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Guo Y, Yao L, Chen X, Xu X, Sang YL, Liu LJ. The transcription factor PagLBD4 represses cell differentiation and secondary cell wall biosynthesis in Populus. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 214:108924. [PMID: 38991593 DOI: 10.1016/j.plaphy.2024.108924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 06/20/2024] [Accepted: 07/07/2024] [Indexed: 07/13/2024]
Abstract
LBD (LATERAL ORGAN BOUNDARIES DOMAIN) transcription factors are key regulators of plant growth and development. In this study, we functionally characterized the PagLBD4 gene in Populus (Populus alba × Populus glandulosa). Overexpression of PagLBD4 (PagLBD4OE) significantly repressed secondary xylem differentiation and secondary cell wall (SCW) deposition, while CRISPR/Cas9-mediated PagLBD4 knockout (PagLBD4KO) significantly increased secondary xylem differentiation and SCW deposition. Consistent with the functional analysis, gene expression analysis revealed that SCW biosynthesis pathways were significantly down-regulated in PagLBD4OE plants but up-regulated in PagLBD4KO plants. We also performed DNA affinity purification followed by sequencing (DAP-seq) to identify genes bound by PagLBD4. Integration of RNA sequencing (RNA-seq) and DAP-seq data identified 263 putative direct target genes (DTGs) of PagLBD4, including important regulatory genes for SCW biosynthesis, such as PagMYB103 and PagIRX12. Together, our results demonstrated that PagLBD4 is a repressor of secondary xylem differentiation and SCW biosynthesis in Populus, which possibly lead to the dramatic growth repression in PagLBD4OE plants.
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Affiliation(s)
- Ying Guo
- State Forestry and Grassland Administration Key Laboratory of Silviculture in downstream areas of the Yellow River, College of Forestry, Shandong Agricultural University, Taian, 271018, China
| | - Lijuan Yao
- State Forestry and Grassland Administration Key Laboratory of Silviculture in downstream areas of the Yellow River, College of Forestry, Shandong Agricultural University, Taian, 271018, China
| | - Xiaoman Chen
- State Forestry and Grassland Administration Key Laboratory of Silviculture in downstream areas of the Yellow River, College of Forestry, Shandong Agricultural University, Taian, 271018, China
| | - Xiaoqi Xu
- State Forestry and Grassland Administration Key Laboratory of Silviculture in downstream areas of the Yellow River, College of Forestry, Shandong Agricultural University, Taian, 271018, China
| | - Ya Lin Sang
- State Forestry and Grassland Administration Key Laboratory of Silviculture in downstream areas of the Yellow River, College of Forestry, Shandong Agricultural University, Taian, 271018, China.
| | - Li-Jun Liu
- State Forestry and Grassland Administration Key Laboratory of Silviculture in downstream areas of the Yellow River, College of Forestry, Shandong Agricultural University, Taian, 271018, China.
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Gao Y, Chen Z, Feng Q, Long T, Ding J, Shu P, Deng H, Yu P, Tan W, Liu S, Rodriguez LG, Wang L, Resco de Dios V, Yao Y. ELONGATED HYPOCOTYL 5a modulates FLOWERING LOCUS T2 and gibberellin levels to control dormancy and bud break in poplar. THE PLANT CELL 2024; 36:1963-1984. [PMID: 38271284 PMCID: PMC11062467 DOI: 10.1093/plcell/koae022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 12/15/2023] [Accepted: 01/16/2024] [Indexed: 01/27/2024]
Abstract
Photoperiod is a crucial environmental cue for phenological responses, including growth cessation and winter dormancy in perennial woody plants. Two regulatory modules within the photoperiod pathway explain bud dormancy induction in poplar (Populus spp.): the circadian oscillator LATE ELONGATED HYPOCOTYL 2 (LHY2) and GIGANTEA-like genes (GIs) both regulate the key target for winter dormancy induction FLOWERING LOCUS T2 (FT2). However, modification of LHY2 and GIs cannot completely prevent growth cessation and bud set under short-day (SD) conditions, indicating that additional regulatory modules are likely involved. We identified PtoHY5a, an orthologs of the photomorphogenesis regulatory factor ELONGATED HYPOCOTYL 5 (HY5) in poplar (Populus tomentosa), that directly activates PtoFT2 expression and represses the circadian oscillation of LHY2, indirectly activating PtoFT2 expression. Thus, PtoHY5a suppresses SD-induced growth cessation and bud set. Accordingly, PtoHY5a knockout facilitates dormancy induction. PtoHY5a also inhibits bud-break in poplar by controlling gibberellic acid (GA) levels in apical buds. Additionally, PtoHY5a regulates the photoperiodic control of seasonal growth downstream of phytochrome PHYB2. Thus, PtoHY5a modulates seasonal growth in poplar by regulating the PtoPHYB2-PtoHY5a-PtoFT2 module to determine the onset of winter dormancy, and by fine-tuning GA levels to control bud-break.
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Affiliation(s)
- Yongfeng Gao
- School of Life Science and Engineering, Southwest University of Science and Technology, 621010 Mianyang, China
| | - Zihao Chen
- School of Life Science and Engineering, Southwest University of Science and Technology, 621010 Mianyang, China
| | - Qian Feng
- School of Life Science and Engineering, Southwest University of Science and Technology, 621010 Mianyang, China
| | - Tao Long
- School of Life Science and Engineering, Southwest University of Science and Technology, 621010 Mianyang, China
| | - Jihua Ding
- College of Horticulture and Forestry, Huazhong Agricultural University, 430070 Wuhan, China
| | - Peng Shu
- Clinical Medical Research Center, Xinqiao Hospital, Army Medical University, 400037 Chongqing, China
| | - Heng Deng
- School of Life Science and Engineering, Southwest University of Science and Technology, 621010 Mianyang, China
| | - Peizhi Yu
- School of Life Science and Engineering, Southwest University of Science and Technology, 621010 Mianyang, China
| | - Wenrong Tan
- School of Life Science and Engineering, Southwest University of Science and Technology, 621010 Mianyang, China
| | - Siqin Liu
- School of Life Science and Engineering, Southwest University of Science and Technology, 621010 Mianyang, China
| | - Lucas Gutierrez Rodriguez
- School of Life Science and Engineering, Southwest University of Science and Technology, 621010 Mianyang, China
| | - Lijun Wang
- School of Life Science and Engineering, Southwest University of Science and Technology, 621010 Mianyang, China
| | - Víctor Resco de Dios
- School of Life Science and Engineering, Southwest University of Science and Technology, 621010 Mianyang, China
| | - Yinan Yao
- School of Life Science and Engineering, Southwest University of Science and Technology, 621010 Mianyang, China
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Kovalev MA, Gladysh NS, Bogdanova AS, Bolsheva NL, Popchenko MI, Kudryavtseva AV. Editing Metabolism, Sex, and Microbiome: How Can We Help Poplar Resist Pathogens? Int J Mol Sci 2024; 25:1308. [PMID: 38279306 PMCID: PMC10816636 DOI: 10.3390/ijms25021308] [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: 11/18/2023] [Revised: 01/14/2024] [Accepted: 01/19/2024] [Indexed: 01/28/2024] Open
Abstract
Poplar (Populus) is a genus of woody plants of great economic value. Due to the growing economic importance of poplar, there is a need to ensure its stable growth by increasing its resistance to pathogens. Genetic engineering can create organisms with improved traits faster than traditional methods, and with the development of CRISPR/Cas-based genome editing systems, scientists have a new highly effective tool for creating valuable genotypes. In this review, we summarize the latest research data on poplar diseases, the biology of their pathogens and how these plants resist pathogens. In the final section, we propose to plant male or mixed poplar populations; consider the genes of the MLO group, transcription factors of the WRKY and MYB families and defensive proteins BbChit1, LJAMP2, MsrA2 and PtDef as the most promising targets for genetic engineering; and also pay attention to the possibility of microbiome engineering.
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Affiliation(s)
- Maxim A. Kovalev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (M.A.K.); (N.S.G.); (A.S.B.); (N.L.B.); (M.I.P.)
- Department of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Natalya S. Gladysh
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (M.A.K.); (N.S.G.); (A.S.B.); (N.L.B.); (M.I.P.)
| | - Alina S. Bogdanova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (M.A.K.); (N.S.G.); (A.S.B.); (N.L.B.); (M.I.P.)
- Institute of Agrobiotechnology, Russian State Agrarian University—Moscow Timiryazev Agricultural Academy, 127434 Moscow, Russia
| | - Nadezhda L. Bolsheva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (M.A.K.); (N.S.G.); (A.S.B.); (N.L.B.); (M.I.P.)
| | - Mikhail I. Popchenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (M.A.K.); (N.S.G.); (A.S.B.); (N.L.B.); (M.I.P.)
| | - Anna V. Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (M.A.K.); (N.S.G.); (A.S.B.); (N.L.B.); (M.I.P.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia
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Yang P, Sun Y, Sun X, Li Y, Wang L. Optimization of preparation and transformation of protoplasts from Populus simonii × P. nigra leaves and subcellular localization of the major latex protein 328 (MLP328). PLANT METHODS 2024; 20:3. [PMID: 38178205 PMCID: PMC10765669 DOI: 10.1186/s13007-023-01128-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 12/19/2023] [Indexed: 01/06/2024]
Abstract
BACKGROUND Populus simonii × P. nigra is an ideal material for studying the molecular mechanisms of woody plants. In recent years, research on Populus simonii × P. nigra has increasingly focused on the application of transgenic technology to improve salt tolerance. However, the rapid characterization of gene functions has been hampered by the long growth cycle and exceedingly poor transformation efficiency. Protoplasts are an important tool for plant gene engineering, which can assist with challenging genetic transformation and the protracted growth cycle of Populus simonii × P. nigra. This study established an optimized system for the preparation and transformation of protoplasts from Populus simonii × P. nigra leaves, making genetic research on Populus simonii × P. nigra faster and more convenient. Major Latex Protein (MLP) family genes play a crucial role in plant salt stress response. In the previous study, we discovered that PsnMLP328 can be induced by salt treatment, which suggested that this gene may be involved in response to salt stress. Protein localization is a suggestion for its function. Therefore, we conducted subcellular localization analysis using protoplasts of Populus simonii × P. nigra to study the function of the PsnMLP328 gene preliminarily. RESULTS This study established an optimized system for the preparation and transformation of Populus simonii × P. nigra protoplasts. The research results indicate that the optimal separation scheme for the protoplasts of Populus simonii × P. nigra leaves included 2.5% cellulase R-10, 0.6% macerozyme R-10, 0.3% pectolyase Y-23, and 0.8 M mannitol. After enzymatic digestion for 5 h, the yield of obtained protoplasts could reach up to 2 × 107 protoplasts/gFW, with a high viability of 98%. We carried out the subcellular localization analysis based on the optimized transient transformation system, and the results indicated that the MLP328 protein is localized in the nucleus and cytoplasm; thereby proving the effectiveness of the transformation system. CONCLUSION In summary, this study successfully established an efficient system for preparing and transforming leaf protoplasts of Populus simonii × P. nigra, laying the foundation for future research on gene function and expression of Populus simonii × P. nigra.
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Affiliation(s)
- Ping Yang
- Department of Biotechnology, Institute of Advanced Technology, Heilongjiang Academy of Sciences, Harbin, 150001, China
| | - Yao Sun
- Department of Biotechnology, Institute of Advanced Technology, Heilongjiang Academy of Sciences, Harbin, 150001, China
| | - Xin Sun
- Department of Biotechnology, Institute of Advanced Technology, Heilongjiang Academy of Sciences, Harbin, 150001, China
| | - Yao Li
- Department of Biotechnology, Institute of Advanced Technology, Heilongjiang Academy of Sciences, Harbin, 150001, China
| | - Lei Wang
- Department of Biotechnology, Institute of Advanced Technology, Heilongjiang Academy of Sciences, Harbin, 150001, China.
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Kumar A, Rawat N, Thakur S, Joshi R, Pandey SS. A highly efficient protocol for isolation of protoplast from China, Assam and Cambod types of tea plants [Camellia sinensis (L.) O. Kuntze]. PLANT METHODS 2023; 19:147. [PMID: 38102681 PMCID: PMC10724972 DOI: 10.1186/s13007-023-01120-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 12/01/2023] [Indexed: 12/17/2023]
Abstract
BACKGROUND Tea is the most popular beverage worldwide second only to water. Its demand is tremendously rising due to increased awareness of its medicinal importance. The quality and uses of tea depend on the tea-types which are mainly three types including China, Assam and Cambod type having distinct compositions of secondary metabolites. Huge variation in secondary metabolites in different tea-types and cultivars limited the successful application of various approaches used for its trait improvement. The efficiency of a protocol for isolation of protoplast is specific to the types and cultivars of tea plants. The existing tea protoplast-isolation protocols [which were optimized for tea-types (China and Assam type) and Chinese cultivars grown in China] were found ineffective on types/cultivars grown in India due to type/cultivar variability. Therefore, optimization of protoplast-isolation protocol is essential for tea-types/cultivars grown in India, as it is the second largest producer of tea and the largest producer of black tea. Here, efforts were made to develop an efficient protoplast-isolation protocol from all major types of tea (China, Assam and Cambod types) grown in India and also from three types of tender leaves obtained from field-grown, hydroponically-grown and tissue culture-grown tea plants. RESULTS Developed protoplast-isolation protocol was effective for different types of leaf tissue obtained from the tender leaves of field-grown, hydroponically-grown and tissue culture-grown tea plants. Moreover, optimized protocol effectively worked on all three types of tea including China, Assam and Cambod types cultivated in India. The digestion of leaves with 3% cellulase R-10, 0.6% macerozyme, 1% hemicellulase and 4% polyvinylpyrrolidone for 12 h at 28ºC yielded approximately 3.8-4.6 × 107 protoplasts per gram fresh tissue and 80-95% viability in selected tea cultivars, and tissue culture plant material was found most appropriate for protoplast isolation. CONCLUSIONS In conclusion, we reported an efficient protocol for isolation of protoplasts from tender tea leaves of all major tea-types (China, Assam and Cambod) grown in India. Moreover, the protocol is also effective for tender-leaf tissue of field-grown, hydroponically-grown and tissue culture-grown tea plants. The findings are expected to contribute to the genetic improvement of tea traits widely.
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Affiliation(s)
- Abhishek Kumar
- Biotechnology Division, Council of Scientific and Industrial Research (CSIR)-Institute of Himalayan Bioresource Technology, Palampur, 176061, India
| | - Nikhil Rawat
- Biotechnology Division, Council of Scientific and Industrial Research (CSIR)-Institute of Himalayan Bioresource Technology, Palampur, 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Shweta Thakur
- Biotechnology Division, Council of Scientific and Industrial Research (CSIR)-Institute of Himalayan Bioresource Technology, Palampur, 176061, India
| | - Rohit Joshi
- Biotechnology Division, Council of Scientific and Industrial Research (CSIR)-Institute of Himalayan Bioresource Technology, Palampur, 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Shiv Shanker Pandey
- Biotechnology Division, Council of Scientific and Industrial Research (CSIR)-Institute of Himalayan Bioresource Technology, Palampur, 176061, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Yang C, Yu R, Li J, Wang K, Liu G. Preparation of leaf protoplasts from Populus (Populus × xiaohei T. S. Hwang et Liang) and establishment of transient expression system. JOURNAL OF PLANT PHYSIOLOGY 2023; 291:154122. [PMID: 37979433 DOI: 10.1016/j.jplph.2023.154122] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 09/12/2023] [Accepted: 10/19/2023] [Indexed: 11/20/2023]
Abstract
Poplar, as a typical woody plant, is an ideal raw material for the production of lignocellulose biofuel. However, the longer life cycle is not conducive to the rapid identification of poplar genes. At present, protoplasts have been used for gene function identification and high-throughput analysis in many model plants. In this paper, a simplified and efficient protoplast isolation and transient expression system of Populus (Populus × xiaohei T. S. Hwang et Liang) is described. Firstly, we proposed an efficient enzyme hydrolysis method for isolating protoplasts from leaves of Populus × xiaohei. Secondly, we optimized the conditions of protoplast transformation mediated by PEG, and established an efficient transient expression system of protoplasts of Populus × xiaohei. Finally, the subcellular localization of three identified Dof transcription factors (PnDof19, PnDof20 and PnDof30) was also observed in the nucleus by using this scheme, which proved that the method was feasible. In general, this efficient method of protoplast isolation and transformation can be used for the study of protein subcellular localization and can be applied to other fields of molecular biology, such as protein interaction, gene activation and so on.
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Affiliation(s)
- Chengjun Yang
- Northeast Asia Biodiversity Research Center, Northeast Forestry University, Harbin, 150040, China; State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, No. 26, Hexing Road, HarBin, 150040, China
| | - Ruiqiang Yu
- Northeast Asia Biodiversity Research Center, Northeast Forestry University, Harbin, 150040, China
| | - Jinbo Li
- Northeast Asia Biodiversity Research Center, Northeast Forestry University, Harbin, 150040, China
| | - Kai Wang
- Northeast Asia Biodiversity Research Center, Northeast Forestry University, Harbin, 150040, China
| | - Guanjun Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, No. 26, Hexing Road, HarBin, 150040, China.
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Chen K, Chen J, Pi X, Huang LJ, Li N. Isolation, Purification, and Application of Protoplasts and Transient Expression Systems in Plants. Int J Mol Sci 2023; 24:16892. [PMID: 38069215 PMCID: PMC10706244 DOI: 10.3390/ijms242316892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 11/23/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
Protoplasts, derived from plant cells, exhibit remarkable totipotency and hold significant value across a wide spectrum of biological and biotechnological applications. These versatile applications encompass protein subcellular localization and interaction analysis, gene expression regulation, functional characterization, gene editing techniques, and single-cell sequencing. Protoplasts' usability stems from their inherent accessibility and their ability to efficiently incorporate exogenous genes. In this review, we provide a comprehensive overview, including details on isolation procedures and influencing factors, purification and viability assessment methodologies, and the utilization of the protoplast transient expression system. The aim is to provide a comprehensive overview of current applications and offer valuable insights into protoplast isolation and the establishment of transient expression systems in a diverse range of plant species, thereby serving as a valuable resource for the plant science community.
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Affiliation(s)
- Kebin Chen
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha 410004, China
- Key Laboratory of Forest Bio-Resources and Integrated Pest Management for Higher Education in Hunan Province, Central South University of Forestry and Technology, Changsha 410004, China
| | - Jiali Chen
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha 410004, China
- Key Laboratory of Forest Bio-Resources and Integrated Pest Management for Higher Education in Hunan Province, Central South University of Forestry and Technology, Changsha 410004, China
| | - Xin Pi
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha 410004, China
| | - Li-Jun Huang
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha 410004, China
| | - Ning Li
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha 410004, China
- Key Laboratory of Forest Bio-Resources and Integrated Pest Management for Higher Education in Hunan Province, Central South University of Forestry and Technology, Changsha 410004, China
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Yuan G, Liu Y, Yao T, Muchero W, Chen JG, Tuskan GA, Yang X. eYGFPuv-Assisted Transgenic Selection in Populus deltoides WV94 and Multiplex Genome Editing in Protoplasts of P. trichocarpa × P. deltoides Clone '52-225'. PLANTS (BASEL, SWITZERLAND) 2023; 12:1657. [PMID: 37111880 PMCID: PMC10145771 DOI: 10.3390/plants12081657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 03/16/2023] [Accepted: 03/30/2023] [Indexed: 06/19/2023]
Abstract
Although CRISPR/Cas-based genome editing has been widely used for plant genetic engineering, its application in the genetic improvement of trees has been limited, partly because of challenges in Agrobacterium-mediated transformation. As an important model for poplar genomics and biotechnology research, eastern cottonwood (Populus deltoides) clone WV94 can be transformed by A. tumefaciens, but several challenges remain unresolved, including the relatively low transformation efficiency and the relatively high rate of false positives from antibiotic-based selection of transgenic events. Moreover, the efficacy of CRISPR-Cas system has not been explored in P. deltoides yet. Here, we first optimized the protocol for Agrobacterium-mediated stable transformation in P. deltoides WV94 and applied a UV-visible reporter called eYGFPuv in transformation. Our results showed that the transgenic events in the early stage of transformation could be easily recognized and counted in a non-invasive manner to narrow down the number of regenerated shoots for further molecular characterization (at the DNA or mRNA level) using PCR. We found that approximately 8.7% of explants regenerated transgenic shoots with green fluorescence within two months. Next, we examined the efficacy of multiplex CRISPR-based genome editing in the protoplasts derived from P. deltoides WV94 and hybrid poplar clone '52-225' (P. trichocarpa × P. deltoides clone '52-225'). The two constructs expressing the Trex2-Cas9 system resulted in mutation efficiency ranging from 31% to 57% in hybrid poplar clone 52-225, but no editing events were observed in P. deltoides WV94 transient assay. The eYGFPuv-assisted plant transformation and genome editing approach demonstrated in this study has great potential for accelerating the genome editing-based breeding process in poplar and other non-model plants species and point to the need for additional CRISPR work in P. deltoides.
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Affiliation(s)
- Guoliang Yuan
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Chemical and Biological Process Development Group, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA 99352, USA
| | - Yang Liu
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN 37831, USA
| | - Tao Yao
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Wellington Muchero
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Jin-Gui Chen
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Gerald A. Tuskan
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Xiaohan Yang
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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D'Ercole C, de Marco A. Isolation of Adhirons Specific for Plant Protoplast Membrane Biomarkers Is Simplified by Phagemid Design. Methods Mol Biol 2023; 2681:33-45. [PMID: 37405641 DOI: 10.1007/978-1-0716-3279-6_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2023]
Abstract
Phage display is an effective method to retrieve binders specific for a target epitope from a large clone library. Nevertheless, the panning process allows for the accumulation of some contaminant clones into the selected phage pool and, consequently, each clone requires individual screening to verify its actual specificity. This step is time-consuming, independently on the chosen method, and relies on the availability of reliable reagents. Since phages display a single binder responsible for the antigen recognition but their coat is formed by several repeats of the same proteins, the targeting of coat epitopes is often exploited to amplify the signal. Commercial anti-M13 antibodies are commonly labeled with peroxidase or FITC but customized antibodies might be necessary for specific applications. Here, we report a protocol describing the selection of anti-protoplast Adhirons that relies on the availability of nanobodies fused to a fluorescent protein to use during flow cytometry screening. Specifically, when preparing our Adhiron synthetic library, we designed a new phagemid that allows the expression of the clones fused to three tags. These can interact with a large variety of commercial and home-made reagents, selected according to the needs of the downstream characterization process. In the described case, we combined the ALFA-tagged Adhirons with an anti-ALFAtag nanobody fused with the fluorescent protein mRuby3.
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Affiliation(s)
- Claudia D'Ercole
- Laboratory of Environmental and Life Sciences, University of Nova Gorica, Rožna Dolina, Nova Gorica, Slovenia
| | - Ario de Marco
- Laboratory of Environmental and Life Sciences, University of Nova Gorica, Rožna Dolina, Nova Gorica, Slovenia.
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Yuan G, Tuskan GA, Yang X. Use of Fluorescent Protein Reporters for Assessing and Detecting Genome Editing Reagents and Transgene Expression in Plants. Methods Mol Biol 2023; 2653:115-127. [PMID: 36995623 DOI: 10.1007/978-1-0716-3131-7_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Fluorescent protein reporters have been widely used for monitoring the expression of target genes in various engineered organisms. Although a wide range of analytical approaches (e.g., genotyping PCR, digital PCR, DNA sequencing) have been utilized to detect and identify genome editing reagents and transgene expression in genetically modified plants, these methods are usually limited to use in the late stages of plant transformation and can only be used invasively. Here we describe GFP- and eYGFPuv-based strategies and methods for assessing and detecting genome editing reagents and transgene expression in plants, including protoplast transformation, leaf infiltration, and stable transformation. These methods and strategies enable easy, noninvasive screening of genome editing and transgenic events in plants.
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Affiliation(s)
- Guoliang Yuan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
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Abstract
Droplet-based single-cell RNA-sequencing (scRNA-seq) empowers transcriptomic profiling with an unprecedented resolution, facilitating insights into the cellular heterogeneity of tissues, developmental progressions, stress-response dynamics, and more at single-cell level. In this chapter, we describe the experimental workflow of processing Arabidopsis root tissue into protoplasts and generating single-cell transcriptomes. We also describe the general computational workflow of visualizing and utilizing scRNA-seq data. This protocol can be used as a starting point for establishing a scRNA-seq workflow.
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Affiliation(s)
- Yuji Ke
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Max Minne
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Thomas Eekhout
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- VIB Single Cell Core, VIB, Ghent/Leuven, Belgium
| | - Bert De Rybel
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium.
- VIB Center for Plant Systems Biology, Ghent, Belgium.
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12
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Ye S, Ding W, Bai W, Lu J, Zhou L, Ma X, Zhu Q. Application of a novel strong promoter from Chinese fir ( Cunninghamia lanceolate) in the CRISPR/Cas mediated genome editing of its protoplasts and transgenesis of rice and poplar. FRONTIERS IN PLANT SCIENCE 2023; 14:1179394. [PMID: 37152166 PMCID: PMC10157052 DOI: 10.3389/fpls.2023.1179394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 03/27/2023] [Indexed: 05/09/2023]
Abstract
Novel constitutive promoters are essential for plant biotechnology. Although in angiosperms, a number of promoters were applied in monocots or dicots genetic engineering, only a few promoters were used in gymnosperm. Here we identified two strong promoters (Cula11 and Cula08) from Chinese fir (C. lanceolate) by screening the transcriptomic data and preliminary promoter activity assays in tobacco. By using the newly established Chinese fir protoplast transient expression technology that enables in vivo molecular biology studies in its homologous system, we compared the activities of Cula11 and Cula08 with that of the commonly used promoters in genetic engineering of monocots or dicots, such as CaM35S, CmYLCV, and ZmUbi, and our results revealed that Cula11 and Cula08 promoters have stronger activities in Chinese fir protoplasts. Furthermore, the vector containing Cas gene driven by Cula11 promoter and sgRNA driven by the newly isolated CulaU6b polyIII promoters were introduced into Chinese fir protoplasts, and CRISPR/Cas mediated gene knock-out event was successfully achieved. More importantly, compared with the commonly used promoters in the genetic engineering in angiosperms, Cula11 promoter has much stronger activity than CaM35S promoter in transgenic poplar, and ZmUbi promoter in transgenic rice, respectively, indicating its potential application in poplar and rice genetic engineering. Overall, the novel putative constitutive gene promoters reported here will have great potential application in gymnosperm and angiosperm biotechnology, and the transient gene expression system established here will serve as a useful tool for the molecular and genetic analyses of Chinese fir genes.
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Affiliation(s)
| | | | | | | | | | | | - Qiang Zhu
- *Correspondence: Xiangqing Ma, ; Qiang Zhu,
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13
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Brazel AJ, Graciet E. Complexity of Abiotic Stress Stimuli: Mimicking Hypoxic Conditions Experimentally on the Basis of Naturally Occurring Environments. Methods Mol Biol 2023; 2642:23-48. [PMID: 36944871 DOI: 10.1007/978-1-0716-3044-0_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Plants require oxygen to respire and produce energy. Plant cells are exposed to low oxygen levels (hypoxia) in different contexts and have evolved conserved molecular responses to hypoxia. Both environmental and developmental factors can influence intracellular oxygen concentrations. In nature, plants can experience hypoxic conditions when the soil becomes saturated with water following heavy precipitation (i.e., waterlogging). Hypoxia can also arise in specific tissues that have poor gas exchange with atmospheric oxygen. In this case, hypoxic niches that are physiologically and developmentally relevant may form. To dissect the molecular mechanisms underlying the regulation of hypoxia response in plants, a wide range of hypoxia-inducing methods have been used in the laboratory setting. Yet, the different characteristics, pros and cons of each of these hypoxia treatments are seldom compared between methods, and with natural forms of hypoxia. In this chapter, we present both environmental and developmental forms of hypoxia that plants encounter in the wild, as well as the different experimental hypoxia treatments used to mimic them in the laboratory setting, with the aim of informing on what experimental approaches might be most appropriate to the questions addressed, including stress signaling and regulation.
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14
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Hyden B, Yuan G, Liu Y, Smart LB, Tuskan GA, Yang X. Protoplast-Based Transient Expression and Gene Editing in Shrub Willow ( Salix purpurea L.). PLANTS (BASEL, SWITZERLAND) 2022; 11:3490. [PMID: 36559601 PMCID: PMC9784668 DOI: 10.3390/plants11243490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 11/30/2022] [Accepted: 12/10/2022] [Indexed: 06/17/2023]
Abstract
Shrub willows (Salix section Vetrix) are grown as a bioenergy crop in multiple countries and as ornamentals across the northern hemisphere. To facilitate the breeding and genetic advancement of shrub willow, there is a strong interest in the characterization and functional validation of genes involved in plant growth and biomass production. While protocols for shoot regeneration in tissue culture and production of stably transformed lines have greatly advanced this research in the closely related genus Populus, a lack of efficient methods for regeneration and transformation has stymied similar advancements in willow functional genomics. Moreover, transient expression assays in willow have been limited to callus tissue and hairy root systems. Here we report an efficient method for protoplast isolation from S. purpurea leaf tissue, along with transient overexpression and CRISPR-Cas9 mediated mutations. This is the first such report of transient gene expression in Salix protoplasts as well as the first application of CRISPR technology in this genus. These new capabilities pave the way for future functional genomics studies in this important bioenergy and ornamental crop.
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Affiliation(s)
- Brennan Hyden
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
- School of Integrative Plant Sciences, Cornell AgriTech, Cornell University, Geneva, NY 14456, USA
| | - Guoliang Yuan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Yang Liu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Lawrence B. Smart
- School of Integrative Plant Sciences, Cornell AgriTech, Cornell University, Geneva, NY 14456, USA
| | - Gerald A. Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
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15
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Chen N, Tong S, Yang J, Qin J, Wang W, Chen K, Shi W, Li J, Liu J, Jiang Y. PtoWRKY40 interacts with PtoPHR1-LIKE3 while regulating the phosphate starvation response in poplar. PLANT PHYSIOLOGY 2022; 190:2688-2705. [PMID: 36040189 PMCID: PMC9706449 DOI: 10.1093/plphys/kiac404] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 08/03/2022] [Indexed: 05/27/2023]
Abstract
Plants usually suffer from phosphorus starvation because of the low inorganic phosphate (Pi) status of most soils. To cope with this, plants have evolved an adaptive phosphate starvation response (PSR) which involves both developmental and metabolic changes regulated mainly by PHOSPHATE STARVATION RESPONSE1 (PHR1) and its homologs. Here, we elucidated how perennial woody plants, such as poplars (Populus spp.), respond to low-Pi stress. We first performed RNA-seq analysis of low-Pi-treated poplars and identified PtoWRKY40 is rapidly downregulated and protein degraded after stress. Overexpressing and knocking-down PtoWRKY40 downregulated and upregulated the expression of Pi starvation signaling genes, respectively, such as PHOSPHATE TRANSPORTER1 (PHT1)-type genes and PURPLE ACID PHOSPHATASE genes. PtoWRKY40 bound to the W box in the promoter of several PtoPHT1s and repressed their expression. Moreover, PtoWRKY40 interacted with PtoPHR1-LIKE3 (PtoPHL3), a PHR1 homolog in poplar, to inhibit the latter binding to the P1BS element and thus reduced PtoPHT1s' transcription under Pi-sufficient conditions. However, Pi deficiency decreased PtoWRKY40 abundance and therefore released its inhibition on PHT1s. In conclusion, we have uncovered a PSR mechanism mediated by PtoWRKY40 and PtoPHL3 which regulates Pi content in poplars, deepening our understanding of how poplars adapt to diverse Pi conditions and regulate appropriate responses to maintain Pi homeostasis.
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Affiliation(s)
- Ningning Chen
- College of Life Science, Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, Sichuan University, Chengdu, 610065, China
| | - Shaofei Tong
- College of Life Science, Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, Sichuan University, Chengdu, 610065, China
| | - Jian Yang
- College of Life Sciences, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065, China
| | - Jiajia Qin
- College of Life Science, Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, Sichuan University, Chengdu, 610065, China
| | - Weiwei Wang
- College of Life Science, Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, Sichuan University, Chengdu, 610065, China
| | - Kai Chen
- College of Life Science, Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, Sichuan University, Chengdu, 610065, China
| | - Wensen Shi
- College of Life Science, Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, Sichuan University, Chengdu, 610065, China
| | - Jiacong Li
- College of Life Science, Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, Sichuan University, Chengdu, 610065, China
| | - Jianquan Liu
- College of Life Science, Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, Sichuan University, Chengdu, 610065, China
- College of Ecology, State Key Laboratory of Grassland Agro-Ecosystem, Lanzhou University, Lanzhou, 730000, China
| | - Yuanzhong Jiang
- College of Life Science, Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, Sichuan University, Chengdu, 610065, China
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16
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Ghose AK, Abdullah SNA, Md Hatta MA, Megat Wahab PE. DNA Free CRISPR/DCAS9 Based Transcriptional Activation System for UGT76G1 Gene in Stevia rebaudiana Bertoni Protoplasts. PLANTS (BASEL, SWITZERLAND) 2022; 11:2393. [PMID: 36145794 PMCID: PMC9501275 DOI: 10.3390/plants11182393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 08/23/2022] [Accepted: 09/01/2022] [Indexed: 06/16/2023]
Abstract
The UDP-glycosyltransferase 76G1 (UGT76G1) is responsible for the conversion of stevioside to rebaudioside A. Four single guide RNAs (sgRNAs) were designed from the UGT76G1 proximal promoter region of stevia by using the online-based tool, benchling. The dCas9 fused with VP64 as a transcriptional activation domain (TAD) was produced and purified for the formation of ribonucleoproteins (RNPs) by mixing with the in vitro transcribed sgRNAs. Protoplast yield was the highest from leaf mesophyll of in vitro grown stevia plantlets (3.16 × 106/g of FW) using ES5 (1.25% cellulase R-10 and 0.75% macerozyme R-10). The RNPs were delivered into the isolated protoplasts through the Polyethylene glycol (PEG)-mediated transfection method. The highest endogenous activation of the UGT76G1 gene was detected at 27.51-fold after 24 h of transfection with RNP30 consisting of CRISPR/dCas9-TAD with sgRNA30 and a similar activation level was obtained using RNP18, RNP33, and RNP34, produced using sgRNA18, sgRNA33, and sgRNA34, respectively. Activation of UGT76G1 by RNP18 led to a significant increase in the expression of the rate-limiting enzyme UGT85C2 by 2.37-fold and there was an increasing trend in the expression of UGT85C2 using RNP30, RNP33, and RNP34. Successful application of CRISPR/dCas9-TAD RNP in activating specific genes can avoid the negative integration effects of introduced DNA in the host genome.
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Affiliation(s)
- Asish Kumar Ghose
- Laboratory of Agronomy and Sustainable Crop Protection, Institute of Plantation Studies, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
- Biotechnology Division, Bangladesh Sugarcrop Research Institute, Ishurdi, Pabna 6620, Bangladesh
| | - Siti Nor Akmar Abdullah
- Laboratory of Agronomy and Sustainable Crop Protection, Institute of Plantation Studies, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
- Department of Agriculture Technology, Faculty of Agriculture, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Muhammad Asyraf Md Hatta
- Department of Agriculture Technology, Faculty of Agriculture, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Puteri Edaroyati Megat Wahab
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
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17
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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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18
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Tong S, Wang Y, Chen N, Wang D, Liu B, Wang W, Chen Y, Liu J, Ma T, Jiang Y. PtoNF-YC9-SRMT-PtoRD26 module regulates the high saline tolerance of a triploid poplar. Genome Biol 2022; 23:148. [PMID: 35799188 PMCID: PMC9264554 DOI: 10.1186/s13059-022-02718-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 06/25/2022] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Sensing and responding to stresses determine the tolerance of plants to adverse environments. The triploid Chinese white poplar is widely cultivated in North China because of its adaptation to a wide range of habitats including highly saline ones. However, its triploid genome complicates any detailed investigation of the molecular mechanisms underlying its adaptations. RESULTS We report a haplotype-resolved genome of this triploid poplar and characterize, using reverse genetics and biochemical approaches, a MYB gene, SALT RESPONSIVE MYB TRANSCRIPTION FACTOR (SRMT), which combines NUCLEAR FACTOR Y SUBUNIT C 9 (PtoNF-YC9) and RESPONSIVE TO DESICCATION 26 (PtoRD26), to regulate an ABA-dependent salt-stress response signaling. We reveal that the salt-inducible PtoRD26 is dependent on ABA signaling. We demonstrate that ABA or salt drives PtoNF-YC9 shuttling into the nucleus where it interacts with SRMT, resulting in the rapid expression of PtoRD26 which in turn directly regulates SRMT. This positive feedback loop of SRMT-PtoRD26 can rapidly amplify salt-stress signaling. Interference with either component of this regulatory module reduces the salt tolerance of this triploid poplar. CONCLUSION Our findings reveal a novel ABA-dependent salt-responsive mechanism, which is mediated by the PtoNF-YC9-SRMT-PtoRD26 module that confers salt tolerance to this triploid poplar. These genes may therefore also serve as potential and important modification targets in breeding programs.
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Affiliation(s)
- Shaofei Tong
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, No. 24 South Section 1, Yihuan Road, Chengdu, 610065, China
| | - Yubo Wang
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, No. 24 South Section 1, Yihuan Road, Chengdu, 610065, China
| | - Ningning Chen
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, No. 24 South Section 1, Yihuan Road, Chengdu, 610065, China
| | - Deyan Wang
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, No. 24 South Section 1, Yihuan Road, Chengdu, 610065, China
| | - Bao Liu
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, No. 24 South Section 1, Yihuan Road, Chengdu, 610065, China
| | - Weiwei Wang
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, No. 24 South Section 1, Yihuan Road, Chengdu, 610065, China
| | - Yang Chen
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, No. 24 South Section 1, Yihuan Road, Chengdu, 610065, China
| | - Jianquan Liu
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, No. 24 South Section 1, Yihuan Road, Chengdu, 610065, China.
| | - Tao Ma
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, No. 24 South Section 1, Yihuan Road, Chengdu, 610065, China.
| | - Yuanzhong Jiang
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, No. 24 South Section 1, Yihuan Road, Chengdu, 610065, China.
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19
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Park SJ, Bae EK, Choi H, Yoon SK, Jang HA, Choi YI, Lee H. Knockdown of PagSAP11 Confers Drought Resistance and Promotes Lateral Shoot Growth in Hybrid Poplar ( Populus alba × Populus tremula var. glandulosa). FRONTIERS IN PLANT SCIENCE 2022; 13:925744. [PMID: 35812954 PMCID: PMC9263715 DOI: 10.3389/fpls.2022.925744] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 05/30/2022] [Indexed: 06/15/2023]
Abstract
Plants have evolved defense mechanisms to overcome unfavorable climatic conditions. The growth and development of plants are regulated in response to environmental stress. In this study, we investigated the molecular and physiological characteristics of a novel gene PagSAP11 in hybrid poplar (Populus alba × Populus tremula var. glandulosa) under drought stress. PagSAP11, a stress-associated protein (SAP) family gene, encodes a putative protein containing an A20 and AN1 zinc-finger domain at its N- and C-termini, respectively. Knockdown of PagSAP11 transgenic poplars (SAP11-Ri) enhanced their tolerance to drought stress compared with wild type plants. Moreover, the RNAi lines showed increased branching of lateral shoots that led to a gain in fresh weight, even when grown in the living modified organism (LMO) field. In SAP11-Ri transgenic plants, the expression levels of genes involved in axillary bud outgrowth and cell proliferation such as DML10, CYP707A and RAX were increased while the DRM gene which involved in bud dormancy was down-regulated. Taken together, these results indicate that PagSAP11 represents a promising candidate gene for engineering trees with improved stress tolerance and growth during unfavorable conditions.
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Affiliation(s)
- Su Jin Park
- Department of Forest Bioresources, National Institute of Forest Science, Suwon, South Korea
| | - Eun-Kyung Bae
- Department of Forest Bioresources, National Institute of Forest Science, Suwon, South Korea
| | - Hyunmo Choi
- Forest Biomaterials Research Center, National Institute of Forest Science, Jinju, South Korea
| | - Seo-Kyung Yoon
- Department of Forest Sciences, Seoul National University, Seoul, South Korea
| | - Hyun-A Jang
- Department of Forest Bioresources, National Institute of Forest Science, Suwon, South Korea
| | - Young-Im Choi
- National Forest Seed and Variety Center, Forest Service, Chungju, South Korea
| | - Hyoshin Lee
- Department of Forest Bioresources, National Institute of Forest Science, Suwon, South Korea
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20
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Nayeri S, Baghban Kohnehrouz B, Ahmadikhah A, Mahna N. CRISPR/Cas9-mediated P-CR domain-specific engineering of CESA4 heterodimerization capacity alters cell wall architecture and improves saccharification efficiency in poplar. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1197-1212. [PMID: 35266285 PMCID: PMC9129088 DOI: 10.1111/pbi.13803] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 02/10/2022] [Accepted: 02/21/2022] [Indexed: 05/21/2023]
Abstract
Cellulose is the most abundant unique biopolymer in nature with widespread applications in bioenergy and high-value bioproducts. The large transmembrane-localized cellulose synthase (CESA) complexes (CSCs) play a pivotal role in the biosynthesis and orientation of the para-crystalline cellulose microfibrils during secondary cell wall (SCW) deposition. However, the hub CESA subunit with high potential homo/heterodimerization capacity and its functional effects on cell wall architecture, cellulose crystallinity, and saccharification efficiency remains unclear. Here, we reported the highly potent binding site containing four residues of Pro435, Trp436, Pro437, and Gly438 in the plant-conserved region (P-CR) of PalCESA4 subunit, which are involved in the CESA4-CESA8 heterodimerization. The CRISPR/Cas9-knockout mutagenesis in the predicted binding site results in physiological abnormalities, stunt growth, and deficient roots. The homozygous double substitution of W436Q and P437S and heterozygous double deletions of W436 and P437 residues potentially reduced CESA4-binding affinity resulting in normal roots, 1.5-2-fold higher plant growth and cell wall regeneration rates, 1.7-fold thinner cell wall, high hemicellulose content, 37%-67% decrease in cellulose content, high cellulose DP, 25%-37% decrease in cellulose crystallinity, and 50% increase in saccharification efficiency. The heterozygous deletion of W436 increases about 2-fold CESA4 homo/heterodimerization capacity led to the 50% decrease in plant growth and increase in cell walls thickness, cellulose content (33%), cellulose DP (20%), and CrI (8%). Our findings provide a strategy for introducing commercial CRISPR/Cas9-mediated bioengineered poplars with promising cellulose applications. We anticipate our results could create an engineering revolution in bioenergy and cellulose-based nanomaterial technologies.
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Affiliation(s)
- Shahnoush Nayeri
- Department of Plant Sciences and BiotechnologyFaculty of Life Sciences and BiotechnologyShahid Beheshti UniversityTehranIran
| | | | - Asadollah Ahmadikhah
- Department of Plant Sciences and BiotechnologyFaculty of Life Sciences and BiotechnologyShahid Beheshti UniversityTehranIran
| | - Nasser Mahna
- Department of Horticultural SciencesFaculty of AgricultureUniversity of TabrizTabrizIran
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21
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One AP2/ERF Transcription Factor Positively Regulates Pi Uptake and Drought Tolerance in Poplar. Int J Mol Sci 2022; 23:ijms23095241. [PMID: 35563632 PMCID: PMC9099566 DOI: 10.3390/ijms23095241] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 04/30/2022] [Accepted: 05/03/2022] [Indexed: 11/17/2022] Open
Abstract
Drought decreases the inorganic phosphate (Pi) supply of soil, resulting in Pi starvation of plants, but the molecular mechanism of how plants, especially the perennial trees, are tolerant to drought stress and Pi starvation, is still elusive. In this study, we identified an AP2/ERF transcription factor gene, PalERF2, from Populus alba var. pyramidalis, and it was induced by both mannitol treatment and Pi starvation. Overexpressing and knocking-down of PalERF2 both enhanced and attenuated tolerance to drought stress and Pi deficiency compared to WT, respectively. Moreover, the overexpression of PalERF2 up-regulated the expression levels of Pi starvation-induced (PSI) genes and increased Pi uptake under drought conditions; however, its RNAi poplar showed the opposite phenotypes. Subsequent analysis indicated that PalERF2 directly modulated expressions of drought-responsive genes PalRD20 and PalSAG113, as well as PSI genes PalPHL2 and PalPHT1;4, through binding to the DRE motifs on their promoters. These results clearly indicate that poplars can recruit PalERF2 to increase the tolerance to drought and also elevate Pi uptake under drought stress.
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22
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Kim MH, Cho JS, Bae EK, Choi YI, Eom SH, Lim YJ, Lee H, Park EJ, Ko JH. PtrMYB120 functions as a positive regulator of both anthocyanin and lignin biosynthetic pathway in a hybrid poplar. TREE PHYSIOLOGY 2021; 41:2409-2423. [PMID: 34100089 DOI: 10.1093/treephys/tpab082] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 06/01/2021] [Indexed: 06/12/2023]
Abstract
Both anthocyanins and lignins are essential secondary metabolites in plant growth and development. Their biosynthesis is metabolically interconnected and diverges in the central metabolite 4-coumaroyl CoA of the phenylpropanoid pathway. Considerable progress has been made in understanding transcriptional regulation of genes involved in lignin and anthocyanin synthesis pathways, but the concerted regulation of these pathways is not yet fully understood. Here, we functionally characterized PtrMYB120, a R2R3-MYB transcription factor from Populus trichocarpa. Overexpression of PtrMYB120 in a hybrid poplar (i.e., 35S::PtrMYB120) was associated with increased anthocyanin (i.e., cyanidin 3-O-glucoside) accumulation and upregulation of anthocyanin biosynthetic genes. However, transgenic poplars with dominant suppression of PtrMYB120 function achieved by fusing the ERF-associated amphiphilic repression motif to PtrMYB120 (i.e., 35S::PtrMYB120-SRDX) had a dramatic decrease in not only anthocyanin but also Klason lignin content with downregulation of both anthocyanin and lignin biosynthetic genes. Indeed, 35S::PtrMYB120-SRDX poplars had irregularly shaped xylem vessels with reduced S-lignin content in stems, which was proportionally related to the level of the introduced PtrMYB120-SRDX gene. Furthermore, protoplast-based transcriptional activation assay using the PtrMYB120-GR system suggested that PtrMYB120 directly regulates genes involved in both anthocyanin and lignin biosynthesis, including chalcone synthase and ferulate-5 hydroxylase. Interestingly, the saccharification efficiency of line #6 of 35S::PtrMYB120-SRDX poplars, which had slightly reduced lignin content with a normal growth phenotype, was dramatically enhanced (>45%) by NaOH treatment. Taken together, our results suggest that PtrMYB120 functions as a positive regulator of both anthocyanin and lignin biosynthetic pathways and can be targeted to enhance saccharification efficiency in woody perennials.
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Affiliation(s)
- Min-Ha Kim
- Department of Plant & Environmental New Resources, Kyung Hee University, 1732 Deogyeong-daero, Yongin 17104, Republic of Korea
| | - Jin-Seong Cho
- Department of Plant & Environmental New Resources, Kyung Hee University, 1732 Deogyeong-daero, Yongin 17104, Republic of Korea
- Abio materials Co., Ltd., 7-44 Jamsil-gil, Cheonan 31005, Republic of Korea
| | - Eun-Kyung Bae
- Division of Forest Biotechnology, National Institute of Forest Science, 39 Onjeong-ro, Suwon 16631, Republic of Korea
| | - Young-Im Choi
- Division of Forest Biotechnology, National Institute of Forest Science, 39 Onjeong-ro, Suwon 16631, Republic of Korea
| | - Seok Hyun Eom
- Department of Horticultural Biotechnology, 1732 Deogyeong-daero, Yongin 17104, Republic of Korea
| | - You Jin Lim
- Department of Horticultural Biotechnology, 1732 Deogyeong-daero, Yongin 17104, Republic of Korea
| | - Hyoshin Lee
- Department of Horticultural Biotechnology, 1732 Deogyeong-daero, Yongin 17104, Republic of Korea
| | - Eung-Jun Park
- Division of Forest Biotechnology, National Institute of Forest Science, 39 Onjeong-ro, Suwon 16631, Republic of Korea
| | - Jae-Heung Ko
- Department of Plant & Environmental New Resources, Kyung Hee University, 1732 Deogyeong-daero, Yongin 17104, Republic of Korea
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23
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Tong S, Chen N, Wang D, Ai F, Liu B, Ren L, Chen Y, Zhang J, Lou S, Liu H, Liu J, Ma T, Jiang Y. The U-box E3 ubiquitin ligase PalPUB79 positively regulates ABA-dependent drought tolerance via ubiquitination of PalWRKY77 in Populus. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:2561-2575. [PMID: 34382303 PMCID: PMC8633511 DOI: 10.1111/pbi.13681] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 08/09/2021] [Indexed: 05/22/2023]
Abstract
The abscisic acid (ABA) signalling pathway is involved in the plant response to osmotic stress caused by drought and/or salinity. Although the ABA signalling pathway has been elucidated in Arabidopsis, it remains elusive in woody poplars. In this study, genome-wide analyses of U-box genes in poplars revealed that a U-box E3 ubiquitin ligase gene, PalPUB79, is significantly induced following drought, salinity and ABA signalling. PalPUB79 overexpression enhanced drought tolerance in transgenic poplars, while PalPUB79 RNAi lines were more sensitive to drought. PalPUB79 positively regulated ABA signalling pathway. Furthermore, PalPUB79 interacted with PalWRKY77, a negative transcriptional regulator of ABA signalling, and mediated its ubiquitination for degradation, therefore counteracting its inhibitory effect on PalRD26 transcription. However, the finding that PalWRKY77 negatively regulates PalPUB79 expression was indicative of a negative feedback loop between PalWRKY77 and PalPUB79 during ABA signalling in poplar. These findings provide novel insight into the mechanism through which PalPUB79 enhances the ABA-mediated stress response in woody poplars.
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Affiliation(s)
- Shaofei Tong
- Key Laboratory for Bio‐resources and Eco‐environment of Ministry of EducationCollege of Life ScienceSichuan UniversityChengduChina
| | - Ningning Chen
- Key Laboratory for Bio‐resources and Eco‐environment of Ministry of EducationCollege of Life ScienceSichuan UniversityChengduChina
| | - Deyan Wang
- Key Laboratory for Bio‐resources and Eco‐environment of Ministry of EducationCollege of Life ScienceSichuan UniversityChengduChina
| | - Fandi Ai
- Key Laboratory for Bio‐resources and Eco‐environment of Ministry of EducationCollege of Life ScienceSichuan UniversityChengduChina
| | - Bao Liu
- Key Laboratory for Bio‐resources and Eco‐environment of Ministry of EducationCollege of Life ScienceSichuan UniversityChengduChina
| | - Liwen Ren
- Key Laboratory for Bio‐resources and Eco‐environment of Ministry of EducationCollege of Life ScienceSichuan UniversityChengduChina
| | - Yang Chen
- Key Laboratory for Bio‐resources and Eco‐environment of Ministry of EducationCollege of Life ScienceSichuan UniversityChengduChina
| | - Junlin Zhang
- Key Laboratory for Bio‐resources and Eco‐environment of Ministry of EducationCollege of Life ScienceSichuan UniversityChengduChina
| | - Shangling Lou
- Key Laboratory for Bio‐resources and Eco‐environment of Ministry of EducationCollege of Life ScienceSichuan UniversityChengduChina
| | - Huanhuan Liu
- Key Laboratory for Bio‐resources and Eco‐environment of Ministry of EducationCollege of Life ScienceSichuan UniversityChengduChina
| | - Jianquan Liu
- Key Laboratory for Bio‐resources and Eco‐environment of Ministry of EducationCollege of Life ScienceSichuan UniversityChengduChina
- State Key Laboratory of Grassland Agro‐EcosystemInstitute of Innovation Ecology & College of Life ScienceLanzhou UniversityLanzhouChina
| | - Tao Ma
- Key Laboratory for Bio‐resources and Eco‐environment of Ministry of EducationCollege of Life ScienceSichuan UniversityChengduChina
| | - Yuanzhong Jiang
- Key Laboratory for Bio‐resources and Eco‐environment of Ministry of EducationCollege of Life ScienceSichuan UniversityChengduChina
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24
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Wang HL, Wang T, Yang Q, Yin W, Xia X, Guo H, Li Z. Preparation and Transfection of Populus tomentosa Mesophyll Protoplasts. Bio Protoc 2021; 11:e4220. [PMID: 34909441 DOI: 10.21769/bioprotoc.4220] [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: 06/15/2021] [Revised: 08/12/2021] [Accepted: 08/17/2021] [Indexed: 11/02/2022] Open
Abstract
Mesophyll protoplasts freshly isolated from leaves are a useful research system in plants. However, cell walls in woody plants contain more pectin, making mesophyll protoplasts isolation difficult in Populus. This has limited their application in biochemical, molecular, cellular, genetic, genomic, transcriptomic, and proteomic assays. In this protocol, a simple and efficient method to prepare and transfect mesophyll protoplasts of Populus tomentosa is presented in detail. Leaves of P. tomentosa plants grown in tissue culture media were pre-treated in D-mannitol solution and then digested with an enzyme solution. After washing with W5 and MMg buffers, the protoplasts were incubated in PEG/Ca2+ solution with plasmid for transfection. The mesophyll protoplasts isolated were used to express the histone variant H2B fused with green fluorescent protein (GFP) for confocal microscopy imaging. This "P. tomentosa mesophyll protoplasts preparation and transfection" system provides a useful tool for studying woody plants using a variety of applications, including gene expression, subcellular localization, protein-protein interaction, chromatin immunoprecipitation, western blot, single-cell sequencing, and genome editing.
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Affiliation(s)
- Hou-Ling Wang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Ting Wang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Qi Yang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Weilun Yin
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Xinli Xia
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Hongwei Guo
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen, Guangdong, 518055, China
| | - Zhonghai Li
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
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25
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Wang HL, Zhang Y, Wang T, Yang Q, Yang Y, Li Z, Li B, Wen X, Li W, Yin W, Xia X, Guo H, Li Z. An alternative splicing variant of PtRD26 delays leaf senescence by regulating multiple NAC transcription factors in Populus. THE PLANT CELL 2021; 33:1594-1614. [PMID: 33793897 PMCID: PMC8254505 DOI: 10.1093/plcell/koab046] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 02/01/2021] [Indexed: 05/05/2023]
Abstract
During leaf senescence, the final stage of leaf development, nutrients are recycled from leaves to other organs, and therefore proper control of senescence is thus critical for plant fitness. Although substantial progress has been achieved in understanding leaf senescence in annual plants, the molecular factors that control leaf senescence in perennial woody plants are largely unknown. Using RNA sequencing, we obtained a high-resolution temporal profile of gene expression during autumn leaf senescence in poplar (Populus tomentosa). Identification of hub transcription factors (TFs) by co-expression network analysis of genes revealed that senescence-associated NAC family TFs (Sen-NAC TFs) regulate autumn leaf senescence. Age-dependent alternative splicing (AS) caused an intron retention (IR) event in the pre-mRNA encoding PtRD26, a NAC-TF. This produced a truncated protein PtRD26IR, which functions as a dominant-negative regulator of senescence by interacting with multiple hub Sen-NAC TFs, thereby repressing their DNA-binding activities. Functional analysis of senescence-associated splicing factors identified two U2 auxiliary factors that are involved in AS of PtRD26IR. Correspondingly, silencing of these factors decreased PtRD26IR transcript abundance and induced early senescence. We propose that an age-dependent increase of IR splice variants derived from Sen-NAC TFs is a regulatory program to fine tune the molecular mechanisms that regulate leaf senescence in trees.
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Affiliation(s)
- Hou-Ling Wang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China
| | - Yi Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China
| | - Ting Wang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Qi Yang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Yanli Yang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Ze Li
- The State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Bosheng Li
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen, Guangdong, 518055, China
| | - Xing Wen
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen, Guangdong, 518055, China
| | - Wenyang Li
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen, Guangdong, 518055, China
| | - Weilun Yin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Xinli Xia
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Hongwei Guo
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen, Guangdong, 518055, China
- Author for correspondence: (Z.L.), (H.G.)
| | - Zhonghai Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China
- Author for correspondence: (Z.L.), (H.G.)
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26
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Yang Y, Lee JH, Poindexter MR, Shao Y, Liu W, Lenaghan SC, Ahkami AH, Blumwald E, Stewart CN. Rational design and testing of abiotic stress-inducible synthetic promoters from poplar cis-regulatory elements. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1354-1369. [PMID: 33471413 PMCID: PMC8313130 DOI: 10.1111/pbi.13550] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 12/31/2020] [Accepted: 01/09/2021] [Indexed: 05/27/2023]
Abstract
Abiotic stress resistance traits may be especially crucial for sustainable production of bioenergy tree crops. Here, we show the performance of a set of rationally designed osmotic-related and salt stress-inducible synthetic promoters for use in hybrid poplar. De novo motif-detecting algorithms yielded 30 water-deficit (SD) and 34 salt stress (SS) candidate DNA motifs from relevant poplar transcriptomes. We selected three conserved water-deficit stress motifs (SD18, SD13 and SD9) found in 16 co-expressed gene promoters, and we discovered a well-conserved motif for salt response (SS16). We characterized several native poplar stress-inducible promoters to enable comparisons with our synthetic promoters. Fifteen synthetic promoters were designed using various SD and SS subdomains, in which heptameric repeats of five-to-eight subdomain bases were fused to a common core promoter downstream, which, in turn, drove a green fluorescent protein (GFP) gene for reporter assays. These 15 synthetic promoters were screened by transient expression assays in poplar leaf mesophyll protoplasts and agroinfiltrated Nicotiana benthamiana leaves under osmotic stress conditions. Twelve synthetic promoters were induced in transient expression assays with a GFP readout. Of these, five promoters (SD18-1, SD9-2, SS16-1, SS16-2 and SS16-3) endowed higher inducibility under osmotic stress conditions than native promoters. These five synthetic promoters were stably transformed into Arabidopsis thaliana to study inducibility in whole plants. Herein, SD18-1 and SD9-2 were induced by water-deficit stress, whereas SS16-1, SS16-2 and SS16-3 were induced by salt stress. The synthetic biology design pipeline resulted in five synthetic promoters that outperformed endogenous promoters in transgenic plants.
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Affiliation(s)
- Yongil Yang
- Center for Agricultural Synthetic BiologyUniversity of Tennessee Institute of AgricultureKnoxvilleTNUSA
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
| | - Jun Hyung Lee
- Center for Agricultural Synthetic BiologyUniversity of Tennessee Institute of AgricultureKnoxvilleTNUSA
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
| | - Magen R. Poindexter
- Center for Agricultural Synthetic BiologyUniversity of Tennessee Institute of AgricultureKnoxvilleTNUSA
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
| | - Yuanhua Shao
- Center for Agricultural Synthetic BiologyUniversity of Tennessee Institute of AgricultureKnoxvilleTNUSA
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
| | - Wusheng Liu
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
- Department of Horticultural ScienceNorth Carolina State UniversityRaleighNCUSA
| | - Scott C. Lenaghan
- Center for Agricultural Synthetic BiologyUniversity of Tennessee Institute of AgricultureKnoxvilleTNUSA
- Department of Food ScienceUniversity of TennesseeKnoxvilleTNUSA
| | - Amir H. Ahkami
- Environmental Molecular Sciences Laboratory (EMSL)Pacific Northwest National Laboratory (PNNL)RichlandWAUSA
| | | | - Charles Neal Stewart
- Center for Agricultural Synthetic BiologyUniversity of Tennessee Institute of AgricultureKnoxvilleTNUSA
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
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27
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Wang H, Chen JG, Chang Y. Identification, Expression, and Interaction Analysis of Ovate Family Proteins in Populus trichocarpa Reveals a Role of PtOFP1 Regulating Drought Stress Response. FRONTIERS IN PLANT SCIENCE 2021; 12:650109. [PMID: 33959141 PMCID: PMC8095670 DOI: 10.3389/fpls.2021.650109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 03/08/2021] [Indexed: 06/12/2023]
Abstract
Ovate family proteins (OFPs) are a family of plant growth regulators that play diverse roles in many aspects of physiological processes. OFPs have been characterized in various plant species including tomato, Arabidopsis, and rice. However, little is known about OFPs in woody species. Here, a total of 30 PtOFP genes were identified from the genome of Populus trichocarpa and were further grouped into four subfamilies based on their sequence similarities. Gene expression analysis indicated that some members of the PtOFP gene family displayed tissue/organ-specific patterns. Analysis of cis-acting elements in the promoter as well as gene expression by hormone treatment revealed putative involvement of PtOFPs in hormonal response. Furthermore, PtOFP1 (Potri.006G107700) was further experimentally demonstrated to act as a transcriptional repressor. Yeast two-hybrid assay showed physical interactions of PtOFP1 with other proteins, which suggests that they might function in various cellular processes by forming protein complexes. In addition, overexpression of PtOFP1 in Arabidopsis conferred enhanced tolerance to PEG-induced drought stress at seedling stage, as well as a higher survival rate than the wild type at mature stage. These results provide a systematic analysis of the Populus OFP gene family and lay a foundation for functional characterization of this gene family.
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Affiliation(s)
- Hemeng Wang
- Northeast Agricultural University, Harbin, China
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Ying Chang
- Northeast Agricultural University, Harbin, China
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28
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Jiang Y, Tong S, Chen N, Liu B, Bai Q, Chen Y, Bi H, Zhang Z, Lou S, Tang H, Liu J, Ma T, Liu H. The PalWRKY77 transcription factor negatively regulates salt tolerance and abscisic acid signaling in Populus. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:1258-1273. [PMID: 33264467 DOI: 10.1111/tpj.15109] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 09/28/2020] [Accepted: 11/04/2020] [Indexed: 06/12/2023]
Abstract
High salinity, one of the most widespread abiotic stresses, inhibits photosynthesis, reduces vegetation growth, blocks respiration and disrupts metabolism in plants. In order to survive their long-term lifecycle, trees, such as Populus species, recruit the abscisic acid (ABA) signaling pathway to adapt to a saline environment. However, the molecular mechanism behind the ABA-mediated salt stress response in woody plants remains elusive. We have isolated a WRKY transcription factor gene, PalWRKY77, from Populus alba var. pyramidalis (poplar), the expression of which is repressed by salt stress. PalWRKY77 decreases salt tolerance in poplar. Furthermore, PalWRKY77 negatively regulated ABA-responsive genes and relieved ABA-mediated growth inhibition, indicating that PalWRKY77 is a repressor of the ABA response. In vivo and in vitro assays revealed that PalWRKY77 targets the ABA- and salt-induced PalNAC002 and PalRD26 genes by binding to the W-boxes in their promoters. In addition, overexpression of both PalNAC002 and PalRD26 could elevate salt tolerance in transgenic poplars. These findings reveal a novel negative regulation mechanism for the ABA signaling pathway mediated by PalWRKY77 that results in more sensitivity to salt stress in poplar. This deepens our understanding of the complex responses of woody species to salt stress.
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Affiliation(s)
- Yuanzhong Jiang
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu, 610065, China
| | - Shaofei Tong
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu, 610065, China
| | - Ningning Chen
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu, 610065, China
| | - Bao Liu
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu, 610065, China
| | - Qiuxian Bai
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and College of Life Science, Lanzhou University, Lanzhou, 730000, China
| | - Yang Chen
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu, 610065, China
| | - Hao Bi
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu, 610065, China
| | - Zhiyang Zhang
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu, 610065, China
| | - Shangling Lou
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu, 610065, China
| | - Hu Tang
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu, 610065, China
| | - Jianquan Liu
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu, 610065, China
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and College of Life Science, Lanzhou University, Lanzhou, 730000, China
| | - Tao Ma
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu, 610065, China
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and College of Life Science, Lanzhou University, Lanzhou, 730000, China
| | - Huanhuan Liu
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu, 610065, China
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29
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Azeez A, Zhao YC, Singh RK, Yordanov YS, Dash M, Miskolczi P, Stojkovič K, Strauss SH, Bhalerao RP, Busov VB. EARLY BUD-BREAK 1 and EARLY BUD-BREAK 3 control resumption of poplar growth after winter dormancy. Nat Commun 2021; 12:1123. [PMID: 33602938 PMCID: PMC7893051 DOI: 10.1038/s41467-021-21449-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 01/22/2021] [Indexed: 01/31/2023] Open
Abstract
Bud-break is an economically and environmentally important process in trees and shrubs from boreal and temperate latitudes, but its molecular mechanisms are poorly understood. Here, we show that two previously reported transcription factors, EARLY BUD BREAK 1 (EBB1) and SHORT VEGETATIVE PHASE-Like (SVL) directly interact to control bud-break. EBB1 is a positive regulator of bud-break, whereas SVL is a negative regulator of bud-break. EBB1 directly and negatively regulates SVL expression. We further report the identification and characterization of the EBB3 gene. EBB3 is a temperature-responsive, epigenetically-regulated, positive regulator of bud-break that provides a direct link to activation of the cell cycle during bud-break. EBB3 is an AP2/ERF transcription factor that positively and directly regulates CYCLIND3.1 gene. Our results reveal the architecture of a putative regulatory module that links temperature-mediated control of bud-break with activation of cell cycle.
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Affiliation(s)
- Abdul Azeez
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, USA
| | - Yiru Chen Zhao
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, USA
| | - Rajesh Kumar Singh
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
- Department of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Yordan S Yordanov
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, USA
- Department of Biological Sciences, Eastern Illinois University, Charleston, IL, USA
| | - Madhumita Dash
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, USA
| | - Pal Miskolczi
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Katja Stojkovič
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Steve H Strauss
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, USA
| | - Rishikesh P Bhalerao
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden.
| | - Victor B Busov
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, USA.
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30
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Ren R, Gao J, Yin D, Li K, Lu C, Ahmad S, Wei Y, Jin J, Zhu G, Yang F. Highly Efficient Leaf Base Protoplast Isolation and Transient Expression Systems for Orchids and Other Important Monocot Crops. FRONTIERS IN PLANT SCIENCE 2021; 12:626015. [PMID: 33659015 PMCID: PMC7917215 DOI: 10.3389/fpls.2021.626015] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 01/25/2021] [Indexed: 05/21/2023]
Abstract
Versatile protoplast platforms greatly facilitate the development of modern botany. However, efficient protoplast-based systems are still challenging for numerous horticultural plants and crops. Orchids are globally cultivated ornamental and medicinal monocot plants, but few efficient protoplast isolation and transient expression systems have been developed. In this study, we established a highly efficient orchid protoplast isolation protocol by selecting suitable source materials and optimizing the enzymatic conditions, which required optimal D-mannitol concentrations (0.4-0.6 M) combined with optimal 1.2% cellulose and 0.6% macerozyme, 5 μM of 2-mercaptoethanol and 6 h digestion. Tissue- and organ-specific protoplasts were successfully isolated from young leaves [∼3.22 × 106/g fresh weight (FW)], flower pedicels (∼5.26 × 106/g FW), and young root tips (∼7.66 × 105/g FW) of Cymbidium orchids. This protocol recommends the leaf base tissues (the tender part of young leaves attached to the stem) as better source materials. High yielding viable protoplasts were isolated from the leaf base of Cymbidium (∼2.50 × 107/g FW), Phalaenopsis (1.83 × 107/g FW), Paphiopedilum (1.10 × 107/g FW), Dendrobium (8.21 × 106/g FW), Arundina (3.78 × 106/g FW) orchids, and other economically important monocot crops including maize (Zea mays) (3.25 × 107/g FW) and rice (Oryza sativa) (4.31 × 107/g FW), which showed marked advantages over previous mesophyll protoplast isolation protocols. Leaf base protoplasts of Cymbidium orchids were used for polyethylene glycol (PEG)-mediated transfection, and a transfection efficiency of more than 80% was achieved. This leaf base protoplast system was applied successfully to analyze the CsDELLA-mediated gibberellin signaling in Cymbidium orchids. We investigated the subcellular localization of the CsDELLA-green fluorescent protein fusion and analyzed the role of CsDELLA in the regulation of gibberellin to flowering-related genes via efficient transient overexpression and gene silencing of CsDELLA in Cymbidium protoplasts. This protoplast isolation and transient expression system is the most efficient based on the documented results to date. It can be widely used for cellular and molecular studies in orchids and other economically important monocot crops, especially for those lacking an efficient genetic transformation system in vivo.
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Affiliation(s)
- Rui Ren
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Jie Gao
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Dongmei Yin
- College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Kai Li
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Chuqiao Lu
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Sagheer Ahmad
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Yonglu Wei
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Jianpeng Jin
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Genfa Zhu
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Fengxi Yang
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
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Chen N, Tong S, Tang H, Zhang Z, Liu B, Lou S, Liu J, Liu H, Ma T, Jiang Y. The PalERF109 transcription factor positively regulates salt tolerance via PalHKT1;2 in Populus alba var. pyramidalis. TREE PHYSIOLOGY 2020; 40:717-730. [PMID: 32083670 DOI: 10.1093/treephys/tpaa018] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Revised: 01/01/2020] [Accepted: 01/31/2020] [Indexed: 05/19/2023]
Abstract
Salinity restricts the growth of trees to varying extents, but the regulatory mechanisms involved in their varying salt tolerance are largely unknown. In an effort to elucidate these mechanisms, we identified a total of 99 genes in the Ethylene Responsive Factor (ERF) family of transcription factors and examined their expression patterns under salt stress in Populus alba var. pyramidalis. We found that a B4 group gene, PalERF109, was rapidly induced by salt treatment and preferentially expressed in stems and petioles, where it is probably involved in transport of ions and water in xylem. Overexpression of PalERF109 enhanced the salt tolerance of the poplar, and further analysis showed that it directly upregulated a high-affinity K+transporter (HKT) gene, PalHKT1;2. The results clearly indicate that PalERF109 enhances salt tolerance at least partially through direct activation of PalHKT1;2 and extends understanding of the roles of ERF genes in tree stress responses.
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Affiliation(s)
- Ningning Chen
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu 610065, China
| | - Shaofei Tong
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu 610065, China
| | - Hu Tang
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu 610065, China
| | - Zhiyang Zhang
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu 610065, China
| | - Bao Liu
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu 610065, China
| | - Shangling Lou
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu 610065, China
| | - Jianquan Liu
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu 610065, China
- State Key Laboratory of Grassland Agro-Ecosystem, College of Life Science, Institute of Innovation Ecology, Lanzhou University, Lanzhou 730000, China
| | - Huanhuan Liu
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu 610065, China
| | - Tao Ma
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu 610065, China
| | - Yuanzhong Jiang
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu 610065, China
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Sultana MS, Frazier TP, Millwood RJ, Lenaghan SC, Stewart CN. Development and validation of a novel and robust cell culture system in soybean (Glycine max (L.) Merr.) for promoter screening. PLANT CELL REPORTS 2019; 38:1329-1345. [PMID: 31396683 DOI: 10.1007/s00299-019-02455-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 07/29/2019] [Indexed: 05/23/2023]
Abstract
KEY MESSAGE A novel soybean cell culture was developed, establishing a reliable and rapid promoter assay to enable high-throughput automated screening in soybean protoplasts relevant to shoot tissues in whole plants. Transient reporter gene assays can be valuable to rapidly estimate expression characteristics of heterologous promoters. The challenge for maximizing the value of such screens is to combine relevant cells or tissues with methods that can be scaled for high-throughput screening, especially for crop-rather than model species. We developed a robust and novel soybean cell suspension culture derived from leaf-derived callus for protoplast production: a platform for promoter screening. The protoplasts were transfected with promoter-reporter constructs, of which were chosen and validated against known promoter expression profiles from tissue-derived protoplasts (leaves, stems, and immature cotyledons) and gene expression data from plants. The cell culture reliably produced 2.82 ± 0.94 × 108 protoplasts/g fresh culture mass with a transfection efficiency of 31.06 ± 7.69% at 48 h post-incubation. The promoter-reporter gene DNA expression levels of transfected cell culture-derived protoplasts were most similar to that of leaf- and stem-derived protoplasts (correlation coefficient of 0.99 and 0.96, respectively) harboring the same constructs. Cell culture expression was also significantly correlated to endogenous promoter-gene expression in leaf tissues as measured by qRT-PCR (correlation coefficient of 0.80). Using the manual protocols that produced these results, we performed early stage experiments to automate protoplast transformation on a robotic system. After optimizing the protocol, we achieved up to 29% transformation efficiency using our robotic system. We conclude that the soybean cell culture-to-protoplast transformation screen is amenable to automate promoter and gene screens in soybean that could be used to accelerate discoveries relevant for crop improvement. Key features of the system include low-cost, facile protoplast isolation, and transformation for soybean shoot tissue-relevant molecular screening.
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Affiliation(s)
- Mst Shamira Sultana
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA
- Center for Agricultural Synthetic Biology, University of Tennessee Institute of Agriculture, Knoxville, TN, USA
| | - Taylor P Frazier
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA
- Center for Agricultural Synthetic Biology, University of Tennessee Institute of Agriculture, Knoxville, TN, USA
- Elo Life Systems, Suite Number 2200, 3054 E Cornwallis Road, Durham, NC, 27709, USA
| | | | - Scott C Lenaghan
- Center for Agricultural Synthetic Biology, University of Tennessee Institute of Agriculture, Knoxville, TN, USA
- Department of Food Science, University of Tennessee, Knoxville, TN, USA
- Department of Mechanical, Aerospace, and Biomedical Engineering, University of Tennessee, Knoxville, TN, USA
| | - C Neal Stewart
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA.
- Center for Agricultural Synthetic Biology, University of Tennessee Institute of Agriculture, Knoxville, TN, 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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Liu Y, Xue Y, Tang J, Chen J, Chen M. Efficient mesophyll protoplast isolation and development of a transient expression system for castor-oil plant (Ricinus communis L.). Biol Futur 2019; 70:8-15. [PMID: 34554435 DOI: 10.1556/019.70.2019.02] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 02/21/2019] [Indexed: 11/19/2022]
Abstract
INTRODUCTION We investigated the main factors affecting the efficacy of protoplast isolation, including leaf-obtaining period, cutting shapes of leaf material, enzyme concentration, enzymolysis time, and centrifugal speed. METHODS Protoplast isolation was optimal on the condition of 20 days of leaf materials, 2-mm filament of leaves, 1.6% RS and 0.8% R-10, 80 min of enzymolysis, and 700 rpm of centrifugation, resulting in the best yield (1.19 X 106 protoplasts/g FW) and vitality (80.34%) of mesophyll protoplasts. The transient expression vector pGFPl with green fluorescent protein was transfected into the obtained protoplasts from castor by polyethylene glycol-mediated method with a transformation efficiency of 12.37%. RESULTS Moreover, the applicability of the system for studying the subcellular localization of Re FATA (an acyl-ACP thioesterase) was validated via the protoplast isolation and transient expression protocol in this study. DISCUSSION Collectively, the efficient mesophyll protoplast isolation and protoplast transient expression system facilitate to analyze the function of specific gene in castor (Ricinus communis L).
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Affiliation(s)
- Ying Liu
- Department of Biotechnology, Faculty of Agricultural Science, Guangdong Ocean University, Zhanjiang, Guangdong, P. R. China
| | - Yingbin Xue
- Department of Biotechnology, Faculty of Agricultural Science, Guangdong Ocean University, Zhanjiang, Guangdong, P. R. China
| | - Jianian Tang
- Department of Biotechnology, Faculty of Agricultural Science, Guangdong Ocean University, Zhanjiang, Guangdong, P. R. China.,State Key Laboratory for Conservation and Utilization of Subtropical Afro-Bioresources, South China Agricultural University, Guangzhou, Guangdong, P. R. China
| | - Jianping Chen
- Department of Food Science and Engineering, College of Food Science and Technology, Guangdong Ocean University, Zhanjiang, Guangdong, P. R. China.
| | - Miao Chen
- Department of Biotechnology, Faculty of Agricultural Science, Guangdong Ocean University, Zhanjiang, Guangdong, P. R. China. .,State Key Laboratory for Conservation and Utilization of Subtropical Afro-Bioresources, South China Agricultural University, Guangzhou, Guangdong, P. R. China.
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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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Muchero W, Sondreli KL, Chen JG, Urbanowicz BR, Zhang J, Singan V, Yang Y, Brueggeman RS, Franco-Coronado J, Abraham N, Yang JY, Moremen KW, Weisberg AJ, Chang JH, Lindquist E, Barry K, Ranjan P, Jawdy S, Schmutz J, Tuskan GA, LeBoldus JM. Association mapping, transcriptomics, and transient expression identify candidate genes mediating plant-pathogen interactions in a tree. Proc Natl Acad Sci U S A 2018; 115:11573-11578. [PMID: 30337484 PMCID: PMC6233113 DOI: 10.1073/pnas.1804428115] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Invasive microbes causing diseases such as sudden oak death negatively affect ecosystems and economies around the world. The deployment of resistant genotypes for combating introduced diseases typically relies on breeding programs that can take decades to complete. To demonstrate how this process can be accelerated, we employed a genome-wide association mapping of ca 1,000 resequenced Populus trichocarpa trees individually challenged with Sphaerulina musiva, an invasive fungal pathogen. Among significant associations, three loci associated with resistance were identified and predicted to encode one putative membrane-bound L-type receptor-like kinase and two receptor-like proteins. A susceptibility-associated locus was predicted to encode a putative G-type D-mannose-binding receptor-like kinase. Multiple lines of evidence, including allele analysis, transcriptomics, binding assays, and overexpression, support the hypothesized function of these candidate genes in the P. trichocarpa response to S. musiva.
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Affiliation(s)
- Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831
| | - Kelsey L Sondreli
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831
| | | | - Jin Zhang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831
| | - Vasanth Singan
- Joint Genome Institute, US Department of Energy, Walnut Creek, CA 94598
| | - Yongil Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831
| | - Robert S Brueggeman
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58102
| | | | - Nivi Abraham
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58102
| | - Jeong-Yeh Yang
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602
| | - Kelley W Moremen
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602
| | - Alexandra J Weisberg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331
| | - Jeff H Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331
| | - Erika Lindquist
- Joint Genome Institute, US Department of Energy, Walnut Creek, CA 94598
| | - Kerrie Barry
- Joint Genome Institute, US Department of Energy, Walnut Creek, CA 94598
| | - Priya Ranjan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831
| | - Sara Jawdy
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831
| | - Jeremy Schmutz
- Joint Genome Institute, US Department of Energy, Walnut Creek, CA 94598
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831
- Joint Genome Institute, US Department of Energy, Walnut Creek, CA 94598
| | - Jared M LeBoldus
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331;
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58102
- Forest Engineering, Resources, and Management, Oregon State University, Corvallis, OR 97331
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Zhang J, Yang Y, Zheng K, Xie M, Feng K, Jawdy SS, Gunter LE, Ranjan P, Singan VR, Engle N, Lindquist E, Barry K, Schmutz J, Zhao N, Tschaplinski TJ, LeBoldus J, Tuskan GA, Chen JG, Muchero W. Genome-wide association studies and expression-based quantitative trait loci analyses reveal roles of HCT2 in caffeoylquinic acid biosynthesis and its regulation by defense-responsive transcription factors in Populus. THE NEW PHYTOLOGIST 2018; 220:502-516. [PMID: 29992670 DOI: 10.1111/nph.15297] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 05/29/2018] [Indexed: 05/18/2023]
Abstract
3-O-caffeoylquinic acid, also known as chlorogenic acid (CGA), functions as an intermediate in lignin biosynthesis in the phenylpropanoid pathway. It is widely distributed among numerous plant species and acts as an antioxidant in both plants and animals. Using GC-MS, we discovered consistent and extreme variation in CGA content across a population of 739 4-yr-old Populus trichocarpa accessions. We performed genome-wide association studies (GWAS) from 917 P. trichocarpa accessions and expression-based quantitative trait loci (eQTL) analyses to identify key regulators. The GWAS and eQTL analyses resolved an overlapped interval encompassing a hydroxycinnamoyl-CoA:shikimate hydroxycinnamoyl transferase 2 (PtHCT2) that was significantly associated with CGA and partially characterized metabolite abundances. PtHCT2 leaf expression was significantly correlated with CGA abundance and it was regulated by cis-eQTLs containing W-box for WRKY binding. Among all nine PtHCT homologs, PtHCT2 is the only one that responds to infection by the fungal pathogen Sphaerulina musiva (a Populus pathogen). Validation using protoplast-based transient expression system suggests that PtHCT2 is regulated by the defense-responsive WRKY. These results are consistent with reports of CGA functioning as an antioxidant in response to biotic stress. This study provides insights into data-driven and omics-based inference of gene function in woody species.
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Affiliation(s)
- Jin Zhang
- Oak Ridge National Laboratory, Biosciences Division and Center for Bioenergy Innovation, Oak Ridge, TN, 37831, USA
| | - Yongil Yang
- Oak Ridge National Laboratory, Biosciences Division and Center for Bioenergy Innovation, Oak Ridge, TN, 37831, USA
| | - Kaijie Zheng
- Oak Ridge National Laboratory, Biosciences Division and Center for Bioenergy Innovation, Oak Ridge, TN, 37831, USA
| | - Meng Xie
- Oak Ridge National Laboratory, Biosciences Division and Center for Bioenergy Innovation, Oak Ridge, TN, 37831, USA
| | - Kai Feng
- Oak Ridge National Laboratory, Biosciences Division and Center for Bioenergy Innovation, Oak Ridge, TN, 37831, USA
| | - Sara S Jawdy
- Oak Ridge National Laboratory, Biosciences Division and Center for Bioenergy Innovation, Oak Ridge, TN, 37831, USA
| | - Lee E Gunter
- Oak Ridge National Laboratory, Biosciences Division and Center for Bioenergy Innovation, Oak Ridge, TN, 37831, USA
| | - Priya Ranjan
- Oak Ridge National Laboratory, Biosciences Division and Center for Bioenergy Innovation, Oak Ridge, TN, 37831, USA
| | - Vasanth R Singan
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Nancy Engle
- Oak Ridge National Laboratory, Biosciences Division and Center for Bioenergy Innovation, Oak Ridge, TN, 37831, USA
| | - Erika Lindquist
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Jeremy Schmutz
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Nan Zhao
- Institute of Agriculture, University of Tennessee, Knoxville, TN, 37996, USA
| | - Timothy J Tschaplinski
- Oak Ridge National Laboratory, Biosciences Division and Center for Bioenergy Innovation, Oak Ridge, TN, 37831, USA
| | - Jared LeBoldus
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Gerald A Tuskan
- Oak Ridge National Laboratory, Biosciences Division and Center for Bioenergy Innovation, Oak Ridge, TN, 37831, USA
| | - Jin-Gui Chen
- Oak Ridge National Laboratory, Biosciences Division and Center for Bioenergy Innovation, Oak Ridge, TN, 37831, USA
| | - Wellington Muchero
- Oak Ridge National Laboratory, Biosciences Division and Center for Bioenergy Innovation, Oak Ridge, TN, 37831, USA
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Wang CC, Ke L, Cao LJ, Yao Y, Geng MT, Wang Y, Xiao Y, Huang W, Liu XH, Cao P, Guo JC, Min Y. Overexpression of MinE gene affects the plastid division in cassava. Biosci Biotechnol Biochem 2018; 83:95-105. [PMID: 30257607 DOI: 10.1080/09168451.2018.1518703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The MinE protein plays an important role in plastid division. In this study, the MinE gene was isolated from the cassava (Manihot esculenta Crantz) genome. We isolated high quality and quantity protoplasts and succeed in performing the transient expression of the GFP-fused Manihot esculenta MinE (MeMinE) protein in cassava mesophyll protoplasts. The transient expression of MeMinE-GFP in cassava protoplasts showed that the MeMinE protein was located in the chloroplast. Due to the abnormal division of chloroplasts, overexpression of MeMinE proteins in cassava mesophyll protoplasts could result in fewer and smaller chloroplasts. Overexpression of MeMinE proteins also showed abnormal cell division characteristics and minicell occurrence in Escherichia coli caused by aberrant septation events in the cell poles.
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Affiliation(s)
- Cong-Cong Wang
- Hainan Key Laboratory for Sustainable Utilisation of Tropical Bioresource, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Lei Ke
- Hainan Key Laboratory for Sustainable Utilisation of Tropical Bioresource, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Liang-Jing Cao
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Yuan Yao
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Meng-Ting Geng
- Hainan Key Laboratory for Sustainable Utilisation of Tropical Bioresource, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Ying Wang
- Hainan Key Laboratory for Sustainable Utilisation of Tropical Bioresource, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Yu Xiao
- Hainan Key Laboratory for Sustainable Utilisation of Tropical Bioresource, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Wu Huang
- Hainan Key Laboratory for Sustainable Utilisation of Tropical Bioresource, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Xiao-Han Liu
- Hainan Key Laboratory for Sustainable Utilisation of Tropical Bioresource, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Peng Cao
- Hainan Key Laboratory for Sustainable Utilisation of Tropical Bioresource, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Jian-Chun Guo
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Yi Min
- Hainan Key Laboratory for Sustainable Utilisation of Tropical Bioresource, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
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Tuskan GA, Mewalal R, Gunter LE, Palla KJ, Carter K, Jacobson DA, Jones PC, Garcia BJ, Weighill DA, Hyatt PD, Yang Y, Zhang J, Reis N, Chen JG, Muchero W. Defining the genetic components of callus formation: A GWAS approach. PLoS One 2018; 13:e0202519. [PMID: 30118526 PMCID: PMC6097687 DOI: 10.1371/journal.pone.0202519] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 08/03/2018] [Indexed: 12/26/2022] Open
Abstract
A characteristic feature of plant cells is the ability to form callus from parenchyma cells in response to biotic and abiotic stimuli. Tissue culture propagation of recalcitrant plant species and genetic engineering for desired phenotypes typically depends on efficient in vitro callus generation. Callus formation is under genetic regulation, and consequently, a molecular understanding of this process underlies successful generation for propagation materials and/or introduction of genetic elements in experimental or industrial applications. Herein, we identified 11 genetic loci significantly associated with callus formation in Populus trichocarpa using a genome-wide association study (GWAS) approach. Eight of the 11 significant gene associations were consistent across biological replications, exceeding a chromosome-wide-log10 (p) = 4.46 [p = 3.47E-05] Bonferroni-adjusted significance threshold. These eight genes were used as hub genes in a high-resolution co-expression network analysis to gain insight into the genome-wide basis of callus formation. A network of positively and negatively co-expressed genes, including several transcription factors, was identified. As proof-of-principle, a transient protoplast assay confirmed the negative regulation of a Chloroplast Nucleoid DNA-binding-related gene (Potri.018G014800) by the LEC2 transcription factor. Many of the candidate genes and co-expressed genes were 1) linked to cell division and cell cycling in plants and 2) showed homology to tumor and cancer-related genes in humans. The GWAS approach based on a high-resolution marker set, and the ability to manipulate targets genes in vitro, provided a catalog of high-confidence genes linked to callus formation that can serve as an important resource for successful manipulation of model and non-model plant species, and likewise, suggests a robust method of discovering common homologous functions across organisms.
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Affiliation(s)
- Gerald A Tuskan
- Plant Systems Biology Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Ritesh Mewalal
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, Oregon, United States of America
| | - Lee E Gunter
- Plant Systems Biology Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Kaitlin J Palla
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Kelsey Carter
- School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan, United States of America
| | - Daniel A Jacobson
- Computational Biology Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Piet C Jones
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee, United States of America.,Computational Biology Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Benjamin J Garcia
- Computational Biology Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Deborah A Weighill
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee, United States of America.,Computational Biology Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Philip D Hyatt
- Computational Biology Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Yongil Yang
- Plant Systems Biology Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Jin Zhang
- Plant Systems Biology Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Nicholas Reis
- Oak Ridge Associated Universities, Oak Ridge, Tennessee, United States of America
| | - Jin-Gui Chen
- Plant Systems Biology Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Wellington Muchero
- Plant Systems Biology Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
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A Variable Polyglutamine Repeat Affects Subcellular Localization and Regulatory Activity of a Populus ANGUSTIFOLIA Protein. G3-GENES GENOMES GENETICS 2018; 8:2631-2641. [PMID: 29884614 PMCID: PMC6071607 DOI: 10.1534/g3.118.200188] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Polyglutamine (polyQ) stretches have been reported to occur in proteins across many organisms including animals, fungi and plants. Expansion of these repeats has attracted much attention due their associations with numerous human diseases including Huntington’s and other neurological maladies. This suggests that the relative length of polyQ stretches is an important modulator of their function. Here, we report the identification of a Populus C-terminus binding protein (CtBP) ANGUSTIFOLIA (PtAN1) which contains a polyQ stretch whose functional relevance had not been established. Analysis of 917 resequenced Populus trichocarpa genotypes revealed three allelic variants at this locus encoding 11-, 13- and 15-glutamine residues. Transient expression assays using Populus leaf mesophyll protoplasts revealed that the 11Q variant exhibited strong nuclear localization whereas the 15Q variant was only found in the cytosol, with the 13Q variant exhibiting localization in both subcellular compartments. We assessed functional implications by evaluating expression changes of putative PtAN1 targets in response to overexpression of the three allelic variants and observed allele-specific differences in expression levels of putative targets. Our results provide evidence that variation in polyQ length modulates PtAN1 function by altering subcellular localization.
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41
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Xie M, Muchero W, Bryan AC, Yee K, Guo HB, Zhang J, Tschaplinski TJ, Singan VR, Lindquist E, Payyavula RS, Barros-Rios J, Dixon R, Engle N, Sykes RW, Davis M, Jawdy SS, Gunter LE, Thompson O, DiFazio SP, Evans LM, Winkeler K, Collins C, Schmutz J, Guo H, Kalluri U, Rodriguez M, Feng K, Chen JG, Tuskan GA. A 5-Enolpyruvylshikimate 3-Phosphate Synthase Functions as a Transcriptional Repressor in Populus. THE PLANT CELL 2018; 30:1645-1660. [PMID: 29891568 PMCID: PMC6096593 DOI: 10.1105/tpc.18.00168] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 04/17/2018] [Accepted: 06/05/2018] [Indexed: 05/21/2023]
Abstract
Long-lived perennial plants, with distinctive habits of inter-annual growth, defense, and physiology, are of great economic and ecological importance. However, some biological mechanisms resulting from genome duplication and functional divergence of genes in these systems remain poorly studied. Here, we discovered an association between a poplar (Populus trichocarpa) 5-enolpyruvylshikimate 3-phosphate synthase gene (PtrEPSP) and lignin biosynthesis. Functional characterization of PtrEPSP revealed that this isoform possesses a helix-turn-helix motif in the N terminus and can function as a transcriptional repressor that regulates expression of genes in the phenylpropanoid pathway in addition to performing its canonical biosynthesis function in the shikimate pathway. We demonstrated that this isoform can localize in the nucleus and specifically binds to the promoter and represses the expression of a SLEEPER-like transcriptional regulator, which itself specifically binds to the promoter and represses the expression of PtrMYB021 (known as MYB46 in Arabidopsis thaliana), a master regulator of the phenylpropanoid pathway and lignin biosynthesis. Analyses of overexpression and RNAi lines targeting PtrEPSP confirmed the predicted changes in PtrMYB021 expression patterns. These results demonstrate that PtrEPSP in its regulatory form and PtrhAT form a transcriptional hierarchy regulating phenylpropanoid pathway and lignin biosynthesis in Populus.
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Affiliation(s)
- Meng Xie
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Wellington Muchero
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Anthony C Bryan
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Kelsey Yee
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Hao-Bo Guo
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996
| | - Jin Zhang
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Timothy J Tschaplinski
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Vasanth R Singan
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California 94598
| | - Erika Lindquist
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California 94598
| | - Raja S Payyavula
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Jaime Barros-Rios
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, Texas 76203
| | - Richard Dixon
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, Texas 76203
| | - Nancy Engle
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Robert W Sykes
- Bioscience Center, National Renewable Energy Laboratory, Golden, Colorado 80401
| | - Mark Davis
- Bioscience Center, National Renewable Energy Laboratory, Golden, Colorado 80401
| | - Sara S Jawdy
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Lee E Gunter
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Olivia Thompson
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Stephen P DiFazio
- Department of Biology, West Virginia University, Morgantown, West Virginia 26506
| | - Luke M Evans
- Department of Biology, West Virginia University, Morgantown, West Virginia 26506
| | | | | | - Jeremy Schmutz
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California 94598
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806
| | - Hong Guo
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996
| | - Udaya Kalluri
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Miguel Rodriguez
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Kai Feng
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Jin-Gui Chen
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Gerald A Tuskan
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California 94598
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Papacek M, Christmann A, Grill E. Interaction network of ABA receptors in grey poplar. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 92:199-210. [PMID: 28746755 DOI: 10.1111/tpj.13646] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 07/17/2017] [Accepted: 07/21/2017] [Indexed: 06/07/2023]
Abstract
The plant hormone abscisic acid (ABA) is a key player in responses to abiotic stress. ABA regulates a plant's water status and mediates drought tolerance by controlling stomatal gas exchange, water conductance and differential gene expression. ABA is recognized and bound by the Regulatory Component of ABA Receptors (RCARs)/PYR1/PYL (Pyrabactin Resistance 1/PYR1-like). Ligand binding stabilizes the interaction of RCARs with type 2C protein phosphatases (PP2C), which are ABA co-receptors. While the core pathway of ABA signalling has been elucidated, the large number of different ABA receptors and co-receptors within a plant species generates a complexity of heteromeric receptor complexes that has not functionally been resolved in any plant species to date. In this study, we characterized ABA receptors and co-receptors of grey poplar (Populus x canescens [Ait.] Sm.) and their capacity to regulate ABA responses. We observed a high number of regulatory combinations of holo-receptor complexes, but also some preferential and selective RCAR-PP2C interactions. Poplar and Arabidopsis ABA receptor components revealed a strong structural and functional conservation. Heterologous receptor complexes of poplar and Arabidopsis components showed functionality in vitro and regulated ABA-responsive gene expression in cells of both species. ABA-responsive promoters of Arabidopsis were also active in poplar, which was explored to generate poplar reporter lines expressing green fluorescent protein in response to ABA. The study presents a detailed analysis of receptor complexes of a tree species and shows high conservation of ABA receptor components between an annual and a perennial plant.
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Affiliation(s)
- Michael Papacek
- Lehrstuhl für Botanik, Technische Universität München, Emil-Ramann Straße 4, D-85354, Freising, Germany
| | - Alexander Christmann
- Lehrstuhl für Botanik, Technische Universität München, Emil-Ramann Straße 4, D-85354, Freising, Germany
| | - Erwin Grill
- Lehrstuhl für Botanik, Technische Universität München, Emil-Ramann Straße 4, D-85354, Freising, Germany
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43
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Huo A, Chen Z, Wang P, Yang L, Wang G, Wang D, Liao S, Cheng T, Chen J, Shi J. Establishment of transient gene expression systems in protoplasts from Liriodendron hybrid mesophyll cells. PLoS One 2017; 12:e0172475. [PMID: 28323890 PMCID: PMC5360215 DOI: 10.1371/journal.pone.0172475] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 02/05/2017] [Indexed: 11/19/2022] Open
Abstract
Liriodendron is a genus of the magnolia family comprised of two flowering tree species that produce hardwoods of great ecological and economic value. However, only a limited amount of genetic research has been performed on the Liriodendron genus partly because transient or stable transgenic trees have been difficult to produce. In general, transient expression systems are indispensable for rapid, high-throughput screening and systematic characterization of gene functions at a low cost; therefore, development of such a system for Liriodendron would provide a necessary step forward for research on Magnoliaceae and other woody trees. Herein, we describe an efficient and rapid protocol for preparing protoplasts from the leaf mesophyll tissue of a Liriodendron hybrid and an optimized system for polyethylene glycol–mediated transient transfection of the protoplasts. Because the leaves of the Liriodendron hybrid are waxy, we formulated an enzyme mix containing 1.5% (w/v) Cellulase R-10, 0.5% (w/v) Macerozyme R-10, and 0.1% (w/v) Pectolyase Y-23 to efficiently isolate protoplasts from the Liriodendron hybrid leaf mesophyll tissue in 3 h. We optimized Liriodendron protoplast transfection efficiency by including 20 μg plasmid DNA per 104 protoplasts, a transformation time of 20 min, and inclusion of 20% (w/v) polyethylene glycol 4000. After integrating the Liriodendron WOX1 gene into pJIT166-GFP to produce a WOX1-GFP fusion product and transfecting it into isolated protoplasts, LhWOX1-GFP was found to localize to the nucleus according to its green fluorescence.
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Affiliation(s)
- Ailing Huo
- Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- School of Life Science, Huaiyin Normal University, Huaian, China
| | - Zhenyu Chen
- Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing, China
| | - Pengkai Wang
- Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing, China
| | - Liming Yang
- School of Life Science, Huaiyin Normal University, Huaian, China
| | - Guangping Wang
- Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing, China
| | - Dandan Wang
- Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing, China
| | - Suchan Liao
- Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Tielong Cheng
- Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Jinhui Chen
- Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing, China
- * E-mail: (J.C.); (J.S.)
| | - Jisen Shi
- Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing, China
- * E-mail: (J.C.); (J.S.)
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Wu JZ, Liu Q, Geng XS, Li KM, Luo LJ, Liu JP. Highly efficient mesophyll protoplast isolation and PEG-mediated transient gene expression for rapid and large-scale gene characterization in cassava (Manihot esculenta Crantz). BMC Biotechnol 2017; 17:29. [PMID: 28292294 PMCID: PMC5351281 DOI: 10.1186/s12896-017-0349-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 03/07/2017] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Cassava (Manihot esculenta Crantz) is a major crop extensively cultivated in the tropics as both an important source of calories and a promising source for biofuel production. Although stable gene expression have been used for transgenic breeding and gene function study, a quick, easy and large-scale transformation platform has been in urgent need for gene functional characterization, especially after the cassava full genome was sequenced. METHODS Fully expanded leaves from in vitro plantlets of Manihot esculenta were used to optimize the concentrations of cellulase R-10 and macerozyme R-10 for obtaining protoplasts with the highest yield and viability. Then, the optimum conditions (PEG4000 concentration and transfection time) were determined for cassava protoplast transient gene expression. In addition, the reliability of the established protocol was confirmed for subcellular protein localization. RESULTS In this work we optimized the main influencing factors and developed an efficient mesophyll protoplast isolation and PEG-mediated transient gene expression in cassava. The suitable enzyme digestion system was established with the combination of 1.6% cellulase R-10 and 0.8% macerozyme R-10 for 16 h of digestion in the dark at 25 °C, resulting in the high yield (4.4 × 107 protoplasts/g FW) and vitality (92.6%) of mesophyll protoplasts. The maximum transfection efficiency (70.8%) was obtained with the incubation of the protoplasts/vector DNA mixture with 25% PEG4000 for 10 min. We validated the applicability of the system for studying the subcellular localization of MeSTP7 (an H+/monosaccharide cotransporter) with our transient expression protocol and a heterologous Arabidopsis transient gene expression system. CONCLUSION We optimized the main influencing factors and developed an efficient mesophyll protoplast isolation and transient gene expression in cassava, which will facilitate large-scale characterization of genes and pathways in cassava.
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Affiliation(s)
- Jun-Zheng Wu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Agriculture, Hainan University, Haikou, Hainan Province, 570228, China
| | - Qin Liu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Agriculture, Hainan University, Haikou, Hainan Province, 570228, China
| | - Xiao-Shan Geng
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Agriculture, Hainan University, Haikou, Hainan Province, 570228, China
| | - Kai-Mian Li
- The Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan Province, 571101, China
| | - Li-Juan Luo
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Agriculture, Hainan University, Haikou, Hainan Province, 570228, China.
| | - Jin-Ping Liu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Agriculture, Hainan University, Haikou, Hainan Province, 570228, China.
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Shen Y, Meng D, McGrouther K, Zhang J, Cheng L. Efficient isolation of Magnolia protoplasts and the application to subcellular localization of MdeHSF1. PLANT METHODS 2017; 13:44. [PMID: 28546825 PMCID: PMC5442663 DOI: 10.1186/s13007-017-0193-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2016] [Accepted: 05/18/2017] [Indexed: 05/21/2023]
Abstract
BACKGROUND Magnolia is a woody ornamental plant, which is widely used in urban landscaping. However, its lengthy juvenile period and recalcitrance to regeneration impedes functional characterization of its genes. RESULTS We developed an efficient protoplast isolation and transient expression system for Magnolia denudata × Magnolia acuminata 'Yellow River'. The highest yield of protoplasts was obtained from young leaves digested in 3% Cellulase R10, 0.8% Macerozyme R10, 0.04% pectinase and 0.4 M mannitol enzymolysis solution for 6 h. For transfection of protoplasts, 20% PEG4000 for 5 min was optimal. To verify the protoplast system and begin to understand heat tolerance in Magnolia, a heat shock transcription factor MdeHSF1 was cloned from 'Yellow River', which belongs to the HSF subfamily A and has significant homology with AtHSFA1A. Subcellular localization analysis indicated that MdeHSF1 was expressed in the cell nucleus. Furthermore, qPCR analysis of the MdeHSF1 transcript level in response to high temperature stress suggested that MdeHSF1 might be involved in regulating heat stress tolerance in 'Yellow River'. CONCLUSION The described protocol provides a simple and straightforward method for isolating protoplast and exploring gene subcellular localization of MdeHSF1 in Magnolia. This expands the new research of protoplast isolation and transfection in Magnolia.
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Affiliation(s)
- Yamei Shen
- School of Landscape and Architecture, Zhejiang A & F University, Lin’an, 311300 Zhejiang China
- Department of Horticulture, Cornell University, Ithaca, NY 14853 USA
| | - Dong Meng
- Department of Horticulture, Cornell University, Ithaca, NY 14853 USA
| | | | - Junhong Zhang
- Department of Horticulture, Cornell University, Ithaca, NY 14853 USA
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin’an, 311300 Zhejiang China
| | - Lailiang Cheng
- Department of Horticulture, Cornell University, Ithaca, NY 14853 USA
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Yu G, Cheng Q, Xie Z, Xu B, Huang B, Zhao B. An efficient protocol for perennial ryegrass mesophyll protoplast isolation and transformation, and its application on interaction study between LpNOL and LpNYC1. PLANT METHODS 2017; 13:46. [PMID: 28592987 PMCID: PMC5460552 DOI: 10.1186/s13007-017-0196-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 05/25/2017] [Indexed: 05/18/2023]
Abstract
BACKGROUND Perennial ryegrass (Lolium perenne L.) is an important temperate grass used for turf and forage purposes. With the increasing accumulation of genomic and transcriptomic data of perennial ryegrass, an efficient protoplast and transient gene expression protocol is highly desirable for in vivo gene functional studies in its homologous system. RESULTS In this report, a highly efficient protoplast isolation (5.6 × 107 protoplasts per gram of leaf material) and transient expression (plasmid transformation efficiency at 55.2%) was developed and the detailed protocol presented. Using this protocol, the subcellular locations of two ryegrass proteins were visualized in chloroplasts and nuclei, respectively, and protein-protein interaction between two chlorophyll catabolic enzymes (LpNOL and LpNYC1) was recorded in its homologous system for the first time. CONCLUSION This efficient protoplast isolation and transformation protocol is sufficient for studies on protein subcellular localization and protein-protein interaction, and shall be suitable for many other molecular biology applications where the mesophyll protoplast system is desirable in perennial ryegrass.
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Affiliation(s)
- Guohui Yu
- College of Agro-grassland Science, Nanjing Agricultural University, Nanjing, 210095 People’s Republic of China
| | - Qiang Cheng
- Jiangsu Key Laboratory for Poplar Germplasm Enhancement and Variety Improvement, Nanjing Forestry University, Nanjing, 210037 People’s Republic of China
| | - Zheni Xie
- College of Agro-grassland Science, Nanjing Agricultural University, Nanjing, 210095 People’s Republic of China
| | - Bin Xu
- College of Agro-grassland Science, Nanjing Agricultural University, Nanjing, 210095 People’s Republic of China
| | - Bingru Huang
- Department of Plant Biology and Pathology, Rutgers, the State University of New Jersey, New Brunswick, NJ 08901 USA
| | - Bingyu Zhao
- Department of Horticulture, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061 USA
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Fesenko I, Seredina A, Arapidi G, Ptushenko V, Urban A, Butenko I, Kovalchuk S, Babalyan K, Knyazev A, Khazigaleeva R, Pushkova E, Anikanov N, Ivanov V, Govorun VM. The Physcomitrella patens Chloroplast Proteome Changes in Response to Protoplastation. FRONTIERS IN PLANT SCIENCE 2016; 7:1661. [PMID: 27867392 PMCID: PMC5095126 DOI: 10.3389/fpls.2016.01661] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 10/21/2016] [Indexed: 05/29/2023]
Abstract
Plant protoplasts are widely used for genetic manipulation and functional studies in transient expression systems. However, little is known about the molecular pathways involved in a cell response to the combined stress factors resulted from protoplast generation. Plants often face more than one type of stress at a time, and how plants respond to combined stress factors is therefore of great interest. Here, we used protoplasts of the moss Physcomitrella patens as a model to study the effects of short-term stress on the chloroplast proteome. Using label-free comparative quantitative proteomic analysis (SWATH-MS), we quantified 479 chloroplast proteins, 219 of which showed a more than 1.4-fold change in abundance in protoplasts. We additionally quantified 1451 chloroplast proteins using emPAI. We observed degradation of a significant portion of the chloroplast proteome following the first hour of stress imposed by the protoplast isolation process. Electron-transport chain (ETC) components underwent the heaviest degradation, resulting in the decline of photosynthetic activity. We also compared the proteome changes to those in the transcriptional level of nuclear-encoded chloroplast genes. Globally, the levels of the quantified proteins and their corresponding mRNAs showed limited correlation. Genes involved in the biosynthesis of chlorophyll and components of the outer chloroplast membrane showed decreases in both transcript and protein abundance. However, proteins like dehydroascorbate reductase 1 and 2-cys peroxiredoxin B responsible for ROS detoxification increased in abundance. Further, genes such as thylakoid ascorbate peroxidase were induced at the transcriptional level but down-regulated at the proteomic level. Together, our results demonstrate that the initial chloroplast reaction to stress is due changes at the proteomic level.
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Affiliation(s)
- Igor Fesenko
- Laboratory of Proteomics, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of SciencesMoscow, Russia
| | - Anna Seredina
- Laboratory of Proteomics, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of SciencesMoscow, Russia
| | - Georgij Arapidi
- Laboratory of Proteomics, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of SciencesMoscow, Russia
| | - Vasily Ptushenko
- Department of Bioenergetics, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State UniversityMoscow, Russia
- Department of Biocatalysis, Emanuel Institute of Biochemical Physics, Russian Academy of SciencesMoscow, Russia
| | - Anatoly Urban
- Laboratory of Proteomics, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of SciencesMoscow, Russia
| | - Ivan Butenko
- Laboratory of the Proteomic Analysis, Research Institute for Physico-Chemical MedicineMoscow, Russia
| | - Sergey Kovalchuk
- Laboratory of Proteomics, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of SciencesMoscow, Russia
| | - Konstantin Babalyan
- Laboratory of Proteomics, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of SciencesMoscow, Russia
| | - Andrey Knyazev
- Laboratory of Proteomics, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of SciencesMoscow, Russia
| | - Regina Khazigaleeva
- Laboratory of Proteomics, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of SciencesMoscow, Russia
| | - Elena Pushkova
- Laboratory of Proteomics, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of SciencesMoscow, Russia
| | - Nikolai Anikanov
- Laboratory of Proteomics, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of SciencesMoscow, Russia
| | - Vadim Ivanov
- Laboratory of Proteomics, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of SciencesMoscow, Russia
| | - Vadim M. Govorun
- Laboratory of Proteomics, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of SciencesMoscow, Russia
- Laboratory of the Proteomic Analysis, Research Institute for Physico-Chemical MedicineMoscow, Russia
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Nanjareddy K, Arthikala MK, Blanco L, Arellano ES, Lara M. Protoplast isolation, transient transformation of leaf mesophyll protoplasts and improved Agrobacterium-mediated leaf disc infiltration of Phaseolus vulgaris: tools for rapid gene expression analysis. BMC Biotechnol 2016; 16:53. [PMID: 27342637 PMCID: PMC4919892 DOI: 10.1186/s12896-016-0283-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 06/14/2016] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Phaseolus vulgaris is one of the most extensively studied model legumes in the world. The P. vulgaris genome sequence is available; therefore, the need for an efficient and rapid transformation system is more imperative than ever. The functional characterization of P. vulgaris genes is impeded chiefly due to the non-amenable nature of Phaseolus sp. to stable genetic transformation. Transient transformation systems are convenient and versatile alternatives for rapid gene functional characterization studies. Hence, the present work focuses on standardizing methodologies for protoplast isolation from multiple tissues and transient transformation protocols for rapid gene expression analysis in the recalcitrant grain legume P. vulgaris. RESULTS Herein, we provide methodologies for the high-throughput isolation of leaf mesophyll-, flower petal-, hypocotyl-, root- and nodule-derived protoplasts from P. vulgaris. The highly efficient polyethylene glycol-mannitol magnesium (PEG-MMG)-mediated transformation of leaf mesophyll protoplasts was optimized using a GUS reporter gene. We used the P. vulgaris SNF1-related protein kinase 1 (PvSnRK1) gene as proof of concept to demonstrate rapid gene functional analysis. An RT-qPCR analysis of protoplasts that had been transformed with PvSnRK1-RNAi and PvSnRK1-OE vectors showed the significant downregulation and ectopic constitutive expression (overexpression), respectively, of the PvSnRK1 transcript. We also demonstrated an improved transient transformation approach, sonication-assisted Agrobacterium-mediated transformation (SAAT), for the leaf disc infiltration of P. vulgaris. Interestingly, this method resulted in a 90 % transformation efficiency and transformed 60-85 % of the cells in a given area of the leaf surface. The constitutive expression of YFP further confirmed the amenability of the system to gene functional characterization studies. CONCLUSIONS We present simple and efficient methodologies for protoplast isolation from multiple P. vulgaris tissues. We also provide a high-efficiency and amenable method for leaf mesophyll transformation for rapid gene functional characterization studies. Furthermore, a modified SAAT leaf disc infiltration approach aids in validating genes and their functions. Together, these methods help to rapidly unravel novel gene functions and are promising tools for P. vulgaris research.
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Affiliation(s)
- Kalpana Nanjareddy
- />Ciencias Agrogenómicas, Escuela Nacional de Estudios Superiores, Universidad Nacional Autónoma de México (UNAM), León, C.P.37684 Guanajuato Mexico
| | - Manoj-Kumar Arthikala
- />Ciencias Agrogenómicas, Escuela Nacional de Estudios Superiores, Universidad Nacional Autónoma de México (UNAM), León, C.P.37684 Guanajuato Mexico
| | - Lourdes Blanco
- />Ciencias Agrogenómicas, Escuela Nacional de Estudios Superiores, Universidad Nacional Autónoma de México (UNAM), León, C.P.37684 Guanajuato Mexico
- />Instituto de Fisiología Celular, Universidad Nacional Autónoma de México (UNAM), Ciudad Universitaria, Coyoacan, Ciudad de México C.P. 62210 Mexico
| | - Elizabeth S. Arellano
- />Instituto Nacional de Salud Pública, Av. Universidad 655, Col. Santa Maria, Cuernavaca, Morelos 62100 Mexico
| | - Miguel Lara
- />Ciencias Agrogenómicas, Escuela Nacional de Estudios Superiores, Universidad Nacional Autónoma de México (UNAM), León, C.P.37684 Guanajuato Mexico
- />Instituto de Biología, Universidad Nacional Autónoma de México (UNAM), Ciudad Universitaria, Coyoacan, Ciudad de México C.P. 04510 Mexico
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Mewalal R, Mizrachi E, Coetzee B, Mansfield SD, Myburg AA. The Arabidopsis Domain of Unknown Function 1218 (DUF1218) Containing Proteins, MODIFYING WALL LIGNIN-1 and 2 (At1g31720/MWL-1 and At4g19370/MWL-2) Function Redundantly to Alter Secondary Cell Wall Lignin Content. PLoS One 2016; 11:e0150254. [PMID: 26930070 PMCID: PMC4773003 DOI: 10.1371/journal.pone.0150254] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Accepted: 02/11/2016] [Indexed: 11/22/2022] Open
Abstract
DUF1218 is a land plant-specific innovation and has previously been shown to be associated with cell wall biology, vasculature patterning and abiotic/biotic stress response. The Arabidopsis genome encodes 15 members, two of which (At1g31720 and At4g27435) are preferentially expressed in the secondary cell wall depositing inflorescence stems. To further our understanding of the roles of DUF1218-containing proteins in secondary cell wall biology, we functionally characterized At1g31720 (herein referred to as MODIFYING WALL LIGNIN-1 or MWL-1). Since related gene family members may contribute to functional redundancy, we also characterized At4g19370 (MWL-2), the most closely related gene to MWL-1 in the protein family. Subcellular localization revealed that both Arabidopsis proteins are targeted to the cell periphery. The single T-DNA knockout lines, mwl-1 and mwl-2, and independent overexpression lines showed no significant differences in plant growth or changes in total lignin content relative to wild-type (WT) control plants. However, the double homozygous mutant, mwl-1/mwl-2, had smaller rosettes with a significant decrease in rosette fresh weight and stem height relative to the WT control at four weeks and six weeks, respectively. Moreover, mwl-1/mwl-2 showed a significant reduction in total lignin content (by ca. 11% relative to WT) and an increase in syringyl/guaiacyl (S/G) monomer ratio relative to the control plants. Our study has identified two additional members of the DUF1218 family in Arabidopsis as novel contributors to secondary cell wall biology, specifically lignin biosynthesis, and these proteins appear to function redundantly.
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Affiliation(s)
- Ritesh Mewalal
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Pretoria, 0028, South Africa
| | - Eshchar Mizrachi
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Pretoria, 0028, South Africa
| | - Berdine Coetzee
- Department of Chemical Engineering, University of Pretoria, Private bag X20, Pretoria, 0028, South Africa.,Sappi Southern Africa, P.O Box 12796, Pretoria, 0087, South Africa
| | - Shawn D Mansfield
- Department of Wood Science, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 4030-2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Alexander A Myburg
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Pretoria, 0028, South Africa
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50
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Abstract
Strigolactones are a new class of plant hormones regulating shoot branching and symbiotic interactions with arbuscular mycorrhizal fungi. Studies of branching mutants in herbaceous plants have identified several key genes involved in strigolactone biosynthesis or signaling. The strigolactone signal is perceived by a member of the α/β-fold hydrolase superfamily, known as DWARF14 (D14). However, little is known about D14 genes in the woody perennial plants. Here we report the identification of D14 homologs in the model woody plant Populus trichocarpa. We showed that there are two D14 homologs in P. trichocarpa, designated as PtD14a and PtD14b that are over 95% similar at the amino acid level. Expression analysis indicated that the transcript level of PtD14a is generally more abundant than that of PtD14b. However, only PtD14a was able to complement Arabidopsis d14 mutants, suggesting that PtD14a is the functional D14 ortholog. Amino acid alignment and structural modeling revealed substitutions of several highly conserved amino acids in the PtD14b protein including a phenylalanine near the catalytic triad of D14 proteins. This study lays a foundation for further characterization of strigolactone pathway and its functions in the woody perennial plants.
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