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Zhu Y, Li L. Wood of trees: Cellular structure, molecular formation, and genetic engineering. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:443-467. [PMID: 38032010 DOI: 10.1111/jipb.13589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 11/28/2023] [Indexed: 12/01/2023]
Abstract
Wood is an invaluable asset to human society due to its renewable nature, making it suitable for both sustainable energy production and material manufacturing. Additionally, wood derived from forest trees plays a crucial role in sequestering a significant portion of the carbon dioxide fixed during photosynthesis by terrestrial plants. Nevertheless, with the expansion of the global population and ongoing industrialization, forest coverage has been substantially decreased, resulting in significant challenges for wood production and supply. Wood production practices have changed away from natural forests toward plantation forests. Thus, understanding the underlying genetic mechanisms of wood formation is the foundation for developing high-quality, fast-growing plantation trees. Breeding ideal forest trees for wood production using genetic technologies has attracted the interest of many. Tremendous studies have been carried out in recent years on the molecular, genetic, and cell-biological mechanisms of wood formation, and considerable progress and findings have been achieved. These studies and findings indicate enormous possibilities and prospects for tree improvement. This review will outline and assess the cellular and molecular mechanisms of wood formation, as well as studies on genetically improving forest trees, and address future development prospects.
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Affiliation(s)
- Yingying Zhu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems and College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Laigeng Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
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2
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Zhou F, Zhang H, Chen S, Fan C. Transcriptome analysis of the transition from primary to secondary growth of vertical stem in Eucalyptus grandis. BMC PLANT BIOLOGY 2024; 24:96. [PMID: 38331783 PMCID: PMC10851593 DOI: 10.1186/s12870-024-04731-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 01/04/2024] [Indexed: 02/10/2024]
Abstract
Eucalyptus was one of the most cultivated hardwood species worldwide, with rapid growth, good wood properties and a wide range of adaptability. Eucalyptus stem undergoes primary growth (longitudinal growth) followed by secondary growth (radial growth), which produces biomass that is an important source of energy worldwide. In order to better understand the genetic regulation of secondary growth in Eucalyptus grandis, Transcriptome analyses in stem segments along a developmental gradient from the third internode to the eleventh internode of E. grandis that spanned primary to secondary growth were carried out. 5,149 genes that were differentially expressed during stem development were identified. Combining the trend analysis by the Mfuzz method and the module-trait correlation analysis by the Weighted Gene Co-expression Network Analysis method, a total of 70 differentially expressed genes (DEGs) selected from 868 DEGs with high connectivity were found to be closely correlated with secondary growth. Results revealed that the differential expression of these DEGs suggests that they may involve in the primary growth or secondary growth. AP1, YAB2 TFs and EXP genes are highly expressed in the IN3, whereas NAC, MYB TFs are likely to be important for secondary growth. These results will expand our understanding of the complex molecular and cellular events of secondary growth and provide a foundation for future studies on wood formation in Eucalyptus.
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Affiliation(s)
- Fangping Zhou
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
- Key Laboratory of State Forestry Administration On Tropical Forestry, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, 510520, China
| | - Haonan Zhang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
- Key Laboratory of State Forestry Administration On Tropical Forestry, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, 510520, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Shanshan Chen
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
- Key Laboratory of State Forestry Administration On Tropical Forestry, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, 510520, China
- State Key Laboratory of Tree Genetics Breeding, Northeast Forestry University, Harbin, China
| | - Chunjie Fan
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China.
- Key Laboratory of State Forestry Administration On Tropical Forestry, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, 510520, China.
- Yuelushan Laboratory, Central South University of Forestry and Technology, Changsha, Hunan, China.
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Liu H, An X, Liu X, Yang S, Liu Y, Wei X, Li X, Chen Q, Wang J. Molecular mechanism of salinity and waterlogging tolerance in mangrove Kandelia obovata. FRONTIERS IN PLANT SCIENCE 2024; 15:1354249. [PMID: 38384752 PMCID: PMC10879410 DOI: 10.3389/fpls.2024.1354249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 01/15/2024] [Indexed: 02/23/2024]
Abstract
Mangrove forests are colloquially referred to as "Earth's kidneys" and serve many important ecological and commercial functions. Salinity and waterlogging stress are the most important abiotic stressors restricting the growth and development of mangroves. Kandelia obovata (K. obovata) is the greatest latitudinally-distributed salt mangrove species in China.Here, morphology and transcriptomics were used to study the response of K. obovata to salt and waterlogging stress. In addition, weighted gene co-expression network analysis of the combined gene expression and phenotypic datasets was used to identify core salinity- and waterlogging-responsive modules. In this study, we observed that both high salinity and waterlogging significantly inhibited growth and development in K. obovata. Notably, growth was negatively correlated with salt concentration and positively correlated with waterlogging duration, and high salinity was significantly more inhibitive than waterlogging. A total of 7, 591 salt-responsive and 228 waterlogging-responsive differentially expressed genes were identified by RNA sequencing. Long-term salt stress was highly correlated with the measured physiological parameters while long-term waterlogging was poorly correlated with these traits. At the same time, 45 salinity-responsive and 16 waterlogging-responsive core genes were identified. All 61 core genes were mainly involved in metabolic and biosynthesis of secondary metabolites pathways. This study provides valuable insight into the molecular mechanisms of salinity and waterlogging tolerance in K. obovata, as well as a useful genetic resource for the improvement of mangrove stress tolerance using molecular breeding techniques.
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Affiliation(s)
- Huizi Liu
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, China
| | - Xia An
- Zhejiang Xiaoshan Institute of Cotton and Bast Fiber Crops, Zhejiang Institute of Landscape Plants and Flowers, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xing Liu
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, China
| | - Sheng Yang
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, China
| | - Yu Liu
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, China
| | - Xin Wei
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, China
| | - Xiaowen Li
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, China
| | - Qiuxia Chen
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, China
| | - Jinwang Wang
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, China
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Li W, Lin YCJ, Chen YL, Zhou C, Li S, De Ridder N, Oliveira DM, Zhang L, Zhang B, Wang JP, Xu C, Fu X, Luo K, Wu AM, Demura T, Lu MZ, Zhou Y, Li L, Umezawa T, Boerjan W, Chiang VL. Woody plant cell walls: Fundamentals and utilization. MOLECULAR PLANT 2024; 17:112-140. [PMID: 38102833 DOI: 10.1016/j.molp.2023.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/12/2023] [Accepted: 12/12/2023] [Indexed: 12/17/2023]
Abstract
Cell walls in plants, particularly forest trees, are the major carbon sink of the terrestrial ecosystem. Chemical and biosynthetic features of plant cell walls were revealed early on, focusing mostly on herbaceous model species. Recent developments in genomics, transcriptomics, epigenomics, transgenesis, and associated analytical techniques are enabling novel insights into formation of woody cell walls. Here, we review multilevel regulation of cell wall biosynthesis in forest tree species. We highlight current approaches to engineering cell walls as potential feedstock for materials and energy and survey reported field tests of such engineered transgenic trees. We outline opportunities and challenges in future research to better understand cell type biogenesis for more efficient wood cell wall modification and utilization for biomaterials or for enhanced carbon capture and storage.
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Affiliation(s)
- Wei Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | | | - Ying-Lan Chen
- Department of Biotechnology and Bioindustry Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan, China
| | - Chenguang Zhou
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Shuang Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Nette De Ridder
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Dyoni M Oliveira
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Lanjun Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Baocai Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jack P Wang
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, USA
| | - Changzheng Xu
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Xiaokang Fu
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Keming Luo
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Ai-Min Wu
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University, Guangzhou 510642, China
| | - Taku Demura
- Center for Digital Green-innovation, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Meng-Zhu Lu
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A & F University, Hangzhou 311300, China
| | - Yihua Zhou
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Laigeng Li
- CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
| | - Toshiaki Umezawa
- Laboratory of Metabolic Science of Forest Plants and Microorganisms, Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Wout Boerjan
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - 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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Chen L, Liu L, Yang G, Li X, Dai X, Xue L, Yin T. Expression Quantitative Trait Locus of Wood Formation-Related Genes in Salix suchowensis. Int J Mol Sci 2023; 25:247. [PMID: 38203430 PMCID: PMC10778782 DOI: 10.3390/ijms25010247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024] Open
Abstract
Shrub willows are widely planted for landscaping, soil remediation, and biomass production, due to their rapid growth rates. Identification of regulatory genes in wood formation would provide clues for genetic engineering of willows for improved growth traits on marginal lands. Here, we conducted an expression quantitative trait locus (eQTL) analysis, using a full sibling F1 population of Salix suchowensis, to explore the genetic mechanisms underlying wood formation. Based on variants identified from simplified genome sequencing and gene expression data from RNA sequencing, 16,487 eQTL blocks controlling 5505 genes were identified, including 2148 cis-eQTLs and 16,480 trans-eQTLs. eQTL hotspots were identified, based on eQTL frequency in genomic windows, revealing one hotspot controlling genes involved in wood formation regulation. Regulatory networks were further constructed, resulting in the identification of key regulatory genes, including three transcription factors (JAZ1, HAT22, MYB36) and CLV1, BAM1, CYCB2;4, CDKB2;1, associated with the proliferation and differentiation activity of cambium cells. The enrichment of genes in plant hormone pathways indicates their critical roles in the regulation of wood formation. Our analyses provide a significant groundwork for a comprehensive understanding of the regulatory network of wood formation in S. suchowensis.
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Affiliation(s)
| | | | | | | | | | - Liangjiao Xue
- State Key Laboratory of Tree Genetics and Breeding, Jiangsu Key Laboratory for Poplar Germplasm Enhancement and Variety Improvement, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Tongming Yin
- State Key Laboratory of Tree Genetics and Breeding, Jiangsu Key Laboratory for Poplar Germplasm Enhancement and Variety Improvement, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
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Zhou C, Niu S, El-Kassaby YA, Li W. Genome-wide identification of late embryogenesis abundant protein family and their key regulatory network in Pinus tabuliformis cold acclimation. TREE PHYSIOLOGY 2023; 43:1964-1985. [PMID: 37565812 DOI: 10.1093/treephys/tpad095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 07/16/2023] [Accepted: 08/03/2023] [Indexed: 08/12/2023]
Abstract
Cold acclimation is a crucial biological process that enables conifers to overwinter safely. The late embryogenesis abundant (LEA) protein family plays a pivotal role in enhancing freezing tolerance during this process. Despite its importance, the identification, molecular functions and regulatory networks of the LEA protein family have not been extensively studied in conifers or gymnosperms. Pinus tabuliformis, a conifer with high ecological and economic values and with high-quality genome sequence, is an ideal candidate for such studies. Here, a total of 104 LEA genes were identified from P. tabuliformis, and we renamed them according to their subfamily group: PtLEA1-PtLEA92 (group LEA1-LEA6), PtSMP1-PtSMP6 (group seed maturation protein) and PtDHN1-PtDHN6 (group Dehydrin). While the sequence structure of P. tabuliformis LEA genes are conserved, their physicochemical properties exhibit unique characteristics within different subfamily groupings. Notably, the abundance of low-temperature responsive elements in PtLEA genes was observed. Using annual rhythm and temperature gradient transcriptome data, PtLEA22 was identified as a key gene that responds to low-temperature induction while conforming to the annual cycle of cold acclimation. Overexpression of PtLEA22 enhanced Arabidopsis freezing tolerance. Furthermore, several transcription factors potentially co-expressed with PtLEA22 were validated using yeast one-hybrid and dual-luciferase assays, revealing that PtDREB1 could directly bind PtLEA22 promoter to positively regulate its expression. These findings reveal the genome-wide characterization of P. tabuliformis LEA genes and their importance in the cold acclimation, while providing a theoretical basis for studying the molecular mechanisms of cold acclimation in conifers.
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Affiliation(s)
- Chengcheng Zhou
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, 85 Qinghua East Road, Beijing, 100083, China
| | - Shihui Niu
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, 85 Qinghua East Road, Beijing, 100083, China
| | - Yousry A El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, 2424 Main Mall, Vancouver, BC V6T 1Z4, Canada
| | - Wei Li
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, 85 Qinghua East Road, Beijing, 100083, China
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Takawira LT, Hadj Bachir I, Ployet R, Tulloch J, San Clemente H, Christie N, Ladouce N, Dupas A, Rai A, Grima-Pettenati J, Myburg AA, Mizrachi E, Mounet F, Hussey SG. Functional investigation of five R2R3-MYB transcription factors associated with wood development in Eucalyptus using DAP-seq-ML. PLANT MOLECULAR BIOLOGY 2023; 113:33-57. [PMID: 37661236 DOI: 10.1007/s11103-023-01376-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 07/31/2023] [Indexed: 09/05/2023]
Abstract
A multi-tiered transcriptional network regulates xylem differentiation and secondary cell wall (SCW) formation in plants, with evidence of both conserved and lineage-specific SCW network architecture. We aimed to elucidate the roles of selected R2R3-MYB transcription factors (TFs) linked to Eucalyptus wood formation by identifying genome-wide TF binding sites and direct target genes through an improved DAP-seq protocol combined with machine learning for target gene assignment (DAP-seq-ML). We applied this to five TFs including a well-studied SCW master regulator (EgrMYB2; homolog of AtMYB83), a repressor of lignification (EgrMYB1; homolog of AtMYB4), a TF affecting SCW thickness and vessel density (EgrMYB137; homolog of PtrMYB074) and two TFs with unclear roles in SCW regulation (EgrMYB135 and EgrMYB122). Each DAP-seq TF peak set (average 12,613 peaks) was enriched for canonical R2R3-MYB binding motifs. To improve the reliability of target gene assignment to peaks, a random forest classifier was developed from Arabidopsis DAP-seq, RNA-seq, chromatin, and conserved noncoding sequence data which demonstrated significantly higher precision and recall to the baseline method of assigning genes to proximal peaks. EgrMYB1, EgrMYB2 and EgrMYB137 predicted targets showed clear enrichment for SCW-related biological processes. As validation, EgrMYB137 overexpression in transgenic Eucalyptus hairy roots increased xylem lignification, while its dominant repression in transgenic Arabidopsis and Populus reduced xylem lignification, stunted growth, and caused downregulation of SCW genes. EgrMYB137 targets overlapped significantly with those of EgrMYB2, suggesting partial functional redundancy. Our results show that DAP-seq-ML identified biologically relevant R2R3-MYB targets supported by the finding that EgrMYB137 promotes SCW lignification in planta.
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Affiliation(s)
- Lazarus T Takawira
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa
| | - Ines Hadj Bachir
- Laboratoire de Recherche en Sciences Végétales, Université Toulouse, CNRS, INP, Castanet-Tolosan, France
| | - Raphael Ployet
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa
| | - Jade Tulloch
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa
| | - Helene San Clemente
- Laboratoire de Recherche en Sciences Végétales, Université Toulouse, CNRS, INP, Castanet-Tolosan, France
| | - Nanette Christie
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa
| | - Nathalie Ladouce
- Laboratoire de Recherche en Sciences Végétales, Université Toulouse, CNRS, INP, Castanet-Tolosan, France
| | - Annabelle Dupas
- Laboratoire de Recherche en Sciences Végétales, Université Toulouse, CNRS, INP, Castanet-Tolosan, France
| | - Avanish Rai
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa
| | - Jacqueline Grima-Pettenati
- Laboratoire de Recherche en Sciences Végétales, Université Toulouse, CNRS, INP, Castanet-Tolosan, France
| | - Alexander A Myburg
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa
| | - Eshchar Mizrachi
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa
| | - Fabien Mounet
- Laboratoire de Recherche en Sciences Végétales, Université Toulouse, CNRS, INP, Castanet-Tolosan, France.
| | - Steven G Hussey
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa.
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Cao X, Zhang L, Islam MK, Zhao M, He C, Zhang K, Liu S, Sha Q, Wei H. TGPred: efficient methods for predicting target genes of a transcription factor by integrating statistics, machine learning and optimization. NAR Genom Bioinform 2023; 5:lqad083. [PMID: 37711605 PMCID: PMC10498345 DOI: 10.1093/nargab/lqad083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 05/30/2023] [Accepted: 08/30/2023] [Indexed: 09/16/2023] Open
Abstract
Four statistical selection methods for inferring transcription factor (TF)-target gene (TG) pairs were developed by coupling mean squared error (MSE) or Huber loss function, with elastic net (ENET) or least absolute shrinkage and selection operator (Lasso) penalty. Two methods were also developed for inferring pathway gene regulatory networks (GRNs) by combining Huber or MSE loss function with a network (Net)-based penalty. To solve these regressions, we ameliorated an accelerated proximal gradient descent (APGD) algorithm to optimize parameter selection processes, resulting in an equally effective but much faster algorithm than the commonly used convex optimization solver. The synthetic data generated in a general setting was used to test four TF-TG identification methods, ENET-based methods performed better than Lasso-based methods. Synthetic data generated from two network settings was used to test Huber-Net and MSE-Net, which outperformed all other methods. The TF-TG identification methods were also tested with SND1 and gl3 overexpression transcriptomic data, Huber-ENET and MSE-ENET outperformed all other methods when genome-wide predictions were performed. The TF-TG identification methods fill the gap of lacking a method for genome-wide TG prediction of a TF, and potential for validating ChIP/DAP-seq results, while the two Net-based methods are instrumental for predicting pathway GRNs.
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Affiliation(s)
- Xuewei Cao
- Department of Mathematical Sciences, Michigan Technological University, Houghton, MI 49931, USA
| | - Ling Zhang
- Computational Science and Engineering Program, Michigan Technological University, Houghton, MI 49931, USA
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA
| | - Md Khairul Islam
- Computational Science and Engineering Program, Michigan Technological University, Houghton, MI 49931, USA
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA
| | - Mingxia Zhao
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
| | - Cheng He
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
| | - Kui Zhang
- Department of Mathematical Sciences, Michigan Technological University, Houghton, MI 49931, USA
| | - Sanzhen Liu
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
| | - Qiuying Sha
- Department of Mathematical Sciences, Michigan Technological University, Houghton, MI 49931, USA
| | - Hairong Wei
- Department of Mathematical Sciences, Michigan Technological University, Houghton, MI 49931, USA
- Computational Science and Engineering Program, Michigan Technological University, Houghton, MI 49931, USA
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA
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Zhao M, Peng Z, Qin Y, Tamang TM, Zhang L, Tian B, Chen Y, Liu Y, Zhang J, Lin G, Zheng H, He C, Lv K, Klaus A, Marcon C, Hochholdinger F, Trick HN, Liu Y, Cho MJ, Park S, Wei H, Zheng J, White FF, Liu S. Bacterium-enabled transient gene activation by artificial transcription factors for resolving gene regulation in maize. THE PLANT CELL 2023; 35:2736-2749. [PMID: 37233025 PMCID: PMC10396389 DOI: 10.1093/plcell/koad155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 04/11/2023] [Accepted: 05/04/2023] [Indexed: 05/27/2023]
Abstract
Understanding gene regulatory networks is essential to elucidate developmental processes and environmental responses. Here, we studied regulation of a maize (Zea mays) transcription factor gene using designer transcription activator-like effectors (dTALes), which are synthetic Type III TALes of the bacterial genus Xanthomonas and serve as inducers of disease susceptibility gene transcription in host cells. The maize pathogen Xanthomonas vasicola pv. vasculorum was used to introduce 2 independent dTALes into maize cells to induced expression of the gene glossy3 (gl3), which encodes a MYB transcription factor involved in biosynthesis of cuticular wax. RNA-seq analysis of leaf samples identified, in addition to gl3, 146 genes altered in expression by the 2 dTALes. Nine of the 10 genes known to be involved in cuticular wax biosynthesis were upregulated by at least 1 of the 2 dTALes. A gene previously unknown to be associated with gl3, Zm00001d017418, which encodes aldehyde dehydrogenase, was also expressed in a dTALe-dependent manner. A chemically induced mutant and a CRISPR-Cas9 mutant of Zm00001d017418 both exhibited glossy leaf phenotypes, indicating that Zm00001d017418 is involved in biosynthesis of cuticular waxes. Bacterial protein delivery of dTALes proved to be a straightforward and practical approach for the analysis and discovery of pathway-specific genes in maize.
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Affiliation(s)
- Mingxia Zhao
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
| | - Zhao Peng
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA
- College of Plant Protection, Jilin Agricultural University, Changchun, Jilin 130118, China
| | - Yang Qin
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Tej Man Tamang
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
| | - Ling Zhang
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA
| | - Bin Tian
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
| | - Yueying Chen
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
| | - Yan Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Junli Zhang
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA
| | - Guifang Lin
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
| | - Huakun Zheng
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
| | - Cheng He
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
| | - Kaiwen Lv
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Heilongjiang 150040, China
| | - Alina Klaus
- INRES, Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, Bonn 53113, Germany
| | - Caroline Marcon
- INRES, Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, Bonn 53113, Germany
| | - Frank Hochholdinger
- INRES, Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, Bonn 53113, Germany
| | - Harold N Trick
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
| | - Yunjun Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Myeong-Je Cho
- Innovative Genomics Institute, University of California, Berkeley, CA 94704, USA
| | - Sunghun Park
- Department of Horticulture and Natural Resources, Kansas State University, Manhattan, KS 66506, USA
| | - Hairong Wei
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA
| | - Jun Zheng
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Frank F White
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA
| | - Sanzhen Liu
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
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10
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Li M, Dong H, Li J, Dai X, Lin J, Li S, Zhou C, Chiang VL, Li W. PtrVCS2 Regulates Drought Resistance by Changing Vessel Morphology and Stomatal Closure in Populus trichocarpa. Int J Mol Sci 2023; 24:ijms24054458. [PMID: 36901889 PMCID: PMC10003473 DOI: 10.3390/ijms24054458] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/12/2023] [Accepted: 02/16/2023] [Indexed: 03/12/2023] Open
Abstract
Drought has severe effects on plant growth, forest productivity, and survival throughout the world. Understanding the molecular regulation of drought resistance in forest trees can enable effective strategic engineering of novel drought-resistant genotypes of tree species. In this study, we identified a gene, PtrVCS2, encoding a zinc finger (ZF) protein of the ZF-homeodomain transcription factor in Populus trichocarpa (Black Cottonwood) Torr. & A. Gray. ex Hook. Overexpression of PtrVCS2 (OE-PtrVCS2) in P. trichocarpa resulted in reduced growth, a higher proportion of smaller stem vessels, and strong drought-resistance phenotypes. Stomatal movement experiments revealed that the OE-PtrVCS2 transgenics showed lower stomata apertures than wild-type plants under drought conditions. RNA-seq analysis of the OE-PtrVCS2 transgenics showed that PtrVCS2 regulates the expression of multiple genes involved in regulation of stomatal opening and closing, particularly the PtrSULTR3;1-1 gene, and several genes related to cell wall biosynthesis, such as PtrFLA11-12 and PtrPR3-3. Moreover, we found that the water use efficiency of the OE-PtrVCS2 transgenic plants was consistently higher than that of wild type plants when subjected to chronic drought stress. Taken together, our results suggest that PtrVCS2 plays a positive role in improving drought adaptability and resistance in P. trichocarpa.
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Affiliation(s)
- Meng Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Hao Dong
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Jiyuan Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Xiufang Dai
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Jiaojiao Lin
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Shuang Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Chenguang Zhou
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - 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
| | - Wei Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- Correspondence:
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11
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Tung CC, Kuo SC, Yang CL, Yu JH, Huang CE, Liou PC, Sun YH, Shuai P, Su JC, Ku C, Lin YCJ. Single-cell transcriptomics unveils xylem cell development and evolution. Genome Biol 2023; 24:3. [PMID: 36624504 PMCID: PMC9830878 DOI: 10.1186/s13059-022-02845-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 12/31/2022] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Xylem, the most abundant tissue on Earth, is responsible for lateral growth in plants. Typical xylem has a radial system composed of ray parenchyma cells and an axial system of fusiform cells. In most angiosperms, fusiform cells comprise vessel elements for water transportation and libriform fibers for mechanical support, while both functions are performed by tracheids in other vascular plants such as gymnosperms. Little is known about the developmental programs and evolutionary relationships of these xylem cell types. RESULTS Through both single-cell and laser capture microdissection transcriptomic profiling, we determine the developmental lineages of ray and fusiform cells in stem-differentiating xylem across four divergent woody angiosperms. Based on cross-species analyses of single-cell clusters and overlapping trajectories, we reveal highly conserved ray, yet variable fusiform, lineages across angiosperms. Core eudicots Populus trichocarpa and Eucalyptus grandis share nearly identical fusiform lineages, whereas the more basal angiosperm Liriodendron chinense has a fusiform lineage distinct from that in core eudicots. The tracheids in the basal eudicot Trochodendron aralioides, an evolutionarily reversed trait, exhibit strong transcriptomic similarity to vessel elements rather than libriform fibers. CONCLUSIONS This evo-devo framework provides a comprehensive understanding of the formation of xylem cell lineages across multiple plant species spanning over a hundred million years of evolutionary history.
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Affiliation(s)
- Chia-Chun Tung
- Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan
| | - Shang-Che Kuo
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, 10617, Taiwan
| | - Chia-Ling Yang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Jhong-He Yu
- Institute of Plant Biology, National Taiwan University, Taipei, 10617, Taiwan
| | - Chia-En Huang
- Institute of Plant Biology, National Taiwan University, Taipei, 10617, Taiwan
| | - Pin-Chien Liou
- Institute of Plant Biology, National Taiwan University, Taipei, 10617, Taiwan
| | - Ying-Hsuan Sun
- Department of Forestry, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Peng Shuai
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jung-Chen Su
- Department of Pharmacy, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan
| | - Chuan Ku
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, 10617, Taiwan.
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan.
| | - Ying-Chung Jimmy Lin
- Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan.
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, 10617, Taiwan.
- Institute of Plant Biology, National Taiwan University, Taipei, 10617, Taiwan.
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12
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Dai X, Zhai R, Lin J, Wang Z, Meng D, Li M, Mao Y, Gao B, Ma H, Zhang B, Sun Y, Li S, Zhou C, Lin YCJ, Wang JP, Chiang VL, Li W. Cell-type-specific PtrWOX4a and PtrVCS2 form a regulatory nexus with a histone modification system for stem cambium development in Populus trichocarpa. NATURE PLANTS 2023; 9:96-111. [PMID: 36624255 PMCID: PMC9873556 DOI: 10.1038/s41477-022-01315-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 11/17/2022] [Indexed: 05/20/2023]
Abstract
Stem vascular cambium cells in forest trees produce wood for materials and energy. WOX4 affects the proliferation of such cells in Populus. Here we show that PtrWOX4a is the most highly expressed stem vascular-cambium-specific (VCS) gene in P. trichocarpa, and its expression is controlled by the product of the second most highly expressed VCS gene, PtrVCS2, encoding a zinc finger protein. PtrVCS2 binds to the PtrWOX4a promoter as part of a PtrWOX13a-PtrVCS2-PtrGCN5-1-PtrADA2b-3 protein tetramer. PtrVCS2 prevented the interaction between PtrGCN5-1 and PtrADA2b-3, resulting in H3K9, H3K14 and H3K27 hypoacetylation at the PtrWOX4a promoter, which led to fewer cambium cell layers. These effects on cambium cell proliferation were consistent across more than 20 sets of transgenic lines overexpressing individual genes, gene-edited mutants and RNA interference lines in P. trichocarpa. We propose that the tetramer-PtrWOX4a system may coordinate genetic and epigenetic regulation to maintain normal vascular cambium development for wood formation.
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Affiliation(s)
- Xiufang Dai
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Rui Zhai
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Jiaojiao Lin
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Zhifeng Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- National Key Laboratory of Plant Molecular Genetics and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Dekai Meng
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Meng Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Yuli Mao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Boyuan Gao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Hongyan Ma
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Baofeng Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Yi Sun
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Shuang Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Chenguang Zhou
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Ying-Chung Jimmy Lin
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- Department of Life Sciences and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, Taiwan, China
| | - Jack P Wang
- 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, USA
| | - 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, USA
| | - Wei Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China.
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13
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Yi N, Yang H, Zhang X, Pian R, Li H, Zeng W, Wu AM. The physiological and transcriptomic study of secondary growth in Neolamarckia cadamba stimulated by the ethylene precursor ACC. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 190:35-46. [PMID: 36096025 DOI: 10.1016/j.plaphy.2022.08.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 08/14/2022] [Accepted: 08/31/2022] [Indexed: 06/15/2023]
Abstract
Though many biological roles of ethylene have been investigated intensively, the molecular mechanism of ethylene's action in woody plants remains unclear. In this study, we investigated the effects of exogenous 1-aminocyclopropane-1-carboxylic acid (ACC), the precursor of ethylene, on the growth of Neolamarckia cadamba seedlings, a fast-growing tropical tree. After 14 days of ACC treatment, the plants showed a reduced physiological morphology while stem diameter increased; however, this did not occur after the addition of 1-MCP. Meanwhile, the lignin content of N. cadamba also increased. Transcriptome analysis revealed that the expression of the ethylene biosynthesis and signaling genes ACC oxidase (ACO) and ethylene insensitive 3 (EIN3) were up-regulated mainly at the 6th hour and the 3rd day of the ACC treatment, respectively. The transcription levels of transcription factors, mainly in the basic helix-loop-helix (bHLH), ethylene response factor (ERF), WRKY and v-myb avian myeloblastosis viral oncogene homolog (MYB) families, involved in the ethylene signaling and secondary growth also increased significantly. Furthermore, in accordance to the increased lignification of the stem, the transcriptional level of key enzymes in the phenylalanine pathway were elevated after the ACC treatment. Our results revealed the physiological and molecular mechanisms underlying the secondary growth stimulated by exogenous ACC treatment on N. cadamba seedlings.
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Affiliation(s)
- Na Yi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Haoqiang Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Xintong Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Ruiqi Pian
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Huiling Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Wei Zeng
- The State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A & F University, Hangzhou, 311300, China.
| | - Ai-Min Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China.
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14
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Payyavula RS, Badmi R, Jawdy SS, Rodriguez M, Gunter L, Sykes RW, Winkeler KA, Collins CM, Rottmann WH, Chen J, Yang X, Tuskan GA, Kalluri UC. Biomass formation and sugar release efficiency of Populus modified by altered expression of a NAC transcription factor. PLANT DIRECT 2022; 6:e419. [PMID: 35979037 PMCID: PMC9373907 DOI: 10.1002/pld3.419] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 05/15/2022] [Accepted: 06/10/2022] [Indexed: 06/15/2023]
Abstract
Woody biomass is an important feedstock for biofuel production. Manipulation of wood properties that enable efficient conversion of biomass to biofuel reduces cost of biofuel production. Wood cell wall composition is regulated at several levels that involve expression of transcription factors such as wood-/secondary cell wall-associated NAC domains (WND or SND). In Arabidopsis thaliana, SND1 regulates cell wall composition through activation of its down-stream targets such as MYBs. The functional aspects of SND1 homologs in the woody Populus have been studied through transgenic manipulation. In this study, we investigated the role of PdWND1B, Populus SND1 sequence ortholog, in wood formation using transgenic manipulation through over-expression or silencing under the control of a vascular-specific 4-coumarate-CoA ligase (4CL) promoter. As compared with control plants, PdWND1B-RNAi plants were shorter in height, with significantly reduced stem diameter and dry biomass, whereas there were no significant differences in growth and productivity of PdWND1B over-expression plants. Conversely, PdWND1B over-expression lines showed a significant reduction in cellulose and increase in lignin content, whereas there was no significant impact on lignin content of downregulated lines. Stem carbohydrate composition analysis revealed a decrease in glucose, mannose, arabinose, and galactose, but an increase in xylose in the over-expression lines. Transcriptome analysis revealed upregulation of several downstream transcription factors and secondary cell wall related structural genes in the PdWND1B over-expression lines, partly explaining the observed phenotypic changes in cell wall chemistry. Relative to the control, glucose release efficiency and ethanol production from stem biomass was significantly reduced in over-expression lines. Our results show that PdWND1B is an important factor determining biomass productivity, cell wall chemistry and its conversion to biofuels in Populus.
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Affiliation(s)
- Raja S. Payyavula
- BioEnergy Science Centre, Center for Bioenergy Innovation and Biosciences DivisionOak Ridge National LaboratoryOak RidgeTennesseeUSA
| | - Raghuram Badmi
- BioEnergy Science Centre, Center for Bioenergy Innovation and Biosciences DivisionOak Ridge National LaboratoryOak RidgeTennesseeUSA
| | - Sara S. Jawdy
- BioEnergy Science Centre, Center for Bioenergy Innovation and Biosciences DivisionOak Ridge National LaboratoryOak RidgeTennesseeUSA
| | - Miguel Rodriguez
- BioEnergy Science Centre, Center for Bioenergy Innovation and Biosciences DivisionOak Ridge National LaboratoryOak RidgeTennesseeUSA
| | - Lee Gunter
- BioEnergy Science Centre, Center for Bioenergy Innovation and Biosciences DivisionOak Ridge National LaboratoryOak RidgeTennesseeUSA
| | - Robert W. Sykes
- The Biosciences CenterNational Renewable Energy LaboratoryGoldenColoradoUSA
| | | | | | | | - Jin‐Gui Chen
- BioEnergy Science Centre, Center for Bioenergy Innovation and Biosciences DivisionOak Ridge National LaboratoryOak RidgeTennesseeUSA
| | - Xiaohan Yang
- BioEnergy Science Centre, Center for Bioenergy Innovation and Biosciences DivisionOak Ridge National LaboratoryOak RidgeTennesseeUSA
| | - Gerald A Tuskan
- BioEnergy Science Centre, Center for Bioenergy Innovation and Biosciences DivisionOak Ridge National LaboratoryOak RidgeTennesseeUSA
| | - Udaya C. Kalluri
- BioEnergy Science Centre, Center for Bioenergy Innovation and Biosciences DivisionOak Ridge National LaboratoryOak RidgeTennesseeUSA
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15
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Xylem Transcriptome Analysis in Contrasting Wood Phenotypes of Eucalyptus urophylla × tereticornis Hybrids. FORESTS 2022. [DOI: 10.3390/f13071102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
An investigation of the effects of two important post-transcriptional regulatory mechanisms, gene transcription and alternative splicing (AS), on the wood formation of Eucalyptusurophylla × tereticornis, an economic tree species widely planted in southern China, was carried out. We performed RNA-seq on E. urophylla × tereticornis hybrids with highly contrasting wood basic density (BD), cellulose content (CC), hemicellulose content (HC), and lignin content (LC). Signals of strong differentially expressed genes (DEGs) and differentially spliced genes (DSGs) were detected in all four groups of wood properties, suggesting that gene transcription and selective splicing may have important regulatory roles in wood properties. We found that there was little overlap between DEGs and DSGs in groups of the same trait. Furthermore, the key DEGs and DSGs that were detected simultaneously in the four groups tended to be enriched in different Gene Ontology terms, Kyoto Encyclopedia of Genes and Genomes pathways, and transcription factors. These results implied that regulation of gene transcription and AS is controlled by independent regulatory systems in wood formation. Lastly, we detected transcript levels of known wood biosynthetic genes and found that 79 genes encoding mainly enzymes or proteins such as UGT, LAC, CAD, and CESA may be involved in the positive or negative regulation of wood properties. This study reveals potential molecular mechanisms that may regulate wood formation and will contribute to the genetic improvement of Eucalyptus.
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16
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Du C, Sun P, Cheng X, Zhang L, Wang L, Hu J. QTL mapping of drought-related traits in the hybrids of Populus deltoides 'Danhong'×Populus simonii 'Tongliao1'. BMC PLANT BIOLOGY 2022; 22:238. [PMID: 35545765 PMCID: PMC9092850 DOI: 10.1186/s12870-022-03613-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 04/21/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Poplar trees provide a large amount of wood material, but many parts of the world are arid or semi-arid areas because of insufficient annual precipitation, which seriously affects the growth of poplar trees. Populus simonii 'Tongliao1' shows strong tolerance to stress environments, and Populus deltoides 'Danhong' shows a stronger growth rate in a suitable environment. To identify drought tolerance-related QTLs and genes, an F1 population derived from the cross between the 'Danhong' and 'Tongliao 1' Populus was assessed under drought stress. RESULTS We measured drought-related traits such as the relative height growth, relative diameter growth, leaf senescence number, specific leaf area, and leaf relative water content in the population under control and drought environments. The results showed that drought stress reduced the plant height relative growth, ground diameter relative growth, specific leaf area and leaf relative water content and increased the number of leaf drops. A total of 208 QTLs were identified by QTL mapping analysis, and they consisted of 92, 63 and 53 QTLs under control, drought stress treatment and drought index conditions, respectively. A molecular identification marker for drought tolerance, np2841, which was associated with a QTL (qDLRWC-LG10-1) for relative leaf water content, was initially developed. We mined 187 candidate genes for QTL regions of five traits under a drought environment. The reference genome annotation for Populus trichocarpa and a homologous gene analysis of Arabidopsis thaliana identified two candidate genes, Potri.003G171300 and Potri.012G123900, with significant functions in response to drought stress. We identified five key regulatory genes (Potri.006G273500, Potri.007G111500, Potri.007G111600, Potri.007G111700, and Potri.007G111800) related to drought tolerance through the poplar coexpression network. CONCLUSION In this study, our results indicate that the QTLs can effectively enhance the drought tolerance of poplar. It is a step closer towards unravelling the genetic basis of poplar drought tolerance-related traits, and to providing validated candidate genes and molecular markers for future genetic improvement.
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Affiliation(s)
- Changjian Du
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Pei Sun
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100093, China
| | - Xingqi Cheng
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Lei Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Lijuan Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Jianjun Hu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China.
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17
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Liu H, Gao J, Sun J, Li S, Zhang B, Wang Z, Zhou C, Sulis DB, Wang JP, Chiang VL, Li W. Dimerization of PtrMYB074 and PtrWRKY19 mediates transcriptional activation of PtrbHLH186 for secondary xylem development in Populus trichocarpa. THE NEW PHYTOLOGIST 2022; 234:918-933. [PMID: 35152419 PMCID: PMC9314101 DOI: 10.1111/nph.18028] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 02/02/2022] [Indexed: 05/28/2023]
Abstract
Wood formation is controlled by transcriptional regulatory networks (TRNs) involving regulatory homeostasis determined by combinations of transcription factor (TF)-DNA and TF-TF interactions. Functions of TF-TF interactions in wood formation are still in the early stages of identification. PtrMYB074 is a woody dicot-specific TF in a TRN for wood formation in Populus trichocarpa. Here, using yeast two-hybrid and bimolecular fluorescence complementation, we conducted a genome-wide screening for PtrMYB074 interactors and identified 54 PtrMYB074-TF pairs. Of these pairs, 53 are novel. We focused on the PtrMYB074-PtrWRKY19 pair, the most highly expressed and xylem-specific interactor, and its direct transregulatory target, PtrbHLH186, the xylem-specific one of the pair's only two direct TF target genes. Using transient and CRISPR-mediated transgenesis in P. trichocarpa coupled with chromatin immunoprecipitation and electrophoretic mobility shift assays, we demonstrated that PtrMYB074 is recruited by PtrWRKY19 and that the PtrMYB074-PtrWRKY19 dimers are required to transactive PtrbHLH186. Overexpressing PtrbHLH186 in P. trichocarpa resulted in retarded plant growth, increased guaiacyl lignin, a higher proportion of smaller stem vessels and strong drought-tolerant phenotypes. Knowledge of the PtrMYB074-PtrWRKY19-PtrbHLH186 regulation may help design genetic controls of optimal growth and wood formation to maximize beneficial wood properties while minimizing negative effects on growth.
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Affiliation(s)
- Huizi Liu
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbin150040China
| | - Jinghui Gao
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbin150040China
| | - Jiatong Sun
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbin150040China
| | - Shuang Li
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbin150040China
| | - Baofeng Zhang
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbin150040China
| | - Zhuwen Wang
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbin150040China
| | - Chenguang Zhou
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbin150040China
| | - Daniel Barletta Sulis
- Forest Biotechnology GroupDepartment of Forestry and Environmental ResourcesNorth Carolina State UniversityRaleighNC27695USA
| | - Jack P. Wang
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbin150040China
- Forest Biotechnology GroupDepartment of Forestry and Environmental ResourcesNorth Carolina State UniversityRaleighNC27695USA
| | - Vincent L. Chiang
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbin150040China
- Forest Biotechnology GroupDepartment of Forestry and Environmental ResourcesNorth Carolina State UniversityRaleighNC27695USA
| | - Wei Li
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbin150040China
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18
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Luo J, Huang S, Wang M, Zhang R, Zhao D, Yang Y, Wang F, Wang Z, Tang R, Wang L, Xiao H, Yang B, Li C. Characterization of the Transcriptome and Proteome of Brassica napus Reveals the Close Relation between DW871 Dwarfing Phenotype and Stalk Tissue. PLANTS (BASEL, SWITZERLAND) 2022; 11:413. [PMID: 35161394 PMCID: PMC8838640 DOI: 10.3390/plants11030413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 01/29/2022] [Accepted: 01/29/2022] [Indexed: 06/14/2023]
Abstract
Rapeseed is a significant oil-bearing cash crop. As a hybrid crop, Brassica napus L. produces a high yield, but it also has drawbacks such as a tall stalk, easy lodging, and is not suitable for mechanized production. To address these concerns, we created the DW871 rapeseed dwarf variety, which has a high yield, high oil content, and is suitable for mechanized production. To fully comprehend the dwarfing mechanism of DW871 and provide a theoretical foundation for future applications of the variety, we used transcriptome and proteome sequencing to identify genes and proteins associated with the dwarfing phenotype, using homologous high-stalk material HW871 as a control. By RNA-seq and iTRAQ, we discovered 8665 DEGs and 50 DAPs. Comprehensive transcription and translation level analysis revealed 25 correlations, 23 of which have the same expression trend, involving monolignin synthesis, pectin-lignin assembly, lignification, glucose modification, cell wall composition and architecture, cell morphology, vascular bundle development, and stalk tissue composition and architecture. As a result of these results, we can formulate a hypothesis about the DW871 dwarfing phenotype: plant hormone signal transduction, such as IAA and BRs, is linked to the formation of dwarf phenotypes, and metabolic pathways related to lignin synthesis, such as phenylpropane biosynthesis, also play a role. Our works will contribute to a better understanding of the genes and proteins involved in the rapeseed dwarf phenotype, and we will propose new insights into the dwarfing mechanism of Brassica napus L.
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Affiliation(s)
- Jing Luo
- Guizhou Oil Crops Institute, Guizhou Academy of Agriculture Sciences, No. 502 Xinzhong Road, Jinxin Community, Huaxi District, Guiyang 550006, China; (J.L.); (S.H.); (Y.Y.); (F.W.); (Z.W.); (R.T.); (L.W.); (H.X.); (B.Y.)
- School of Life Sciences, Guizhou Normal University, Huaxi University City, Gui’an New District, Guiyang 550025, China;
- Guizhou Plant Conservation Technology Center, Guizhou Academy of Agricultural Sciences, No. 502 Xinzhong Road, Jinxin Community, Huaxi District, Guiyang 550006, China;
| | - Sha Huang
- Guizhou Oil Crops Institute, Guizhou Academy of Agriculture Sciences, No. 502 Xinzhong Road, Jinxin Community, Huaxi District, Guiyang 550006, China; (J.L.); (S.H.); (Y.Y.); (F.W.); (Z.W.); (R.T.); (L.W.); (H.X.); (B.Y.)
- Guizhou Plant Conservation Technology Center, Guizhou Academy of Agricultural Sciences, No. 502 Xinzhong Road, Jinxin Community, Huaxi District, Guiyang 550006, China;
| | - Min Wang
- School of Life Sciences, Guizhou Normal University, Huaxi University City, Gui’an New District, Guiyang 550025, China;
| | - Ruimao Zhang
- Guizhou Rapeseed Institute, Guizhou Academy of Agriculture Sciences, No. 111 Duyun Road, Guanshanhu District, Guiyang 520115, China;
| | - Degang Zhao
- Guizhou Plant Conservation Technology Center, Guizhou Academy of Agricultural Sciences, No. 502 Xinzhong Road, Jinxin Community, Huaxi District, Guiyang 550006, China;
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation Center for Mountainous Region (Ministry of Education), Institute of Agro-Bioengineering, College of Life Sciences, Guizhou University, 2708 Huaxi Avenue South Section, Huaxi District, Guiyang 550025, China
| | - Yuanyu Yang
- Guizhou Oil Crops Institute, Guizhou Academy of Agriculture Sciences, No. 502 Xinzhong Road, Jinxin Community, Huaxi District, Guiyang 550006, China; (J.L.); (S.H.); (Y.Y.); (F.W.); (Z.W.); (R.T.); (L.W.); (H.X.); (B.Y.)
- Guizhou Plant Conservation Technology Center, Guizhou Academy of Agricultural Sciences, No. 502 Xinzhong Road, Jinxin Community, Huaxi District, Guiyang 550006, China;
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation Center for Mountainous Region (Ministry of Education), Institute of Agro-Bioengineering, College of Life Sciences, Guizhou University, 2708 Huaxi Avenue South Section, Huaxi District, Guiyang 550025, China
| | - Fang Wang
- Guizhou Oil Crops Institute, Guizhou Academy of Agriculture Sciences, No. 502 Xinzhong Road, Jinxin Community, Huaxi District, Guiyang 550006, China; (J.L.); (S.H.); (Y.Y.); (F.W.); (Z.W.); (R.T.); (L.W.); (H.X.); (B.Y.)
- Guizhou Plant Conservation Technology Center, Guizhou Academy of Agricultural Sciences, No. 502 Xinzhong Road, Jinxin Community, Huaxi District, Guiyang 550006, China;
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation Center for Mountainous Region (Ministry of Education), Institute of Agro-Bioengineering, College of Life Sciences, Guizhou University, 2708 Huaxi Avenue South Section, Huaxi District, Guiyang 550025, China
| | - Zhuanzhuan Wang
- Guizhou Oil Crops Institute, Guizhou Academy of Agriculture Sciences, No. 502 Xinzhong Road, Jinxin Community, Huaxi District, Guiyang 550006, China; (J.L.); (S.H.); (Y.Y.); (F.W.); (Z.W.); (R.T.); (L.W.); (H.X.); (B.Y.)
- Guizhou Plant Conservation Technology Center, Guizhou Academy of Agricultural Sciences, No. 502 Xinzhong Road, Jinxin Community, Huaxi District, Guiyang 550006, China;
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation Center for Mountainous Region (Ministry of Education), Institute of Agro-Bioengineering, College of Life Sciences, Guizhou University, 2708 Huaxi Avenue South Section, Huaxi District, Guiyang 550025, China
| | - Rong Tang
- Guizhou Oil Crops Institute, Guizhou Academy of Agriculture Sciences, No. 502 Xinzhong Road, Jinxin Community, Huaxi District, Guiyang 550006, China; (J.L.); (S.H.); (Y.Y.); (F.W.); (Z.W.); (R.T.); (L.W.); (H.X.); (B.Y.)
| | - Lulu Wang
- Guizhou Oil Crops Institute, Guizhou Academy of Agriculture Sciences, No. 502 Xinzhong Road, Jinxin Community, Huaxi District, Guiyang 550006, China; (J.L.); (S.H.); (Y.Y.); (F.W.); (Z.W.); (R.T.); (L.W.); (H.X.); (B.Y.)
| | - Huagui Xiao
- Guizhou Oil Crops Institute, Guizhou Academy of Agriculture Sciences, No. 502 Xinzhong Road, Jinxin Community, Huaxi District, Guiyang 550006, China; (J.L.); (S.H.); (Y.Y.); (F.W.); (Z.W.); (R.T.); (L.W.); (H.X.); (B.Y.)
| | - Bin Yang
- Guizhou Oil Crops Institute, Guizhou Academy of Agriculture Sciences, No. 502 Xinzhong Road, Jinxin Community, Huaxi District, Guiyang 550006, China; (J.L.); (S.H.); (Y.Y.); (F.W.); (Z.W.); (R.T.); (L.W.); (H.X.); (B.Y.)
| | - Chao Li
- Guizhou Oil Crops Institute, Guizhou Academy of Agriculture Sciences, No. 502 Xinzhong Road, Jinxin Community, Huaxi District, Guiyang 550006, China; (J.L.); (S.H.); (Y.Y.); (F.W.); (Z.W.); (R.T.); (L.W.); (H.X.); (B.Y.)
- Guizhou Plant Conservation Technology Center, Guizhou Academy of Agricultural Sciences, No. 502 Xinzhong Road, Jinxin Community, Huaxi District, Guiyang 550006, China;
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Zhuang Y, Chen S, Lian W, Xu L, Wang D, Wang C, Meng J, Tang X, Xu H, Wang S, Du L, Zhang Y, Zhou G, Chai G. A High-Throughput Screening System for Populus Wood-Associated Transcription Factors and Its Application to Lignin Regulation. FRONTIERS IN PLANT SCIENCE 2022; 12:715809. [PMID: 35095939 PMCID: PMC8795814 DOI: 10.3389/fpls.2021.715809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 12/09/2021] [Indexed: 06/14/2023]
Abstract
Wood formation of trees is a complex and costly developmental process, whose regulatory network is involved in the protein-protein and protein-DNA interactions. To detect such interactions in wood development, we developed a high-throughput screening system with 517 Gal4-AD-wood-associated transcription factors (TFs) library from Populus alba × P. glandulosa cv "84K." This system can be used for screening the upstream regulators and interacting proteins of targets by mating-based yeast-one hybrid (Y1H) and yeast-two-hybrid (Y2H) method, respectively. Multiple regulatory modules of lignin biosynthesis were identified based on this Populus system. Five TFs interacted with the 500-bp promoter fragment of PHENYLALANINE AMMONIA-LYASE 2 (PAL2), the first rate-limiting enzyme gene in the lignin biosynthesis pathway, and 10 TFs interacted with PaMYB4/LTF1, a key regulator of lignin biosynthesis. Some of these interactions were further validated by EMSA and BiFC assays. The TF-PaPAL2 promoter interaction and TF-PaMYB4 interaction revealed a complex mechanism governing the regulation of lignin synthesis in wood cells. Our high-throughput Y1H/Y2H screening system may be an efficient tool for studying regulatory network of wood formation in tree species.
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Affiliation(s)
- Yamei Zhuang
- College of Resources and Environment, Qingdao Agricultural University, Qingdao, China
- Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Sihui Chen
- Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Wenjun Lian
- College of Resources and Environment, Qingdao Agricultural University, Qingdao, China
| | - Li Xu
- College of Resources and Environment, Qingdao Agricultural University, Qingdao, China
| | - Dian Wang
- Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
| | - Congpeng Wang
- College of Resources and Environment, Qingdao Agricultural University, Qingdao, China
- Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Jie Meng
- College of Resources and Environment, Qingdao Agricultural University, Qingdao, China
- Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Xianfeng Tang
- Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Hua Xu
- Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Shumin Wang
- Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Lin Du
- Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Yang Zhang
- Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Gongke Zhou
- College of Resources and Environment, Qingdao Agricultural University, Qingdao, China
- Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Academy of Dongying Efficient Agricultural Technology and Industry on Saline and Alkaline Land in Collaboration With Qingdao Agricultural University, Dongying, China
| | - Guohua Chai
- College of Resources and Environment, Qingdao Agricultural University, Qingdao, China
- Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Academy of Dongying Efficient Agricultural Technology and Industry on Saline and Alkaline Land in Collaboration With Qingdao Agricultural University, Dongying, China
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20
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Yu J, Zhou C, Li D, Li S, Jimmy Lin YC, Wang JP, Chiang VL, Li W. A PtrLBD39-mediated transcriptional network regulates tension wood formation in Populus trichocarpa. PLANT COMMUNICATIONS 2022; 3:100250. [PMID: 35059630 PMCID: PMC8760142 DOI: 10.1016/j.xplc.2021.100250] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 09/10/2021] [Accepted: 10/19/2021] [Indexed: 05/29/2023]
Abstract
Tension wood (TW) is a specialized xylem tissue formed in angiosperm trees under gravitational stimulus or mechanical stresses (e.g., bending). The genetic regulation that underlies this important mechanism remains poorly understood. Here, we used laser capture microdissection of stem xylem cells coupled with full transcriptome RNA-sequencing to analyze TW formation in Populus trichocarpa. After tree bending, PtrLBD39 was the most significantly induced transcription factor gene; it has a phylogenetically paired homolog, PtrLBD22. CRISPR-based knockout of PtrLBD39/22 severely inhibited TW formation, reducing cellulose and increasing lignin content. Transcriptomic analyses of CRISPR-based PtrLBD39/22 double mutants showed that these two genes regulate a set of TW-related genes. Chromatin immunoprecipitation sequencing (ChIP-seq) was used to identify direct targets of PtrLBD39. We integrated transcriptomic analyses and ChIP-seq assays to construct a transcriptional regulatory network (TRN) mediated by PtrLBD39. In this TRN, PtrLBD39 directly regulates 26 novel TW-responsive transcription factor genes. Our work suggests that PtrLBD39 and PtrLBD22 specifically control TW formation by mediating a TW-specific TRN in Populus.
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Affiliation(s)
- Jing Yu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Chenguang Zhou
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Danning Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Shuang Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Ying-Chung Jimmy Lin
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- Department of Life Sciences and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, Taiwan 10617, China
| | - Jack P. Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- Department of Forestry and Environmental Resources, Forest Biotechnology Group, North Carolina State University, Raleigh, NC 27695, USA
| | - Vincent L. Chiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- Department of Forestry and Environmental Resources, Forest Biotechnology Group, North Carolina State University, Raleigh, NC 27695, USA
| | - Wei Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
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21
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Shen T, Xu M, Qi H, Feng Y, Yang Z, Xu M. Protoplast isolation and transcriptome analysis of developing xylem in Pinus massoniana (Pinaceae). Mol Biol Rep 2021; 49:1857-1869. [PMID: 34826048 DOI: 10.1007/s11033-021-06995-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 11/19/2021] [Indexed: 10/19/2022]
Abstract
BACKGROUND With active physiological and biochemical activities, tissue-specific protoplasts from cambial derivatives, could serve as a specific source for information on xylogenesis for softwood species resistant to stable genetic transformation and lacking available mutants. METHODS AND RESULTS In this study, protoplasts were isolated from developing xylem of the Chinese red pine, Pinus massoniana, by enzymolysis. High-quality RNAs were extracted from developing xylem and their protoplasts for constructing transcriptome libraries. Using Illumina HiSeq 2500 PE150 platform, a total of 362,328,426 clean paired-end reads (54.35G) were generated from multiple cDNA libraries and assembled into 146,422 unigenes. The transcriptome data were further analysed to identify 1567 differentially expressed genes (DEGs) between the isolated protoplasts and developing xylem of P. massoniana (Masson pine), 1126 DEGs were upregulated in protoplasts relative to developing xylem cells and 441 were downregulated. Most of the differentially expressed genes in biological process terms are related to plant response, which may be due to the response to cell wall removal. Further, the expression pattern of 71 unigenes involved in lignin biosynthesis was verified by RNA-seq. CONCLUSIONS This study is the first to report the transcriptome profiles of the developing xylem and its protoplasts of coniferous trees, which provide a new perspective and valuable resource for tracking transcriptional regulatory events in wood formation of Masson pine.
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Affiliation(s)
- Tengfei Shen
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, Nanning, 530002, China.,Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology Ministry of Education, Nanjing Forestry University, Nanjing, 210037, China
| | - Mengxuan Xu
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology Ministry of Education, Nanjing Forestry University, Nanjing, 210037, China
| | - Haoran Qi
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology Ministry of Education, Nanjing Forestry University, Nanjing, 210037, China
| | - Yuanheng Feng
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, Nanning, 530002, China
| | - Zhangqi Yang
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, Nanning, 530002, China
| | - Meng Xu
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology Ministry of Education, Nanjing Forestry University, Nanjing, 210037, China.
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22
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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. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 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] [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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23
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Liu Y, Cao S, Liu X, Li Y, Wang B, Sun Y, Zhang C, Guo X, Li H, Lu H. PtrLAC16 plays a key role in catalyzing lignin polymerization in the xylem cell wall of Populus. Int J Biol Macromol 2021; 188:983-992. [PMID: 34403677 DOI: 10.1016/j.ijbiomac.2021.08.077] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 08/06/2021] [Accepted: 08/10/2021] [Indexed: 10/20/2022]
Abstract
Plant laccases have been proposed to participate in lignin biosynthesis. However, there is no direct evidence that individual laccases in Populus can polymerize lignin monomers and alter cell wall structure. Here, a Populus laccase, PtrLAC16, was expressed and purified in a eukaryotic system. Enzymatic analysis of PtrLAC16 showed that it could polymerize lignin monomers in vitro. PtrLAC16 preferred sinapyl alcohol, and this preference is associated with an altered S/G ratio in transgenic Populus lines. PtrLAC16 was localized exclusively in the cell walls of stem vascular tissue, and a reduction in PtrLAC16 expression led to a significant decrease in lignin content and altered cell wall structure. There was a direct correlation between the inhibition of PtrLAC16 expression and structural changes in the stem cell wall of Populus. This study provides direct evidence that PtrLAC16 plays a key role in the polymerization of lignin monomers, especially for sinapyl lignin, and affects the formation of xylem cell walls in Populus.
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Affiliation(s)
- Yadi Liu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China; College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Shan Cao
- School of Management, Qingdao Agricultural University, Shandong 266109, China
| | - Xiatong Liu
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Ying Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
| | - Bing Wang
- Guizhou Academy of Tobacco Science, Molecular Genetics Key Laboratory of China Tobacco, Guiyang 550081, China
| | - Yu Sun
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Chong Zhang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Xiaorui Guo
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Hui Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China; College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Hai Lu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China; College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China.
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24
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Tsai NC, Hsu TS, Kuo SC, Kao CT, Hung TH, Lin DG, Yeh CS, Chu CC, Lin JS, Lin HH, Ko CY, Chang TH, Su JC, Lin YCJ. Large-scale data analysis for robotic yeast one-hybrid platforms and multi-disciplinary studies using GateMultiplex. BMC Biol 2021; 19:214. [PMID: 34560855 PMCID: PMC8461970 DOI: 10.1186/s12915-021-01140-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 09/03/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Yeast one-hybrid (Y1H) is a common technique for identifying DNA-protein interactions, and robotic platforms have been developed for high-throughput analyses to unravel the gene regulatory networks in many organisms. Use of these high-throughput techniques has led to the generation of increasingly large datasets, and several software packages have been developed to analyze such data. We previously established the currently most efficient Y1H system, meiosis-directed Y1H; however, the available software tools were not designed for processing the additional parameters suggested by meiosis-directed Y1H to avoid false positives and required programming skills for operation. RESULTS We developed a new tool named GateMultiplex with high computing performance using C++. GateMultiplex incorporated a graphical user interface (GUI), which allows the operation without any programming skills. Flexible parameter options were designed for multiple experimental purposes to enable the application of GateMultiplex even beyond Y1H platforms. We further demonstrated the data analysis from other three fields using GateMultiplex, the identification of lead compounds in preclinical cancer drug discovery, the crop line selection in precision agriculture, and the ocean pollution detection from deep-sea fishery. CONCLUSIONS The user-friendly GUI, fast C++ computing speed, flexible parameter setting, and applicability of GateMultiplex facilitate the feasibility of large-scale data analysis in life science fields.
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Affiliation(s)
- Ni-Chiao Tsai
- Department of Life Science and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, 10617, Taiwan
| | - Tzu-Shu Hsu
- Department of Pharmacy, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan
| | - Shang-Che Kuo
- Department of Pharmacy, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, 10617, Taiwan
| | - Chung-Ting Kao
- Department of Life Science and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, 10617, Taiwan
| | - Tzu-Huan Hung
- Biotechnology Division, Taiwan Agricultural Research Institute, Taichung, 41362, Taiwan
| | - Da-Gin Lin
- Biotechnology Division, Taiwan Agricultural Research Institute, Taichung, 41362, Taiwan
| | - Chung-Shu Yeh
- Genomics Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Chia-Chen Chu
- Department of Life Science and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, 10617, Taiwan
| | - Jeng-Shane Lin
- Department of Life Sciences, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Hsin-Hung Lin
- Department of Horticulture and Biotechnology, Chinese Culture University, Taipei, 11114, Taiwan
| | - Chia-Ying Ko
- Department of Life Sciences and Institute of Fisheries Science, National Taiwan University, Taipei, 10617, Taiwan
| | - Tien-Hsien Chang
- Genomics Research Center, Academia Sinica, Taipei, 11529, Taiwan.
| | - Jung-Chen Su
- Department of Pharmacy, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan.
| | - Ying-Chung Jimmy Lin
- Department of Life Science and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, 10617, Taiwan.
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, 10617, Taiwan.
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25
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Liu X, Gao Y, Liao J, Miao M, Chen K, Xi F, Wei W, Wang H, Wang Y, Xu X, Reddy ASN, Gu L. Genome-wide profiling of circular RNAs, alternative splicing, and R-loops in stem-differentiating xylem of Populus trichocarpa. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:1294-1308. [PMID: 33570252 DOI: 10.1111/jipb.13081] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 02/08/2021] [Indexed: 06/12/2023]
Abstract
Circular RNAs (circRNAs) are a recently discovered type of non-coding RNA derived from pre-mRNAs. R-loops consist of a DNA:RNA hybrid and the associated single-stranded DNA. In Arabidopsis thaliana, circRNA:DNA R-loops regulate alternative splicing (AS) of SEPALLATA3 (SEP3). However, the occurrence and functions of circRNAs and R-loops in Populus trichocarpa are largely unexplored. Here, we performed circRNA-enriched sequencing in the stem-differentiating xylem (SDX) of P. trichocarpa and identified 2,742 distinct circRNAs, including circ-CESA4, circ-IRX7, and circ-GUX1, which are generated from genes involved in cellulose, and hemicellulose biosynthesis, respectively. To investigate the roles of circRNAs in modulating alternative splicing (AS), we detected 7,836 AS events using PacBio Iso-Seq and identified 634 circRNAs that overlapped with 699 AS events. Furthermore, using DNA:RNA hybrid immunoprecipitation followed by sequencing (DRIP-seq), we identified 8,932 R-loop peaks that overlapped with 181 circRNAs and 672 AS events. Notably, several SDX-related circRNAs overlapped with R-loop peaks, pointing to their possible roles in modulating AS in SDX. Indeed, overexpressing circ-IRX7 increased the levels of R-loop structures and decreased the frequency of intron retention in linear IRX7 transcripts. This study provides a valuable R-loop atlas resource and uncovers the interplay between circRNAs and AS in SDX of P. trichocarpa.
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Affiliation(s)
- Xuqing Liu
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yubang Gao
- Basic Forestry and Proteomics Research Center, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jiakai Liao
- Basic Forestry and Proteomics Research Center, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Miao Miao
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Kai Chen
- Basic Forestry and Proteomics Research Center, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Feihu Xi
- Basic Forestry and Proteomics Research Center, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wentao Wei
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Huihui Wang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yongsheng Wang
- Basic Forestry and Proteomics Research Center, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xi Xu
- Basic Forestry and Proteomics Research Center, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Anireddy S N Reddy
- Department of Biology and Program in Cell and Molecular Biology, Colorado State University, Fort Collins, Colorado, 80523, USA
| | - Lianfeng Gu
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
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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. FRONTIERS IN PLANT SCIENCE 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] [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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27
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Liu YL, Wang LJ, Li Y, Guo YH, Cao Y, Zhao ST. A Small Guanosine Triphosphate Binding Protein PagRabE1b Promotes Xylem Development in Poplar. FRONTIERS IN PLANT SCIENCE 2021; 12:686024. [PMID: 34149786 PMCID: PMC8213388 DOI: 10.3389/fpls.2021.686024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 05/14/2021] [Indexed: 06/12/2023]
Abstract
Rab GTPases are the subfamily of the small guanosine triphosphate (GTP)-binding proteins which participated in the regulation of various biological processes. Recent studies have found that plant Rabs play some specific functions. However, the functions of Rabs in xylem development in trees remain unclear. In this study, functional identification of PagRabE1b in Populus was performed. Quantitative reverse transcription PCR (qRT-PCR) results showed that PagRabE1b was highly accumulated in stems, especially in phloem and xylem tissues. Overexpression of PagRabE1b in poplar enhanced programmed cell death (PCD) and increased the growth rate and the secondary cell wall (SCW) thickness. Quantitative analysis of monosaccharide content showed that various monosaccharides were significantly increased in secondary xylem tissues of the overexpressed lines. Flow cytometry analysis revealed that the number of apoptotic cells in PagRabE1b-OE lines is more than a wild type (WT), which indicated that PagRabE1b may play an important role in PCD. Further studies showed that overexpression of PagRabE1b increased the expression level of genes involved in SCW biosynthesis, PCD, and autophagy. Collectively, the results suggest that PagRabE1b plays a positive role in promoting the xylem development of poplar.
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Affiliation(s)
- Ying-Li Liu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Li-Juan Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Co-innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Yu Li
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Ying-Hua Guo
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Yuan Cao
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Shu-Tang Zhao
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Co-innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
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28
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Liu B, Liu J, Yu J, Wang Z, Sun Y, Li S, Lin YCJ, Chiang VL, Li W, Wang JP. Transcriptional reprogramming of xylem cell wall biosynthesis in tension wood. PLANT PHYSIOLOGY 2021; 186:250-269. [PMID: 33793955 PMCID: PMC8154086 DOI: 10.1093/plphys/kiab038] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 01/04/2021] [Indexed: 05/02/2023]
Abstract
Tension wood (TW) is a specialized xylem tissue developed under mechanical/tension stress in angiosperm trees. TW development involves transregulation of secondary cell wall genes, which leads to altered wood properties for stress adaptation. We induced TW in the stems of black cottonwood (Populus trichocarpa, Nisqually-1) and identified two significantly repressed transcription factor (TF) genes: class B3 heat-shock TF (HSFB3-1) and MYB092. Transcriptomic analysis and chromatin immunoprecipitation (ChIP) were used to identify direct TF-DNA interactions in P. trichocarpa xylem protoplasts overexpressing the TFs. This analysis established a transcriptional regulatory network in which PtrHSFB3-1 and PtrMYB092 directly activate 8 and 11 monolignol genes, respectively. The TF-DNA interactions were verified for their specificity and transactivator roles in 35 independent CRISPR-based biallelic mutants and overexpression transgenic lines of PtrHSFB3-1 and PtrMYB092 in P. trichocarpa. The gene-edited trees (mimicking the repressed PtrHSFB3-1 and PtrMYB092 under tension stress) have stem wood composition resembling that of TW during normal growth and under tension stress (i.e., low lignin and high cellulose), whereas the overexpressors showed an opposite effect (high lignin and low cellulose). Individual overexpression of the TFs impeded lignin reduction under tension stress and restored high levels of lignin biosynthesis in the TW. This study offers biological insights to further uncover how metabolism, growth, and stress adaptation are coordinately regulated in trees.
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Affiliation(s)
- Baoguang Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- Department of Forestry, Beihua University, Jilin 132013, China
| | - Juan Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Jing Yu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Zhifeng Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Yi Sun
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Shuang Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Ying-Chung Jimmy Lin
- Department of Life Sciences, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - 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
| | - Wei Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - 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
- Author for communication:
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Wu W, Li J, Wang Q, Lv K, Du K, Zhang W, Li Q, Kang X, Wei H. Growth-regulating factor 5 (GRF5)-mediated gene regulatory network promotes leaf growth and expansion in poplar. THE NEW PHYTOLOGIST 2021; 230:612-628. [PMID: 33423287 PMCID: PMC8048564 DOI: 10.1111/nph.17179] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 12/28/2020] [Indexed: 05/07/2023]
Abstract
Although polyploid plants have larger leaves than their diploid counterparts, the molecular mechanisms underlying this difference (or trait) remain elusive. Differentially expressed genes (DEGs) between triploid and full-sib diploid poplar trees were identified from two transcriptomic data sets followed by a gene association study among DEGs to identify key leaf growth regulators. Yeast one-hybrid system, electrophoretic mobility shift assay, and dual-luciferase assay were employed to substantiate that PpnGRF5-1 directly regulated PpnCKX1. The interactions between PpnGRF5-1 and growth-regulating factor (GRF)-interacting factors (GIFs) were experimentally validated and a multilayered hierarchical regulatory network (ML-hGRN)-mediated by PpnGRF5-1 was constructed with top-down graphic Gaussian model (GGM) algorithm by combining RNA-sequencing data from its overexpression lines and DAP-sequencing data. PpnGRF5-1 is a negative regulator of PpnCKX1. Overexpression of PpnGRF5-1 in diploid transgenic lines resulted in larger leaves resembling those of triploids, and significantly increased zeatin and isopentenyladenine in the apical buds and third leaves. PpnGRF5-1 also interacted with GIFs to increase its regulatory diversity and capacity. An ML-hGRN-mediated by PpnGRF5-1 was obtained and could largely elucidate larger leaves. PpnGRF5-1 and the ML-hGRN-mediated by PpnGRF5-1 were underlying the leaf growth and development.
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Affiliation(s)
- Wenqi Wu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignBeijing Forestry UniversityBeijing100083China
| | - Jiang Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignBeijing Forestry UniversityBeijing100083China
| | - Qiao Wang
- State Key Laboratory of Tree Genetics and BreedingChinese Academy of ForestryBeijing100091China
| | - Kaiwen Lv
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbinHeilongjiang150040China
| | - Kang Du
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignBeijing Forestry UniversityBeijing100083China
| | - Wenli Zhang
- State Key Laboratory for Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjingJiangsu210095China
| | - Quanzi Li
- State Key Laboratory of Tree Genetics and BreedingChinese Academy of ForestryBeijing100091China
| | - Xiangyang Kang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignBeijing Forestry UniversityBeijing100083China
| | - Hairong Wei
- College of Forest Resources and Environmental ScienceMichigan Technological UniversityHoughtonMI49931USA
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30
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Kong L, Li Z, Song Q, Li X, Luo K. Construction of a Full-Length cDNA Over-Expressing Library to Identify Valuable Genes from Populus tomentosa. Int J Mol Sci 2021; 22:ijms22073448. [PMID: 33810585 PMCID: PMC8036549 DOI: 10.3390/ijms22073448] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/17/2021] [Accepted: 03/24/2021] [Indexed: 11/16/2022] Open
Abstract
Poplar wood is the main source of renewable biomass energy worldwide, and is also considered to be a model system for studying woody plants. The Full-length cDNA Over-eXpressing (FOX) gene hunting system is an effective method for generating gain-of-function mutants. Large numbers of novel genes have successfully been identified from many herbaceous plants according to the phenotype of gain-of-function mutants under normal or abiotic stress conditions using this system. However, the system has not been used for functional gene identification with high-throughput mutant screening in woody plants. In this study, we constructed a FOX library from the Chinese white poplar, Populus tomentosa. The poplar cDNA library was constructed into the plant expression vector pEarleyGate101 and further transformed into Arabidopsis thaliana (thale cress). We collected 1749 T1 transgenic plants identified by PCR. Of these, 593 single PCR bands from different transgenic lines were randomly selected for sequencing, and 402 diverse sequences of poplar genes were isolated. Most of these genes were involved in photosynthesis, environmental adaptation, and ribosome biogenesis based on Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotation. We characterized in detail two mutant lines carrying PtoCPCa or PtoWRKY13 cDNA insertions. Phenotypic characterization showed that overexpression of these genes in A. thaliana affected trichome development or secondary cell wall (SCW) deposition, respectively. Together, the Populus-FOX-Arabidopsis library generated in our experiments will be helpful for efficient discovery of novel genes in poplar.
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Affiliation(s)
| | | | | | | | - Keming Luo
- Correspondence: ; Tel.: +86-23-6825-3021; Fax: +86-23-6825-2365
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Li J, Wang Y, Wei H, Kang X. Comparative proteomic analysis provides insight into the molecular mechanism of vegetative growth advantage in allotriploid Populus. Genomics 2021; 113:1180-1192. [PMID: 33677055 DOI: 10.1016/j.ygeno.2021.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 01/04/2021] [Accepted: 03/02/2021] [Indexed: 10/22/2022]
Abstract
Though allotriploid poplar shows a salient vegetative growth advantage that impacts biomass and lumber yield, the proteomic data of Populus allotriploids have not been scrutinized for identifying the underlying molecular mechanisms. We conducted a large-scale label-free proteomics profiling of the 5th, 10th, and 25th leaves of allotriploids and diploids, and identified 4587 protein groups. Among 932 differentially expressed proteins (DEPs), 22 are transcription factors (TFs) that could regulate vegetative growth advantage in allotriploids. The DEPs involved in light reaction, Calvin cycle, and photorespiration, protein synthesis, sucrose synthesis, starch synthesis, and starch decomposition displayed elevated expression in Populus allotriploids. However, the DEPs functioning in sucrose decomposition, tricarboxylic acid (TCA) cycle, and protein degradation exhibited significantly downregulated expression. The alternations of these DEPs augmented efficiency of photosynthesis, carbon fixation, sucrose and starch accumulation, and decreased capacity of carbohydrate consumption, leading to larger volume of biomass and vigorous growth in Populus allotriploids.
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Affiliation(s)
- Jiang Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, PR China
| | - Yi Wang
- Zhongkai University of Agriculture and Engineering, Guangzhou 510225, PR China
| | - Hairong Wei
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton 49931, USA
| | - Xiangyang Kang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, PR China; National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, PR China; College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, PR China.
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32
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Wang H, Liu S, Dai X, Yang Y, Luo Y, Gao Y, Liu X, Wei W, Wang H, Xu X, Reddy ASN, Jaiswal P, Li W, Liu B, Gu L. PSDX: A Comprehensive Multi-Omics Association Database of Populus trichocarpa With a Focus on the Secondary Growth in Response to Stresses. FRONTIERS IN PLANT SCIENCE 2021; 12:655565. [PMID: 34122478 PMCID: PMC8195342 DOI: 10.3389/fpls.2021.655565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 04/26/2021] [Indexed: 05/16/2023]
Abstract
Populus trichocarpa (P. trichocarpa) is a model tree for the investigation of wood formation. In recent years, researchers have generated a large number of high-throughput sequencing data in P. trichocarpa. However, no comprehensive database that provides multi-omics associations for the investigation of secondary growth in response to diverse stresses has been reported. Therefore, we developed a public repository that presents comprehensive measurements of gene expression and post-transcriptional regulation by integrating 144 RNA-Seq, 33 ChIP-seq, and six single-molecule real-time (SMRT) isoform sequencing (Iso-seq) libraries prepared from tissues subjected to different stresses. All the samples from different studies were analyzed to obtain gene expression, co-expression network, and differentially expressed genes (DEG) using unified parameters, which allowed comparison of results from different studies and treatments. In addition to gene expression, we also identified and deposited pre-processed data about alternative splicing (AS), alternative polyadenylation (APA) and alternative transcription initiation (ATI). The post-transcriptional regulation, differential expression, and co-expression network datasets were integrated into a new P. trichocarpa Stem Differentiating Xylem (PSDX) database (http://forestry.fafu.edu.cn/db/SDX), which further highlights gene families of RNA-binding proteins and stress-related genes. The PSDX also provides tools for data query, visualization, a genome browser, and the BLAST option for sequence-based query. Much of the data is also available for bulk download. The availability of PSDX contributes to the research related to the secondary growth in response to stresses in P. trichocarpa, which will provide new insights that can be useful for the improvement of stress tolerance in woody plants.
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Affiliation(s)
- Huiyuan Wang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Sheng Liu
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiufang Dai
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Yongkang Yang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yunjun Luo
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yubang Gao
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xuqing Liu
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wentao Wei
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Huihui Wang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xi Xu
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Anireddy S. N. Reddy
- Department of Biology and Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO, United States
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Wei Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Bo Liu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- *Correspondence: Bo Liu,
| | - Lianfeng Gu
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Lianfeng Gu,
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Wang S, Huang J, Wang X, Fan Y, Liu Q, Han Y. PagERF16 of Populus Promotes Lateral Root Proliferation and Sensitizes to Salt Stress. FRONTIERS IN PLANT SCIENCE 2021; 12:669143. [PMID: 34149765 PMCID: PMC8213033 DOI: 10.3389/fpls.2021.669143] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 04/19/2021] [Indexed: 05/17/2023]
Abstract
The aggravation of soil salinization limits the growth and development of plants. The AP2/ERF transcription factors (TFs) have been identified and play essential roles in plant development and stress response processes. In this study, the function of PagERF16 was detected using the overexpressing (OX) and RNAi transgenic poplar 84K hybrids. Plant growth, stomatal conductance, antioxidant enzymes activity, and PagERF16 co-expressed TFs were analyzed using morphological, physiological, and molecular methods. OX showed a more robust lateral root system with a bigger diameter and volume compared to the wild-type plants (WT). Physiological parameters indicated the bigger stomatal aperture and lower stomatal density of OX along with the lower Catalase (CAT) activity and higher malondialdehyde (MDA) content contributed to the salt sensitivity. The plant height and rooting rate of OX and RNAi were significantly worse compared to WT. Other than that, the morphology and physiology of RNAi plants were similar to WTs, suggesting that the function of PagERF16 may be redundant with other TFs. Our results indicate that when PagERF16 expression is either too high or too low, poplar growth and rooting is negatively affected. In addition, a downstream target TF, NAC45, involved in Auxin biosynthesis, was identified and PagERF16 could directly bind to its promoter to negatively regulate its expression. These results shed new light on the function of ERF TFs in plant root growth and salt stress tolerance.
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Affiliation(s)
- Shengji Wang
- College of Forestry, Shanxi Agricultural University, Jinzhong, China
| | - Juanjuan Huang
- College of Forestry, Shanxi Agricultural University, Jinzhong, China
| | - Xingdou Wang
- College of Forestry, Shanxi Agricultural University, Jinzhong, China
| | - Yan Fan
- College of Forestry, Shanxi Agricultural University, Jinzhong, China
| | - Qiang Liu
- College of Forestry, Hebei Agricultural University, Baoding, China
| | - Youzhi Han
- College of Forestry, Shanxi Agricultural University, Jinzhong, China
- *Correspondence: Youzhi Han
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34
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Identifying transcription factors that reduce wood recalcitrance and improve enzymatic degradation of xylem cell wall in Populus. Sci Rep 2020; 10:22043. [PMID: 33328495 PMCID: PMC7744511 DOI: 10.1038/s41598-020-78781-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 10/21/2020] [Indexed: 12/28/2022] Open
Abstract
Developing an efficient deconstruction step of woody biomass for biorefinery has been drawing considerable attention since its xylem cell walls display highly recalcitrance nature. Here, we explored transcriptional factors (TFs) that reduce wood recalcitrance and improve saccharification efficiency in Populus species. First, 33 TF genes up-regulated during poplar wood formation were selected as potential regulators of xylem cell wall structure. The transgenic hybrid aspens (Populus tremula × Populus tremuloides) overexpressing each selected TF gene were screened for in vitro enzymatic saccharification. Of these, four transgenic seedlings overexpressing previously uncharacterized TF genes increased total glucan hydrolysis on average compared to control. The best performing lines overexpressing Pt × tERF123 and Pt × tZHD14 were further grown to form mature xylem in the greenhouse. Notably, the xylem cell walls exhibited significantly increased total xylan hydrolysis as well as initial hydrolysis rates of glucan. The increased saccharification of Pt × tERF123-overexpressing lines could reflect the improved balance of cell wall components, i.e., high cellulose and low xylan and lignin content, which could be caused by upregulation of cellulose synthase genes upon the expression of Pt × tERF123. Overall, we successfully identified Pt × tERF123 and Pt × tZHD14 as effective targets for reducing cell wall recalcitrance and improving the enzymatic degradation of woody plant biomass.
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Wei M, Liu Q, Wang Z, Yang J, Li W, Chen Y, Lu H, Nie J, Liu B, Lv K, Mao X, Chen S, Sanders J, Wei H, Li C. PuHox52-mediated hierarchical multilayered gene regulatory network promotes adventitious root formation in Populus ussuriensis. THE NEW PHYTOLOGIST 2020; 228:1369-1385. [PMID: 32589766 DOI: 10.1111/nph.16778] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 06/15/2020] [Indexed: 05/25/2023]
Abstract
Adventitious root (AR) formation is critically important in vegetative propagation through cuttings in some plants, especially woody species. However, the underlying molecular mechanisms remain elusive. Here, we report the identification of a poplar homeobox gene, PuHox52, which was induced rapidly (within 15 min) at the basal ends of stems upon cutting and played a key regulatory role in adventitious rooting. We demonstrated that overexpression of PuHox52 significantly increased the number of ARs while suppression of PuHox52 had the opposite effect. A multilayered hierarchical gene regulatory network (ML-hGRN) mediated by PuHox52 was reverse-engineered and demonstrated to govern AR formation. PuHox52 regulated AR formation through upregulation of nine hub regulators, including a jasmonate signaling pathway gene, PuMYC2, and an auxin signaling pathway gene, PuAGL12. We also identified coherent type 4 feed-forward loops within this ML-hGRN; PuHox52 repressed PuHDA9, which encodes a histone deacetylase, and led to an increase in acetylation and presumably expression of three hub regulators, PuWRKY51, PuLBD21 and PuIAA7. Our results indicate that the ML-hGRN mediated by PuHox52 governs AR formation at the basal ends of stem cuttings from poplar trees.
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Affiliation(s)
- Ming Wei
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Quangang Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
- College of Forestry, Shenyang Agricultural University, Shenyang, 110866, China
| | - Zhanchao Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Jingli Yang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Wenlong Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Yingxi Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Han Lu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Jinfu Nie
- Anhui Province Key Laboratory of Medical Physics and Technology, Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230000, China
- Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510000, China
| | - Baoguang Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Kaiwen Lv
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Xuliang Mao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Su Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Jennifer Sanders
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA
| | - Hairong Wei
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA
| | - Chenghao Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
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Wang Z, Mao Y, Guo Y, Gao J, Liu X, Li S, Lin YCJ, Chen H, Wang JP, Chiang VL, Li W. MYB Transcription Factor161 Mediates Feedback Regulation of Secondary wall-associated NAC-Domain1 Family Genes for Wood Formation. PLANT PHYSIOLOGY 2020; 184:1389-1406. [PMID: 32943464 PMCID: PMC7608153 DOI: 10.1104/pp.20.01033] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 09/09/2020] [Indexed: 05/03/2023]
Abstract
Wood formation is a complex process that involves cell differentiation, cell expansion, secondary wall deposition, and programmed cell death. We constructed a four-layer wood formation transcriptional regulatory network (TRN) in Populus trichocarpa (black cottonwood) that has four Secondary wall-associated NAC-Domain1 (PtrSND1) transcription factor (TF) family members as the top-layer regulators. We characterized the function of a MYB (PtrMYB161) TF in this PtrSND1-TRN, using transgenic P trichocarpa cells and whole plants. PtrMYB161 is a third-layer regulator that directly transactivates five wood formation genes. Overexpression of PtrMYB161 in P. trichocarpa (OE-PtrMYB161) led to reduced wood, altered cell type proportions, and inhibited growth. Integrative analysis of wood cell-based chromatin-binding assays with OE-PtrMYB161 transcriptomics revealed a feedback regulation system in the PtrSND1-TRN, where PtrMYB161 represses all four top-layer regulators and one second-layer regulator, PtrMYB021, possibly affecting many downstream TFs in, and likely beyond, the TRN, to generate the observed phenotypic changes. Our data also suggested that the PtrMYB161's repressor function operates through interaction of the base PtrMYB161 target-binding system with gene-silencing cofactors. PtrMYB161 protein does not contain any known negative regulatory domains. CRISPR-based mutants of PtrMYB161 in P. trichocarpa exhibited phenotypes similar to the wild type, suggesting that PtrMYB161's activator functions are redundant among many TFs. Our work demonstrated that PtrMYB161 binds to multiple sets of target genes, a feature that allows it to function as an activator as well as a repressor. The balance of the two functions may be important to the establishment of regulatory homeostasis for normal growth and development.
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Affiliation(s)
- Zhifeng Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Yuli Mao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Yanjiao Guo
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Jinghui Gao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Xinying Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Shuang Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Ying-Chung Jimmy Lin
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- Department of Life Science and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - 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
| | - 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
| | - 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
| | - Wei Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
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Sulis DB, Wang JP. Regulation of Lignin Biosynthesis by Post-translational Protein Modifications. FRONTIERS IN PLANT SCIENCE 2020; 11:914. [PMID: 32714349 PMCID: PMC7343852 DOI: 10.3389/fpls.2020.00914] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 06/04/2020] [Indexed: 05/24/2023]
Abstract
Post-translational modification of proteins exerts essential roles in many biological processes in plants. The function of these chemical modifications has been extensively characterized in many physiological processes, but how these modifications regulate lignin biosynthesis for wood formation remained largely unknown. Over the past decade, post-translational modification of several proteins has been associated with lignification. Phosphorylation, ubiquitination, glycosylation, and S-nitrosylation of transcription factors, monolignol enzymes, and peroxidases were shown to have primordial roles in the regulation of lignin biosynthesis. The main discoveries of post-translational modifications in lignin biosynthesis are discussed in this review.
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Liu B, Wang JP. Tracheid-associated transcription factors in loblolly pine. TREE PHYSIOLOGY 2020; 40:700-703. [PMID: 32050028 DOI: 10.1093/treephys/tpaa014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 01/02/2020] [Accepted: 01/31/2020] [Indexed: 06/10/2023]
Affiliation(s)
- Baoguang Liu
- Department of Forestry, Beihua University, 3999 East Binjiang Road, Fengman District, Jilin 132013, China
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 51 Hexing Road, Harbin 150040, China
| | - Jack P Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 51 Hexing Road, Harbin 150040, China
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, 840 Main Campus Drive, Raleigh, NC 27695, USA
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Jin Y, Yu C, Jiang C, Guo X, Li B, Wang C, Kong F, Zhang H, Wang H. PtiCYP85A3, a BR C-6 Oxidase Gene, Plays a Critical Role in Brassinosteroid-Mediated Tension Wood Formation in Poplar. FRONTIERS IN PLANT SCIENCE 2020; 11:468. [PMID: 32391036 PMCID: PMC7193022 DOI: 10.3389/fpls.2020.00468] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 03/30/2020] [Indexed: 05/21/2023]
Abstract
In angiosperm trees, the gelatinous layer (G-layer) takes a great part of the fiber cell wall in the tension wood (TW). However, the mechanism underlying G-layer formation in poplar is largely unknown. In this work, we demonstrate that G-layer formation in poplar TW cells is regulated by brassinosteroid (BR) and its signaling. PtiCYP85A3, a key BR biosynthesis gene, was predominantly expressed in the xylem of TW, accompanied with a relatively higher castasterone (CS) accumulation, than in the xylem of opposite wood (OW). A wider expression zone of BZR1, a key transcriptional factor in BR singling pathway, was also observed in G-fiber cells on TW side than in wood fiber cells on the OW side, as indicated by immunohistochemistry assays. Transgenic poplar plants overexpressing PtiCYP85A3 produced thicker G-layer with higher cellulose proportion, and accumulated more BZR1 protein in the xylem of TW than did the wild type (WT) plants. Expression of most TW-associated CesAs, which were induced by 2, 4-epibrassinolide, an active BR, and inhibited by brassinazole, a BR biosynthesis inhibitor, were also up-regulated in the xylem of TW in transgenic plants compared to that in WT plants. Further studies with dual-luciferase assays demonstrated that the promoters of PtiCesAs were activated by PtiMYB128, a TW specific transcription factor, which was then regulated by BZR1. All these results indicate that BR plays a crucial role in the G-layer formation of TW fiber cells by regulating the expression of BZR1, PtiMYB128, and PtiCesAs in poplar.
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Affiliation(s)
- Yanli Jin
- College of Agriculture, Ludong University, Yantai, China
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- The Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in the Universities of Shandong, Institute for Advanced Study of Coastal Ecology, Ludong University, Yantai, China
| | - Chunyan Yu
- College of Agriculture, Ludong University, Yantai, China
- The Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in the Universities of Shandong, Institute for Advanced Study of Coastal Ecology, Ludong University, Yantai, China
| | - Chunmei Jiang
- College of Agriculture, Ludong University, Yantai, China
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, College of Life Sciences, Hubei University, Wuhan, China
| | - Xiaotong Guo
- College of Agriculture, Ludong University, Yantai, China
- The Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in the Universities of Shandong, Institute for Advanced Study of Coastal Ecology, Ludong University, Yantai, China
| | - Bei Li
- College of Agriculture, Ludong University, Yantai, China
- The Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in the Universities of Shandong, Institute for Advanced Study of Coastal Ecology, Ludong University, Yantai, China
| | - Cuiting Wang
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Fanjing Kong
- Ministry of Natural Resources Key Laboratory of Saline Lake Resources and Environments, Institute of Mineral Resources, Chinese Academy of Geological Sciences, Beijing, China
| | - Hongxia Zhang
- College of Agriculture, Ludong University, Yantai, China
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- The Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in the Universities of Shandong, Institute for Advanced Study of Coastal Ecology, Ludong University, Yantai, China
| | - Haihai Wang
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
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40
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Wei H. Construction of a hierarchical gene regulatory network centered around a transcription factor. Brief Bioinform 2020; 20:1021-1031. [PMID: 29186304 DOI: 10.1093/bib/bbx152] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 10/11/2017] [Indexed: 12/24/2022] Open
Abstract
We have modified a multitude of transcription factors (TFs) in numerous plant species and some animal species, and obtained transgenic lines that exhibit phenotypic alterations. Whenever we observe phenotypic changes in a TF's transgenic lines, we are always eager to identify its target genes, collaborative regulators and even upstream high hierarchical regulators. This issue can be addressed by establishing a multilayered hierarchical gene regulatory network (ML-hGRN) centered around a given TF. In this article, a practical approach for constructing an ML-hGRN centered on a TF using a combined approach of top-down and bottom-up network construction methods is described. Strategies for constructing ML-hGRNs are vitally important, as these networks provide key information to advance our understanding of how biological processes are regulated.
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Affiliation(s)
- Hairong Wei
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, China.,School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, USA
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Zhao Y, Song X, Zhou H, Wei K, Jiang C, Wang J, Cao Y, Tang F, Zhao S, Lu MZ. KNAT2/6b, a class I KNOX gene, impedes xylem differentiation by regulating NAC domain transcription factors in poplar. THE NEW PHYTOLOGIST 2020; 225:1531-1544. [PMID: 31257603 DOI: 10.1111/nph.16036] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 06/22/2019] [Indexed: 05/21/2023]
Abstract
Wood formation is the terminal differentiation of xylem mother cells derived from cambial initials, and negative regulators play important roles in xylem differentiation. The molecular mechanism of the negative regulator of xylem differentiation PagKNAT2/6b was investigated. PagKNAT2/6b is an ortholog of Arabidopsis KNAT2 and KNAT6 that is highly expressed in phloem and xylem. Compared to nontransgenic control plants, transgenic poplar plants overexpressing PagKNAT2/6b present with altered vascular patterns, characterized by decreased secondary xylem with thin cell walls containing less cellulose, xylose and lignin. RNA sequencing analyses revealed that differentially expressed genes are enriched in xylem differentiation and secondary wall synthesis functions. Expression of NAM/ATAF/CUC (NAC) domain genes including PagSND1-A1, PagSND1-A2, PagSND1-B2 and PagVND6-C1 is downregulated by PagKNAT2/6b, while PagXND1a is directly upregulated. Accordingly, the dominant repression form of PagKNAT2/6b leads to increased xylem width per stem diameter through downregulation of PagXND1a. PagKNAT2/6b can inhibit cell differentiation and secondary wall deposition during wood formation in poplar by modulating the expression of NAC domain transcription factors. Direct activation of PagXND1a by PagKNAT2/6b is a key node in the negative regulatory network of xylem differentiation by KNOXs.
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Affiliation(s)
- Yanqiu Zhao
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Xueqin Song
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Jiangsu, 210037, China
| | - Houjun Zhou
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Kaili Wei
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Cheng Jiang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Zhejiang Agriculture & Forestry University, Hangzhou, 311300, China
| | - Jinnan Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Yuan Cao
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Fang Tang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Jiangsu, 210037, China
| | - Shutang Zhao
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Jiangsu, 210037, China
| | - Meng-Zhu Lu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Jiangsu, 210037, China
- Zhejiang Agriculture & Forestry University, Hangzhou, 311300, China
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Barco B, Clay NK. Hierarchical and Dynamic Regulation of Defense-Responsive Specialized Metabolism by WRKY and MYB Transcription Factors. FRONTIERS IN PLANT SCIENCE 2020; 10:1775. [PMID: 32082343 PMCID: PMC7005594 DOI: 10.3389/fpls.2019.01775] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 12/19/2019] [Indexed: 05/07/2023]
Abstract
The plant kingdom produces hundreds of thousands of specialized bioactive metabolites, some with pharmaceutical and biotechnological importance. Their biosynthesis and function have been studied for decades, but comparatively less is known about how transcription factors with overlapping functions and contrasting regulatory activities coordinately control the dynamics and output of plant specialized metabolism. Here, we performed temporal studies on pathogen-infected intact host plants with perturbed transcription factors. We identified WRKY33 as the condition-dependent master regulator and MYB51 as the dual functional regulator in a hierarchical gene network likely responsible for the gene expression dynamics and metabolic fluxes in the camalexin and 4-hydroxy-indole-3-carbonylnitrile (4OH-ICN) pathways. This network may have also facilitated the regulatory capture of the newly evolved 4OH-ICN pathway in Arabidopsis thaliana by the more-conserved transcription factor MYB51. It has long been held that the plasticity of plant specialized metabolism and the canalization of development should be differently regulated; our findings imply a common hierarchical regulatory architecture orchestrated by transcription factors for specialized metabolism and development, making it an attractive target for metabolic engineering.
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Affiliation(s)
| | - Nicole K. Clay
- Department of Molecular, Cellular & Developmental Biology, Yale University, New Haven, CT, United States
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Tonfack LB, Hussey SG, Veale A, Myburg AA, Mizrachi E. Analysis of Orthologous SECONDARY WALL-ASSOCIATED NAC DOMAIN1 (SND1) Promotor Activity in Herbaceous and Woody Angiosperms. Int J Mol Sci 2019; 20:E4623. [PMID: 31540430 PMCID: PMC6770381 DOI: 10.3390/ijms20184623] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 07/26/2019] [Accepted: 07/29/2019] [Indexed: 12/20/2022] Open
Abstract
SECONDARY WALL-ASSOCIATED NAC DOMAIN1 (SND1) is a master regulator of fibre secondary wall deposition in Arabidopsis thaliana (Arabidopsis), with homologs in other angiosperms and gymnosperms. However, it is poorly understood to what extent the fibre-specific regulation of the SND1 promoter, and that of its orthologs, is conserved between diverged herbaceous and woody lineages. We performed a reciprocal reporter gene analysis of orthologous SND1 promoters from Arabidopsis (AthSND1), Eucalyptus grandis (EgrNAC61) and Populus alba × P. grandidentata (PagWND1A) relative to secondary cell wall-specific Cellulose Synthase4 (CesA4) and CesA7 promoters, in both a non-woody (Arabidopsis) and a woody (poplar) system. β-glucuronidase (GUS) reporter analysis in Arabidopsis showed that the SND1 promoter was active in vascular tissues as previously reported and showed interfascicular and xylary fibre-specific expression in inflorescence stems, while reporter constructs of the woody plant-derived promoters were partial to the (pro)cambium-phloem and protoxylem. In transgenic P. tremula × P. alba plants, all three orthologous SND1 promoters expressed the GUS reporter similarly and preferentially in developing secondary xylem, ray parenchyma and cork cambium. Ours is the first study to reciprocally test orthologous SND1 promoter specificity in herbaceous and woody species, revealing diverged regulatory functions in the herbaceous system.
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Affiliation(s)
- Libert B Tonfack
- Plant Physiology and Improvement Unit, Laboratory of Biotechnology and Environment, Department of Plant Biology, University of Yaoundé I, Yaoundé 0812, Cameroon.
| | - Steven G Hussey
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Pretoria 0002, South Africa.
| | - Adri Veale
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Pretoria 0002, South Africa.
| | - Alexander A Myburg
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Pretoria 0002, South Africa.
| | - Eshchar Mizrachi
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Pretoria 0002, South Africa.
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44
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Liu JG, Han X, Yang T, Cui WH, Wu AM, Fu CX, Wang BC, Liu LJ. Genome-wide transcriptional adaptation to salt stress in Populus. BMC PLANT BIOLOGY 2019; 19:367. [PMID: 31429697 PMCID: PMC6701017 DOI: 10.1186/s12870-019-1952-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 07/29/2019] [Indexed: 05/05/2023]
Abstract
BACKGROUND Adaptation to abiotic stresses is crucial for the survival of perennial plants in a natural environment. However, very little is known about the underlying mechanisms. Here, we adopted a liquid culture system to investigate plant adaptation to repeated salt stress in Populus trees. RESULTS We first evaluated phenotypic responses and found that plants exhibit better stress tolerance after pre-treatment of salt stress. Time-course RNA sequencing (RNA-seq) was then performed to profile changes in gene expression over 12 h of salt treatments. Analysis of differentially expressed genes (DEGs) indicated that significant transcriptional reprogramming and adaptation to repeated salt treatment occurred. Clustering analysis identified two modules of co-expressed genes that were potentially critical for repeated salt stress adaptation, and one key module for salt stress response in general. Gene Ontology (GO) enrichment analysis identified pathways including hormone signaling, cell wall biosynthesis and modification, negative regulation of growth, and epigenetic regulation to be highly enriched in these gene modules. CONCLUSIONS This study illustrates phenotypic and transcriptional adaptation of Populus trees to salt stress, revealing novel gene modules which are potentially critical for responding and adapting to salt stress.
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Affiliation(s)
- Jin-Gui Liu
- State Forestry and Grassland Administration Key Laboratory of Silviculture in downstream areas of the Yellow River, College of Forestry, Shandong Agriculture University, Taian, 271018 Shandong China
| | - Xiao Han
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Lin’an, Hangzhou, 311300 China
| | - Tong Yang
- State Forestry and Grassland Administration Key Laboratory of Silviculture in downstream areas of the Yellow River, College of Forestry, Shandong Agriculture University, Taian, 271018 Shandong China
| | - Wen-Hui Cui
- State Forestry and Grassland Administration Key Laboratory of Silviculture in downstream areas of the Yellow River, College of Forestry, Shandong Agriculture University, Taian, 271018 Shandong China
| | - Ai-Min Wu
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642 China
| | - Chun-Xiang Fu
- Key Laboratory of Biofuels, Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 Shandong China
| | - Bai-Chen Wang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China
| | - Li-Jun Liu
- State Forestry and Grassland Administration Key Laboratory of Silviculture in downstream areas of the Yellow River, College of Forestry, Shandong Agriculture University, Taian, 271018 Shandong China
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Yeh CS, Wang Z, Miao F, Ma H, Kao CT, Hsu TS, Yu JH, Hung ET, Lin CC, Kuan CY, Tsai NC, Zhou C, Qu GZ, Jiang J, Liu G, Wang JP, Li W, Chiang VL, Chang TH, Lin YCJ. A novel synthetic-genetic-array-based yeast one-hybrid system for high discovery rate and short processing time. Genome Res 2019; 29:1343-1351. [PMID: 31186303 PMCID: PMC6673709 DOI: 10.1101/gr.245951.118] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 06/06/2019] [Indexed: 12/18/2022]
Abstract
Eukaryotic gene expression is often tightly regulated by interactions between transcription factors (TFs) and their DNA cis targets. Yeast one-hybrid (Y1H) is one of the most extensively used methods to discover these interactions. We developed a high-throughput meiosis-directed yeast one-hybrid system using the Magic Markers of the synthetic genetic array analysis. The system has a transcription factor–DNA interaction discovery rate twice as high as the conventional diploid-mating approach and a processing time nearly one-tenth of the haploid-transformation method. The system also offers the highest accuracy in identifying TF–DNA interactions that can be authenticated in vivo by chromatin immunoprecipitation. With these unique features, this meiosis-directed Y1H system is particularly suited for constructing novel and comprehensive genome-scale gene regulatory networks for various organisms.
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Affiliation(s)
- Chung-Shu Yeh
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Zhifeng Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Fang Miao
- Department of Life Sciences and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Hongyan Ma
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Chung-Ting Kao
- Department of Life Sciences and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Tzu-Shu Hsu
- Department of Life Sciences and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 10617, Taiwan.,Institute of Biomedical Informatics and Center for Systems and Synthetic Biology, National Yang-Ming University, Taipei 11221, Taiwan
| | - Jhong-He Yu
- Department of Life Sciences and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Er-Tsi Hung
- Department of Life Sciences and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Chia-Chang Lin
- Department of Life Sciences and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Chen-Yu Kuan
- Department of Life Sciences and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Ni-Chiao Tsai
- Department of Life Sciences and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Chenguang Zhou
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Guan-Zheng Qu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Jing Jiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Guifeng Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - 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, USA
| | - Wei Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - 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, USA
| | | | - Ying-Chung Jimmy Lin
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China.,Department of Life Sciences and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 10617, Taiwan.,Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina 27695, USA
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Zheng L, Chen Y, Ding D, Zhou Y, Ding L, Wei J, Wang H. Endoplasmic reticulum-localized UBC34 interaction with lignin repressors MYB221 and MYB156 regulates the transactivity of the transcription factors in Populus tomentosa. BMC PLANT BIOLOGY 2019; 19:97. [PMID: 30866808 PMCID: PMC6416899 DOI: 10.1186/s12870-019-1697-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 02/27/2019] [Indexed: 05/06/2023]
Abstract
BACKGROUND Regulation of lignin biosynthesis is known to occur at the level of transcription factors (TFs), of which R2R3-MYB family members have been proposed to play a central role via the AC cis-elements. Despite the important roles of TFs in lignin biosynthesis, the post-translational regulation of these TFs, particularly their ubiquitination regulation, has not been thoroughly explored. RESULTS We describe the discovery of a Populus tomentosa E2 ubiquitin-conjugating enzyme 34 (PtoUBC34), which is involved in the post-translational regulation of transactivation activity of lignin-associated transcriptional repressors PtoMYB221 and PtoMYB156. PtoUBC34 is localized at the endoplasmic reticulum (ER) membrane where it interacts with transcriptional repressors PtoMYB221 and PtoMYB156. This specific interaction allows for the translocation of TFs PtoMYB221 and PtoMYB156 to the ER and reduces their repression activity in a PtoUBC34 abundance-dependent manner. By taking a molecular biology approach with quantitative real-time polymerase chain reaction (qRT-PCR) analysis, we found that PtoUBC34 is expressed in all aboveground tissues of trees in P. tomentosa, and in particular, it is ubiquitous in all distinct differentiation stages across wood formation, including phloem differentiation, cambium maintaining, early and developing xylem differentiation, secondary cell wall thickening, and programmed cell death. Additionally, we discovered that PtoUBC34 is induced by treatment with sodium chloride and heat shock. CONCLUSIONS Our data suggest a possible mechanism by which lignin biosynthesis is regulated by ER-localized PtoUBC34 in poplar, probably through the ER-associated degradation (ERAD) of lignin-associated repressors PtoMYB221 and PtoMYB156.
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Affiliation(s)
- Lin Zheng
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agricultural and Forestry Sciences, No. 9, Shuguang Huayuan Middle Road, Haidian District, Beijing, 100097 People’s Republic of China
| | - Yajuan Chen
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agricultural and Forestry Sciences, No. 9, Shuguang Huayuan Middle Road, Haidian District, Beijing, 100097 People’s Republic of China
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agricultural and Forestry Sciences, No. 9, Shuguang Huayuan Middle Road, Haidian District, Beijing, 100097 People’s Republic of China
| | - Dong Ding
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agricultural and Forestry Sciences, No. 9, Shuguang Huayuan Middle Road, Haidian District, Beijing, 100097 People’s Republic of China
| | - Ying Zhou
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agricultural and Forestry Sciences, No. 9, Shuguang Huayuan Middle Road, Haidian District, Beijing, 100097 People’s Republic of China
| | - Liping Ding
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agricultural and Forestry Sciences, No. 9, Shuguang Huayuan Middle Road, Haidian District, Beijing, 100097 People’s Republic of China
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agricultural and Forestry Sciences, No. 9, Shuguang Huayuan Middle Road, Haidian District, Beijing, 100097 People’s Republic of China
| | - Jianhua Wei
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agricultural and Forestry Sciences, No. 9, Shuguang Huayuan Middle Road, Haidian District, Beijing, 100097 People’s Republic of China
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agricultural and Forestry Sciences, No. 9, Shuguang Huayuan Middle Road, Haidian District, Beijing, 100097 People’s Republic of China
| | - Hongzhi Wang
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agricultural and Forestry Sciences, No. 9, Shuguang Huayuan Middle Road, Haidian District, Beijing, 100097 People’s Republic of China
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agricultural and Forestry Sciences, No. 9, Shuguang Huayuan Middle Road, Haidian District, Beijing, 100097 People’s Republic of China
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47
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Daly P, McClellan C, Maluk M, Oakey H, Lapierre C, Waugh R, Stephens J, Marshall D, Barakate A, Tsuji Y, Goeminne G, Vanholme R, Boerjan W, Ralph J, Halpin C. RNAi-suppression of barley caffeic acid O-methyltransferase modifies lignin despite redundancy in the gene family. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:594-607. [PMID: 30133138 PMCID: PMC6381794 DOI: 10.1111/pbi.13001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 08/18/2018] [Indexed: 05/12/2023]
Abstract
Caffeic acid O-methyltransferase (COMT), the lignin biosynthesis gene modified in many brown-midrib high-digestibility mutants of maize and sorghum, was targeted for downregulation in the small grain temperate cereal, barley (Hordeum vulgare), to improve straw properties. Phylogenetic and expression analyses identified the barley COMT orthologue(s) expressed in stems, defining a larger gene family than in brachypodium or rice with three COMT genes expressed in lignifying tissues. RNAi significantly reduced stem COMT protein and enzyme activity, and modestly reduced stem lignin content while dramatically changing lignin structure. Lignin syringyl-to-guaiacyl ratio was reduced by ~50%, the 5-hydroxyguaiacyl (5-OH-G) unit incorporated into lignin at 10--15-fold higher levels than normal, and the amount of p-coumaric acid ester-linked to cell walls was reduced by ~50%. No brown-midrib phenotype was observed in any RNAi line despite significant COMT suppression and altered lignin. The novel COMT gene family structure in barley highlights the dynamic nature of grass genomes. Redundancy in barley COMTs may explain the absence of brown-midrib mutants in barley and wheat. The barley COMT RNAi lines nevertheless have the potential to be exploited for bioenergy applications and as animal feed.
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Affiliation(s)
- Paul Daly
- Division of Plant SciencesSchool of Life SciencesUniversity of Dundee at the James Hutton InstituteDundeeUK
- Present address:
Fungal PhysiologyWesterdijk Fungal Biodiversity Institute and Fungal Molecular PhysiologyUtrecht UniversityUtrechtThe Netherlands
| | - Christopher McClellan
- Division of Plant SciencesSchool of Life SciencesUniversity of Dundee at the James Hutton InstituteDundeeUK
| | - Marta Maluk
- Division of Plant SciencesSchool of Life SciencesUniversity of Dundee at the James Hutton InstituteDundeeUK
| | - Helena Oakey
- Division of Plant SciencesSchool of Life SciencesUniversity of Dundee at the James Hutton InstituteDundeeUK
- Faculty of SciencesSchool of Agriculture, Food and WineUniversity of AdelaideAdelaideAustralia
| | - Catherine Lapierre
- UMR1318 INRA‐AgroParistechIJPBUniversite Paris‐SaclayVersailles CedexFrance
| | - Robbie Waugh
- Division of Plant SciencesSchool of Life SciencesUniversity of Dundee at the James Hutton InstituteDundeeUK
- Cell and Molecular SciencesJames Hutton InstituteDundeeUK
| | | | - David Marshall
- Information and Computational SciencesJames Hutton InstituteDundeeUK
| | - Abdellah Barakate
- Division of Plant SciencesSchool of Life SciencesUniversity of Dundee at the James Hutton InstituteDundeeUK
| | - Yukiko Tsuji
- Department of BiochemistryUniversity of Wisconsin‐MadisonMadisonWIUSA
- Department of Energy's Great Lakes Bioenergy Research CenterThe Wisconsin Energy InstituteUniversity of Wisconsin‐MadisonMadisonWIUSA
| | - Geert Goeminne
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - Ruben Vanholme
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - Wout Boerjan
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - John Ralph
- Department of BiochemistryUniversity of Wisconsin‐MadisonMadisonWIUSA
- Department of Energy's Great Lakes Bioenergy Research CenterThe Wisconsin Energy InstituteUniversity of Wisconsin‐MadisonMadisonWIUSA
| | - Claire Halpin
- Division of Plant SciencesSchool of Life SciencesUniversity of Dundee at the James Hutton InstituteDundeeUK
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48
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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). THE PLANT CELL 2019; 31:602-626. [PMID: 30755461 PMCID: PMC6482634 DOI: 10.1105/tpc.18.00620] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [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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49
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Li S, Lin YCJ, Wang P, Zhang B, Li M, Chen S, Shi R, Tunlaya-Anukit S, Liu X, Wang Z, Dai X, Yu J, Zhou C, Liu B, Wang JP, Chiang VL, Li W. The AREB1 Transcription Factor Influences Histone Acetylation to Regulate Drought Responses and Tolerance in Populus trichocarpa. THE PLANT CELL 2019; 31:663-686. [PMID: 30538157 PMCID: PMC6482633 DOI: 10.1105/tpc.18.00437] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 10/29/2018] [Accepted: 11/24/2018] [Indexed: 05/18/2023]
Abstract
Plants develop tolerance to drought by activating genes with altered levels of epigenetic modifications. Specific transcription factors are involved in this activation, but the molecular connections within the regulatory system are unclear. Here, we analyzed genome-wide acetylated lysine residue 9 of histone H3 (H3K9ac) enrichment and examined its association with transcriptomes in Populus trichocarpa under drought stress. We revealed that abscisic acid-Responsive Element (ABRE) motifs in promoters of the drought-responsive genes PtrNAC006, PtrNAC007, and PtrNAC120 are involved in H3K9ac enhancement and activation of these genes. Overexpressing these PtrNAC genes in P trichocarpa resulted in strong drought-tolerance phenotypes. We showed that the ABRE binding protein PtrAREB1-2 binds to ABRE motifs associated with these PtrNAC genes and recruits the histone acetyltransferase unit ADA2b-GCN5, forming AREB1-ADA2b-GCN5 ternary protein complexes. Moreover, this recruitment enables GCN5-mediated histone acetylation to enhance H3K9ac and enrich RNA polymerase II specifically at these PtrNAC genes for the development of drought tolerance. CRISPR editing or RNA interference-mediated downregulation of any of the ternary members results in highly drought-sensitive P trichocarpa Thus, the combinatorial function of the ternary proteins establishes a coordinated histone acetylation and transcription factor-mediated gene activation for drought response and tolerance in Populus species.
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Affiliation(s)
- Shuang Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Ying-Chung Jimmy Lin
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina 27695
- Department of Life Sciences and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Pengyu Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Baofeng Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Meng Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Su Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Rui Shi
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina 27695
- Department of Crop and Soil Science, North Carolina State University, Raleigh, North Carolina 27695
| | - Sermsawat Tunlaya-Anukit
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina 27695
| | - Xinying Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Zhifeng Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Xiufang Dai
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Jing Yu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Chenguang Zhou
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Baoguang Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - 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
| | - 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
| | - Wei Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
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50
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Badmi R, Payyavula RS, Bali G, Guo HB, Jawdy SS, Gunter LE, Yang X, Winkeler KA, Collins C, Rottmann WH, Yee K, Rodriguez M, Sykes RW, Decker SR, Davis MF, Ragauskas AJ, Tuskan GA, Kalluri UC. A New Calmodulin-Binding Protein Expresses in the Context of Secondary Cell Wall Biosynthesis and Impacts Biomass Properties in Populus. FRONTIERS IN PLANT SCIENCE 2018; 9:1669. [PMID: 30568662 PMCID: PMC6290091 DOI: 10.3389/fpls.2018.01669] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 10/26/2018] [Indexed: 05/21/2023]
Abstract
A greater understanding of biosynthesis, signaling and regulatory pathways involved in determining stem growth and secondary cell wall chemistry is important for enabling pathway engineering and genetic optimization of biomass properties. The present study describes a new functional role of PdIQD10, a Populus gene belonging to the IQ67-Domain1 family of IQD genes, in impacting biomass formation and chemistry. Expression studies showed that PdIQD10 has enhanced expression in developing xylem and tension-stressed tissues in Populus deltoides. Molecular dynamics simulation and yeast two-hybrid interaction experiments suggest interactions with two calmodulin proteins, CaM247 and CaM014, supporting the sequence-predicted functional role of the PdIQD10 as a calmodulin-binding protein. PdIQD10 was found to interact with specific Populus isoforms of the Kinesin Light Chain protein family, shown previously to function as microtubule-guided, cargo binding and delivery proteins in Arabidopsis. Subcellular localization studies showed that PdIQD10 localizes in the nucleus and plasma membrane regions. Promoter-binding assays suggest that a known master transcriptional regulator of secondary cell wall biosynthesis (PdWND1B) may be upstream of an HD-ZIP III gene that is in turn upstream of PdIQD10 gene in the transcriptional network. RNAi-mediated downregulation of PdIQD10 expression resulted in plants with altered biomass properties including higher cellulose, wall glucose content and greater biomass quantity. These results present evidence in support of a new functional role for an IQD gene family member, PdIQD10, in secondary cell wall biosynthesis and biomass formation in Populus.
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Affiliation(s)
- Raghuram Badmi
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- The Center for Bioenergy Innovation and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Raja S. Payyavula
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- The Center for Bioenergy Innovation and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Garima Bali
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Georgia Institute of Technology, Atlanta, GA, United States
| | - Hao-Bo Guo
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Sara S. Jawdy
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- The Center for Bioenergy Innovation and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Lee E. Gunter
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- The Center for Bioenergy Innovation and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Xiaohan Yang
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- The Center for Bioenergy Innovation and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | | | | | | | - Kelsey Yee
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- The Center for Bioenergy Innovation and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Miguel Rodriguez
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- The Center for Bioenergy Innovation and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Robert W. Sykes
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- National Renewable Energy Laboratory, Golden, CO, United States
| | - Stephen R. Decker
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- National Renewable Energy Laboratory, Golden, CO, United States
| | - Mark F. Davis
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- National Renewable Energy Laboratory, Golden, CO, United States
| | - Arthur J. Ragauskas
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Department of Chemical and Biomolecular Engineering, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Gerald A. Tuskan
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- The Center for Bioenergy Innovation and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Udaya C. Kalluri
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- The Center for Bioenergy Innovation and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
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