype cDNA pool. Diversity estimates in non-synonymous nucleotides were on average 4x smaller than in synonymous, suggesting purifying selection. Non-synonymous to synonymous substitutions (Ka/Ks) among 2,001 contigs averaged 0.30 and was skewed to the right, further supporting that most genes are under purifying selection. Comparison of these estimates among contigs identified major functional classes of genes under purifying and diversifying selection in agreement with previous researches. Conclusion In providing an abundance of foundational transcript sequences where limited prior genomic information existed, this work created part of the foundation for the annotation of the E. grandis genome that is being sequenced by the US Department of Energy. In addition we demonstrated that SNPs sampled in large-scale with 454 pyrosequencing can be used to detect evolutionary signatures among genes, providing one of the first genome-wide assessments of nucleotide diversity and Ka/Ks for a non-model plant species.
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Affiliation(s)
- Evandro Novaes
- School of Forest Resources and Conservation, University of Florida, PO Box 110410, Gainesville, USA.
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Kirst M, Basten CJ, Myburg AA, Zeng ZB, Sederoff RR. Genetic architecture of transcript-level variation in differentiating xylem of a eucalyptus hybrid. Genetics 2005; 169:2295-303. [PMID: 15687266 PMCID: PMC1449597 DOI: 10.1534/genetics.104.039198] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Species diversity may have evolved by differential regulation of a similar set of genes. To analyze and compare the genetic architecture of transcript regulation in different genetic backgrounds of Eucalyptus, microarrays were used to examine variation in mRNA abundance in the differentiating xylem of a E. grandis pseudobackcross population [E. grandis x F(1) hybrid (E. grandis x E. globulus)]. Least-squares mean estimates of transcript levels were generated for 2608 genes in 91 interspecific backcross progeny. The quantitative measurements of variation in transcript abundance for specific genes were mapped as expression QTL (eQTL) in two single-tree genetic linkage maps (F(1) hybrid paternal and E. grandis maternal). EQTL were identified for 1067 genes in the two maps, of which 811 were located in the F(1) hybrid paternal map, and 451 in the E. grandis maternal map. EQTL for 195 genes mapped to both parental maps, the majority of which localized to nonhomologous linkage groups, suggesting trans-regulation by different loci in the two genetic backgrounds. For 821 genes, a single eQTL that explained up to 70% of the transcript-level variation was identified. Hotspots with colocalized eQTL were identified in both maps and typically contained genes associated with specific metabolic and regulatory pathways, suggesting coordinated genetic regulation.
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Affiliation(s)
- Matias Kirst
- Forest Biotechnology Group, North Carolina State University, Raleigh, 27695, USA
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Myburg AA, Vogl C, Griffin AR, Sederoff RR, Whetten RW. Genetics of postzygotic isolation in Eucalyptus: whole-genome analysis of barriers to introgression in a wide interspecific cross of Eucalyptus grandis and E. globulus. Genetics 2004; 166:1405-18. [PMID: 15082559 PMCID: PMC1470765 DOI: 10.1534/genetics.166.3.1405] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The genetic architecture of hybrid fitness characters can provide valuable insights into the nature and evolution of postzygotic reproductive barriers in diverged species. We determined the genome-wide distribution of barriers to introgression in an F(1) hybrid of two Eucalyptus tree species, Eucalyptus grandis (W. Hill ex Maiden.) and E. globulus (Labill.). Two interspecific backcross families (N = 186) were used to construct comparative, single-tree, genetic linkage maps of an F(1) hybrid individual and two backcross parents. A total of 1354 testcross AFLP marker loci were evaluated in the three parental maps and a substantial proportion (27.7% average) exhibited transmission ratio distortion (alpha = 0.05). The distorted markers were located in distinct regions of the parental maps and marker alleles within each region were all biased toward either of the two parental species. We used a Bayesian approach to estimate the position and effect of transmission ratio distorting loci (TRDLs) in the distorted regions of each parental linkage map. The relative viability of TRDL alleles ranged from 0.20 to 0.72. Contrary to expectation, heterospecific (donor) alleles of TRDLs were favored as often as recurrent alleles in both backcrosses, suggesting that positive and negative heterospecific interactions affect introgression rates in this wide interspecific pedigree.
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Affiliation(s)
- Alexander A Myburg
- Department of Forestry, North Carolina State University, Raleigh, North Carolina 27695, USA.
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Stasolla C, Bozhkov PV, Chu TM, Van Zyl L, Egertsdotter U, Suarez MF, Craig D, Wolfinger RD, Von Arnold S, Sederoff RR. Variation in transcript abundance during somatic embryogenesis in gymnosperms. Tree Physiol 2004. [PMID: 15294754 DOI: 10.1093/treephys/24.10.1093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Somatic embryogenesis of Norway spruce (Picea abies L.) is a versatile model system to study molecular mechanisms regulating embryo development because it proceeds through defined developmental stages corresponding to specific culture treatments. Normal embryonic development involves early differentiation of proembryogenic masses (PEMs) into somatic embryos, followed by early and late embryogeny leading to the formation of mature cotyledonary embryos. In some cell lines there is a developmental arrest at the PEM-somatic embryo transition. To learn more about the molecular mechanisms regulating embryogenesis, we compared the transcript profiles of two normal lines and one developmentally arrested line. Ribonucleic acid, extracted from these cell lines at successive developmental stages, was analyzed on DNA microarrays containing 2178 expressed sequence tags (ESTs) (corresponding to 2110 unique cDNAs) from loblolly pine (Pinus taeda L.). Hybridization between spruce and pine species on microarrays has been shown to be effective (van Zyl et al. 2002, Stasolla et al. 2003). In contrast to the developmentally arrested line, the early phases of normal embryo development are characterized by a precise pattern of gene expression, i.e., repression followed by induction. Comparison of transcript levels between successive stages of embryogenesis allowed us to identify several genes that showed unique expression responses during normal development. Several of these genes encode proteins involved in detoxification processes, methionine synthesis and utilization, and carbohydrate metabolism. The potential role of these genes in embryo development is discussed.
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Affiliation(s)
- Claudio Stasolla
- Department of Plant Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.
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Stasolla C, Bozhkov PV, Chu TM, Van Zyl L, Egertsdotter U, Suarez MF, Craig D, Wolfinger RD, Von Arnold S, Sederoff RR. Variation in transcript abundance during somatic embryogenesis in gymnosperms. Tree Physiol 2004; 24:1073-85. [PMID: 15294754 DOI: 10.1093/treephys/24.10.1073] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Somatic embryogenesis of Norway spruce (Picea abies L.) is a versatile model system to study molecular mechanisms regulating embryo development because it proceeds through defined developmental stages corresponding to specific culture treatments. Normal embryonic development involves early differentiation of proembryogenic masses (PEMs) into somatic embryos, followed by early and late embryogeny leading to the formation of mature cotyledonary embryos. In some cell lines there is a developmental arrest at the PEM-somatic embryo transition. To learn more about the molecular mechanisms regulating embryogenesis, we compared the transcript profiles of two normal lines and one developmentally arrested line. Ribonucleic acid, extracted from these cell lines at successive developmental stages, was analyzed on DNA microarrays containing 2178 expressed sequence tags (ESTs) (corresponding to 2110 unique cDNAs) from loblolly pine (Pinus taeda L.). Hybridization between spruce and pine species on microarrays has been shown to be effective (van Zyl et al. 2002, Stasolla et al. 2003). In contrast to the developmentally arrested line, the early phases of normal embryo development are characterized by a precise pattern of gene expression, i.e., repression followed by induction. Comparison of transcript levels between successive stages of embryogenesis allowed us to identify several genes that showed unique expression responses during normal development. Several of these genes encode proteins involved in detoxification processes, methionine synthesis and utilization, and carbohydrate metabolism. The potential role of these genes in embryo development is discussed.
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Affiliation(s)
- Claudio Stasolla
- Department of Plant Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.
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Brinker M, van Zyl L, Liu W, Craig D, Sederoff RR, Clapham DH, von Arnold S. Microarray analyses of gene expression during adventitious root development in Pinus contorta. Plant Physiol 2004; 135:1526-39. [PMID: 15247392 PMCID: PMC519068 DOI: 10.1104/pp.103.032235] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2003] [Revised: 04/15/2004] [Accepted: 04/15/2004] [Indexed: 05/18/2023]
Abstract
In order to investigate the gene expression pattern during adventitious root development, RNA of Pinus contorta hypocotyls, pulse-treated with the auxin indole-3-butyric acid and harvested at distinct developmental time points of root development, was hybridized to microarrays containing 2,178 cDNAs from Pinus taeda. Over the period of observation of root development, the transcript levels of 220 genes changed significantly. During the root initiation phase, genes involved in cell replication and cell wall weakening and a transcript encoding a PINHEAD/ZWILLE-like protein were up-regulated, while genes related to auxin transport, photosynthesis, and cell wall synthesis were down-regulated. In addition, there were changes in transcript abundance of genes related to water stress. During the root meristem formation phase the transcript abundances of genes involved in auxin transport, auxin responsive transcription, and cell wall synthesis, and of a gene encoding a B-box zinc finger-like protein, increased, while those encoding proteins involved in cell wall weakening decreased. Changes of transcript abundance of genes related to water stress during the root meristem formation and root formation phase indicate that the plant roots had become functional in water transport. Simultaneously, genes involved in auxin transport were up-regulated, while genes related to cell wall modification were down-regulated. Finally, during the root elongation phase down-regulation of transcripts encoding proteins involved in cell replication and stress occurred. Based on the observed changes in transcript abundances, we suggest hypotheses about the relative importance of various physiological processes during the auxin-induced development of roots in P. contorta.
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Affiliation(s)
- Monika Brinker
- Department of Plant Biology and Forest Genetics, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden.
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