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Cazares-Álvarez JE, Báez-Astorga PA, Arroyo-Becerra A, Maldonado-Mendoza IE. Genome-Wide Identification of a Maize Chitinase Gene Family and the Induction of Its Expression by Fusarium verticillioides (Sacc.) Nirenberg (1976) Infection. Genes (Basel) 2024; 15:1087. [PMID: 39202446 PMCID: PMC11353892 DOI: 10.3390/genes15081087] [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: 07/24/2024] [Revised: 08/09/2024] [Accepted: 08/13/2024] [Indexed: 09/03/2024] Open
Abstract
Maize chitinases are involved in chitin hydrolysis. Chitinases are distributed across various organisms including animals, plants, and fungi and are grouped into different glycosyl hydrolase families and classes, depending on protein structure. However, many chitinase functions and their interactions with other plant proteins remain unknown. The economic importance of maize (Zea mays L.) makes it relevant for studying the function of plant chitinases and their biological roles. This work aims to identify chitinase genes in the maize genome to study their gene structure, family/class classification, cis-related elements, and gene expression under biotic stress, such as Fusarium verticillioides infection. Thirty-nine chitinase genes were identified and found to be distributed in three glycosyl hydrolase (GH) families (18, 19 and 20). Likewise, the conserved domains and motifs were identified in each GH family member. The identified cis-regulatory elements are involved in plant development, hormone response, defense, and abiotic stress response. Chitinase protein-interaction network analysis predicted that they interact mainly with cell wall proteins. qRT-PCR analysis confirmed in silico data showing that ten different maize chitinase genes are induced in the presence of F. verticillioides, and that they could have several roles in pathogen infection depending on chitinase structure and cell wall localization.
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Affiliation(s)
- Jesús Eduardo Cazares-Álvarez
- Departamento de Biotecnología Agrícola, Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional (CIIDIR), Unidad Sinaloa, Instituto Politécnico Nacional, Guasave 81049, Sinaloa, Mexico;
| | - Paúl Alán Báez-Astorga
- CONAHCYT—Departamento de Biotecnología Agrícola, Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional (CIIDIR), Unidad Sinaloa, Instituto Politécnico Nacional, Guasave 81049, Sinaloa, Mexico;
| | - Analilia Arroyo-Becerra
- Laboratorio de Genómica Funcional y Biotecnología de Plantas, Centro de Investigación en Biotecnología Aplicada, Instituto Politécnico Nacional, Ex-Hacienda San Juan Molino Carretera Estatal Km 1.5, Santa Inés-Tecuexcomac-Tepetitla 90700, Tlaxcala, Mexico;
| | - Ignacio Eduardo Maldonado-Mendoza
- Departamento de Biotecnología Agrícola, Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional (CIIDIR), Unidad Sinaloa, Instituto Politécnico Nacional, Guasave 81049, Sinaloa, Mexico;
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Sobrino-Mengual G, Alvarez D, Twyman RM, Gerrish C, Fraser PD, Capell T, Christou P. Activation of the native PHYTOENE SYNTHASE 1 promoter by modifying near-miss cis-acting elements induces carotenoid biosynthesis in embryogenic rice callus. PLANT CELL REPORTS 2024; 43:118. [PMID: 38632121 PMCID: PMC11024007 DOI: 10.1007/s00299-024-03199-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 03/13/2024] [Indexed: 04/19/2024]
Abstract
KEY MESSAGE Modification of silent latent endosperm-enabled promoters (SLEEPERs) allows the ectopic activation of non-expressed metabolic genes in rice callus Metabolic engineering in plants typically involves transgene expression or the mutation of endogenous genes. An alternative is promoter modification, where small changes in the promoter sequence allow genes to be switched on or off in particular tissues. To activate silent genes in rice endosperm, we screened native promoters for near-miss cis-acting elements that can be converted to endosperm-active regulatory motifs. We chose rice PHYTOENE SYNTHASE 1 (PSY1), encoding the enzyme responsible for the first committed step in the carotenoid biosynthesis pathway, because it is not expressed in rice endosperm. We identified six motifs within a 120-bp region, upstream of the transcriptional start site, which differed from endosperm-active elements by up to four nucleotides. We mutated four motifs to match functional elements in the endosperm-active BCH2 promoter, and this promoter was able to drive GFP expression in callus and in seeds of regenerated plants. The 4 M promoter was not sufficient to drive PSY1 expression, so we mutated the remaining two elements and used the resulting 6 M promoter to drive PSY1 expression in combination with a PDS transgene. This resulted in deep orange callus tissue indicating the accumulation of carotenoids, which was subsequently confirmed by targeted metabolomics analysis. PSY1 expression driven by the uncorrected or 4 M variants of the promoter plus a PDS transgene produced callus that lacked carotenoids. These results confirm that the adjustment of promoter elements can facilitate the ectopic activation of endogenous plant promoters in rice callus and endosperm and most likely in other tissues and plant species.
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Affiliation(s)
- Guillermo Sobrino-Mengual
- Applied Plant Biotechnology Group, Department of Agricultural and Forest Sciences and Engineering, University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
| | - Derry Alvarez
- Applied Plant Biotechnology Group, Department of Agricultural and Forest Sciences and Engineering, University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
- Division of Biological and Environmental Sciences and Engineering, Center for Desert Agriculture, BioActives Lab, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | | | - Christopher Gerrish
- Department of Biological Sciences, Royal Holloway University of London, Egham Hill, Egham, Surrey, TW20 0EX, UK
| | - Paul D Fraser
- Department of Biological Sciences, Royal Holloway University of London, Egham Hill, Egham, Surrey, TW20 0EX, UK
| | - Teresa Capell
- Applied Plant Biotechnology Group, Department of Agricultural and Forest Sciences and Engineering, University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
| | - Paul Christou
- Applied Plant Biotechnology Group, Department of Agricultural and Forest Sciences and Engineering, University of Lleida-Agrotecnio CERCA Center, Lleida, Spain.
- ICREA, Catalan Institute for Research and Advanced Studies, Barcelona, Spain.
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Qu G, Wang K, Mu J, Zhuo J, Wang X, Li S, Ye X, Li Y, Yan Y, Li X. Identifying cis-Acting Elements Associated with the High Activity and Endosperm Specificity of the Promoters of Genes Encoding Low-Molecular-Weight Glutenin Subunits in Common Wheat ( Triticum aestivum). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023. [PMID: 37919930 DOI: 10.1021/acs.jafc.3c04209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2023]
Abstract
Low-molecular-weight glutenin subunits (LMW-GSs) associated with bread-baking quality and flour nutrient quality accumulate in endosperms of common wheat and related species. However, the mechanism underlying the expression regulation of genes encoding LMW-GSs has not been fully elucidated. In this study, we identified LMW-D2 and LMW-D7, which are highly and weakly expressed, respectively, via the analysis of RNA-sequencing data of Chinese Spring wheat and wheat transgenic lines transformed with 5' deletion promoter fragments and GUS fusion constructs. The 605-bp fragment upstream of the LMW-D2 start codon could drive high levels of GUS expression in the endosperm. The truncated endosperm box located at the -300 site resulted in the loss of LMW-D2 promoter activity, and a single-nucleotide polymorphism on the GCN4 motif was closely related to the expression of LMW-GSs. TCT and TGACG motifs, as well as the others located on the 5' distal end, might also be involved in the transcription regulation of LMW-GSs. In transgenic lines, fusion proteins of LMW-GS and GUS were deposited into protein bodies. Our findings provide new insights into the mechanism underlying the transcription regulation of LMW-GSs and will contribute to the development of wheat endosperm as a bioreactor for the production of nutraceuticals, antibodies, vaccines, and medicinal proteins.
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Affiliation(s)
- Ge Qu
- Key Laboratory of Genetics and Biotechnology, College of Life Science, Capital Normal University, Beijing 100048, China
| | - Ke Wang
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Junyi Mu
- Key Laboratory of Genetics and Biotechnology, College of Life Science, Capital Normal University, Beijing 100048, China
| | - Jiahui Zhuo
- Key Laboratory of Genetics and Biotechnology, College of Life Science, Capital Normal University, Beijing 100048, China
| | - Xinyu Wang
- Key Laboratory of Genetics and Biotechnology, College of Life Science, Capital Normal University, Beijing 100048, China
| | - Shasha Li
- Key Laboratory of Genetics and Biotechnology, College of Life Science, Capital Normal University, Beijing 100048, China
| | - Xingguo Ye
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yaxuan Li
- Key Laboratory of Genetics and Biotechnology, College of Life Science, Capital Normal University, Beijing 100048, China
| | - Yueming Yan
- Key Laboratory of Genetics and Biotechnology, College of Life Science, Capital Normal University, Beijing 100048, China
| | - Xiaohui Li
- Key Laboratory of Genetics and Biotechnology, College of Life Science, Capital Normal University, Beijing 100048, China
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Chen Q, Guo Y, Zhang J, Zheng N, Wang J, Liu Y, Lu J, Zhen S, Du X, Li L, Fu J, Wang G, Gu R, Wang J, Liu Y. RNA polymerase common subunit ZmRPABC5b is transcriptionally activated by Opaque2 and essential for endosperm development in maize. Nucleic Acids Res 2023; 51:7832-7850. [PMID: 37403778 PMCID: PMC10450181 DOI: 10.1093/nar/gkad571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 06/08/2023] [Accepted: 06/24/2023] [Indexed: 07/06/2023] Open
Abstract
Maize (Zea mays) kernel size is an important factor determining grain yield; although numerous genes regulate kernel development, the roles of RNA polymerases in this process are largely unclear. Here, we characterized the defective kernel 701 (dek701) mutant that displays delayed endosperm development but normal vegetative growth and flowering transition, compared to its wild type. We cloned Dek701, which encoded ZmRPABC5b, a common subunit to RNA polymerases I, II and III. Loss-of-function mutation of Dek701 impaired the function of all three RNA polymerases and altered the transcription of genes related to RNA biosynthesis, phytohormone response and starch accumulation. Consistent with this observation, loss-of-function mutation of Dek701 affected cell proliferation and phytohormone homeostasis in maize endosperm. Dek701 was transcriptionally regulated in the endosperm by the transcription factor Opaque2 through binding to the GCN4 motif within the Dek701 promoter, which was subjected to strong artificial selection during maize domestication. Further investigation revealed that DEK701 interacts with the other common RNA polymerase subunit ZmRPABC2. The results of this study provide substantial insight into the Opaque2-ZmRPABC5b transcriptional regulatory network as a central hub for regulating endosperm development in maize.
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Affiliation(s)
- Quanquan Chen
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs; State Key Laboratory of Maize Bio-breeding; Center for Seed Science and Technology, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yingmei Guo
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs; State Key Laboratory of Maize Bio-breeding; Center for Seed Science and Technology, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Jie Zhang
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs; State Key Laboratory of Maize Bio-breeding; Center for Seed Science and Technology, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Nannan Zheng
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs; State Key Laboratory of Maize Bio-breeding; Center for Seed Science and Technology, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Jie Wang
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs; State Key Laboratory of Maize Bio-breeding; Center for Seed Science and Technology, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Yan Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jiawen Lu
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs; State Key Laboratory of Maize Bio-breeding; Center for Seed Science and Technology, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Sihan Zhen
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs; State Key Laboratory of Maize Bio-breeding; Center for Seed Science and Technology, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Xuemei Du
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs; State Key Laboratory of Maize Bio-breeding; Center for Seed Science and Technology, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Li Li
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs; State Key Laboratory of Maize Bio-breeding; Center for Seed Science and Technology, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Junjie Fu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Guoying Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Riliang Gu
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs; State Key Laboratory of Maize Bio-breeding; Center for Seed Science and Technology, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Jianhua Wang
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs; State Key Laboratory of Maize Bio-breeding; Center for Seed Science and Technology, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Yunjun Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Xu M, Zuo D, Wang Q, Lv L, Zhang Y, Jiao H, Zhang X, Yang Y, Song G, Cheng H. Identification and molecular evolution of the GLX genes in 21 plant species: a focus on the Gossypium hirsutum. BMC Genomics 2023; 24:474. [PMID: 37608304 PMCID: PMC10464159 DOI: 10.1186/s12864-023-09524-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 07/19/2023] [Indexed: 08/24/2023] Open
Abstract
BACKGROUND The glyoxalase system includes glyoxalase I (GLXI), glyoxalase II (GLXII) and glyoxalase III (GLXIII), which are responsible for methylglyoxal (MG) detoxification and involved in abiotic stress responses such as drought, salinity and heavy metal. RESULTS In this study, a total of 620 GLX family genes were identified from 21 different plant species. The results of evolutionary analysis showed that GLX genes exist in all species from lower plants to higher plants, inferring that GLX genes might be important for plants, and GLXI and GLXII account for the majority. In addition, motif showed an expanding trend in the process of evolution. The analysis of cis-acting elements in 21 different plant species showed that the promoter region of the GLX genes were rich in phytohormones and biotic and abiotic stress-related elements, indicating that GLX genes can participate in a variety of life processes. In cotton, GLXs could be divided into two groups and most GLXIs distributed in group I, GLXIIs and GLXIIIs mainly belonged to group II, indicating that there are more similarities between GLXII and GLXIII in cotton evolution. The transcriptome data analysis and quantitative real-time PCR analysis (qRT-PCR) show that some members of GLX family would respond to high temperature treatment in G.hirsutum. The protein interaction network of GLXs in G.hirsutum implied that most members can participate in various life processes through protein interactions. CONCLUSIONS The results elucidated the evolutionary history of GLX family genes in plants and lay the foundation for their functions analysis in cotton.
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Affiliation(s)
- Menglin Xu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
- State Key Laboratory of Cotton Biology, Cotton Research Institute of Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Dongyun Zuo
- State Key Laboratory of Cotton Biology, Cotton Research Institute of Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Qiaolian Wang
- State Key Laboratory of Cotton Biology, Cotton Research Institute of Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Limin Lv
- State Key Laboratory of Cotton Biology, Cotton Research Institute of Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Youping Zhang
- State Key Laboratory of Cotton Biology, Cotton Research Institute of Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Huixin Jiao
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
- State Key Laboratory of Cotton Biology, Cotton Research Institute of Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Xiang Zhang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
- State Key Laboratory of Cotton Biology, Cotton Research Institute of Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Yi Yang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
- State Key Laboratory of Cotton Biology, Cotton Research Institute of Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Guoli Song
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China.
- State Key Laboratory of Cotton Biology, Cotton Research Institute of Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
| | - Hailiang Cheng
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China.
- State Key Laboratory of Cotton Biology, Cotton Research Institute of Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
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Ran C, Zhang Y, Chang F, Yang X, Liu Y, Wang Q, Zhu W. Genome-Wide Analyses of SlFWL Family Genes and Their Expression Profiles under Cold, Heat, Salt and Drought Stress in Tomato. Int J Mol Sci 2023; 24:11783. [PMID: 37511542 PMCID: PMC10380795 DOI: 10.3390/ijms241411783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 07/04/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
PLAC8 is a cysteine-rich protein that serves as a central mediator of tumor evolution in mammals. PLAC8 motif-containing proteins widely distribute in fungi, algae, higher plants and animals that have been described to be implicated in fruit size, cell number and the transport of heavy metals such as cadmium or zinc. In tomatoes, FW2.2 is a PLAC8 motif-containing gene that negatively controls fruit size by regulating cell division and expansion in the carpel ovary during fruit development. However, despite FW2.2, other FWL (FW2.2-Like) genes in tomatoes have not been investigated. In this study, we identified the 21 SlFWL genes, including FW2.2, examined their expression profiles under various abiotic adversity-related conditions. The SlFWL gene structures and motif compositions are conserved, indicating that tomato SlFWL genes may have similar roles. Cis-acting element analysis revealed that the SlFWL genes may participate in light and abiotic stress responses, and they also interacted with a variety of phytohormone-responsive proteins and plant development elements. Phylogenetic analyses were performed on five additional plant species, including Arabidopsis, pepper, soybean, rice and maize, these genes were classified into five subfamilies. Based on the results of collinearity analyses, the SlFWL genes have a tighter homologous evolutionary relationship with soybean, and these orthologous FWL gene pairs might have the common ancestor. Expression profiling of SlFWL genes show that they were all responsive to abiotic stresses, each subgroup of genes exhibited a different expression trend. Our findings provide a strong foundation for investigating the function and abiotic stress responses of the SlFWL family genes.
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Affiliation(s)
- Chunxia Ran
- Shanghai Collaborative Innovation Center of Plant Germplasm Resources Development, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
- Shanghai Key Laboratory of Protected Horticulture Technology, The Protected Horticulture Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Yingying Zhang
- Shanghai Collaborative Innovation Center of Plant Germplasm Resources Development, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
- Shanghai Key Laboratory of Protected Horticulture Technology, The Protected Horticulture Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Feifei Chang
- Shanghai Key Laboratory of Protected Horticulture Technology, The Protected Horticulture Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Xuedong Yang
- Shanghai Key Laboratory of Protected Horticulture Technology, The Protected Horticulture Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Yahui Liu
- Shanghai Key Laboratory of Protected Horticulture Technology, The Protected Horticulture Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Quanhua Wang
- Shanghai Collaborative Innovation Center of Plant Germplasm Resources Development, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Weimin Zhu
- Shanghai Collaborative Innovation Center of Plant Germplasm Resources Development, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
- Shanghai Key Laboratory of Protected Horticulture Technology, The Protected Horticulture Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
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Yu L, Zhang H, Guan R, Li Y, Guo Y, Qiu L. Genome-Wide Tissue-Specific Genes Identification for Novel Tissue-Specific Promoters Discovery in Soybean. Genes (Basel) 2023; 14:1150. [PMID: 37372330 DOI: 10.3390/genes14061150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/18/2023] [Accepted: 05/23/2023] [Indexed: 06/29/2023] Open
Abstract
Promoters play a crucial role in controlling the spatial and temporal expression of genes at transcriptional levels in the process of higher plant growth and development. The spatial, efficient, and correct regulation of exogenous genes expression, as desired, is the key point in plant genetic engineering research. Constitutive promoters widely used in plant genetic transformation are limited because, sometimes, they may cause potential negative effects. This issue can be solved, to a certain extent, by using tissue-specific promoters. Compared with constitutive promoters, a few tissue-specific promoters have been isolated and applied. In this study, based on the transcriptome data, a total of 288 tissue-specific genes were collected, expressed in seven tissues, including the leaves, stems, flowers, pods, seeds, roots, and nodules of soybean (Glycine max). KEGG pathway enrichment analysis was carried out, and 52 metabolites were annotated. A total of 12 tissue-specific genes were selected via the transcription expression level and validated through real-time quantitative PCR, of which 10 genes showed tissue-specific expression. The 3-kb 5' upstream regions of ten genes were obtained as putative promoters. Further analysis showed that all the 10 promoters contained many tissue-specific cis-elements. These results demonstrate that high-throughput transcriptional data can be used as effective tools, providing a guide for high-throughput novel tissue-specific promoter discovery.
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Affiliation(s)
- Lili Yu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Hao Zhang
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Rongxia Guan
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yinghui Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yong Guo
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Lijuan Qiu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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8
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Chakraborty S, Gangwar R, Zahra S, Poddar N, Singh A, Kumar S. Genome-wide characterization and comparative analysis of the OSCA gene family and identification of its potential stress-responsive members in legumes. Sci Rep 2023; 13:5914. [PMID: 37041245 PMCID: PMC10090146 DOI: 10.1038/s41598-023-33226-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 04/10/2023] [Indexed: 04/13/2023] Open
Abstract
Cicer arietinum, Cajanus cajan, Vigna radiata, and Phaseolus vulgaris are economically important legume crops with high nutritional value. They are negatively impacted globally by different biotic and abiotic stresses. Hyperosmolality-gated calcium-permeable channels (OSCA) have been characterized as osmosensors in Arabidopsis thaliana but have not previously reported in legumes. This study provides a genome-wide identification, characterization, and comparative analysis of OSCA genes in legumes. Our study identified and characterized 13 OSCA genes in C. cajan, V. radiata, P. vulgaris, and 12 in C. arietinum, classified into four distinct clades. We found evidence to suggest that the OSCAs might be involved in the interaction between hormone signalling pathways and stress signalling pathways. Furthermore, they play a major role in plant growth and development. The expression levels of the OSCAs vary under different stress conditions in a tissue-specific manner. Our study can be used to develop a detailed understanding of stress regulatory mechanisms of the OSCA gene family in legumes.
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Affiliation(s)
- Srija Chakraborty
- Bioinformatics Lab, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Rashmi Gangwar
- Bioinformatics Lab, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Shafaque Zahra
- Bioinformatics Lab, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Nikita Poddar
- Bioinformatics Lab, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Amarjeet Singh
- Stress Signalling Lab, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Shailesh Kumar
- Bioinformatics Lab, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India.
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9
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Kumari A, Sharma D, Sharma P, Wang C, Verma V, Patil A, Imran M, Singh MP, Kumar K, Paritosh K, Caragea D, Kapoor S, Chandel G, Grover A, Jagadish SVK, Katiyar-Agarwal S, Agarwal M. Meta-QTL and haplo-pheno analysis reveal superior haplotype combinations associated with low grain chalkiness under high temperature in rice. FRONTIERS IN PLANT SCIENCE 2023; 14:1133115. [PMID: 36968399 PMCID: PMC10031497 DOI: 10.3389/fpls.2023.1133115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 02/17/2023] [Indexed: 06/18/2023]
Abstract
Chalk, an undesirable grain quality trait in rice, is primarily formed due to high temperatures during the grain-filling process. Owing to the disordered starch granule structure, air spaces and low amylose content, chalky grains are easily breakable during milling thereby lowering head rice recovery and its market price. Availability of multiple QTLs associated with grain chalkiness and associated attributes, provided us an opportunity to perform a meta-analysis and identify candidate genes and their alleles contributing to enhanced grain quality. From the 403 previously reported QTLs, 64 Meta-QTLs encompassing 5262 non-redundant genes were identified. MQTL analysis reduced the genetic and physical intervals and nearly 73% meta-QTLs were narrower than 5cM and 2Mb, revealing the hotspot genomic regions. By investigating expression profiles of 5262 genes in previously published datasets, 49 candidate genes were shortlisted on the basis of their differential regulation in at least two of the datasets. We identified non-synonymous allelic variations and haplotypes in 39 candidate genes across the 3K rice genome panel. Further, we phenotyped a subset panel of 60 rice accessions by exposing them to high temperature stress under natural field conditions over two Rabi cropping seasons. Haplo-pheno analysis uncovered haplotype combinations of two starch synthesis genes, GBSSI and SSIIa, significantly contributing towards the formation of grain chalk in rice. We, therefore, report not only markers and pre-breeding material, but also propose superior haplotype combinations which can be introduced using either marker-assisted breeding or CRISPR-Cas based prime editing to generate elite rice varieties with low grain chalkiness and high HRY traits.
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Affiliation(s)
- Anita Kumari
- Department of Botany, University of Delhi, Delhi, India
| | - Divya Sharma
- Department of Botany, University of Delhi, Delhi, India
| | - Priya Sharma
- Department of Botany, University of Delhi, Delhi, India
| | - Sahil
- Department of Botany, University of Delhi, Delhi, India
| | - Chaoxin Wang
- Department of Computer Science, Kansas State University, Manhattan, KS, United States
| | - Vibha Verma
- Department of Plant Molecular Biology, University of Delhi, New Delhi, India
| | - Arun Patil
- Department of Plant Molecular Biology and Biotechnology, Indira Gandhi Krishi Vishwavidyalaya, Chattisgarh, India
| | - Md Imran
- Department of Botany, University of Delhi, Delhi, India
| | - Madan Pal Singh
- Division of Plant Physiology, Indian Council of Agricultural Research (ICAR), New Delhi, India
| | - Kuldeep Kumar
- National Institute for Plant Biotechnology, Indian Council of Agricultural Research (ICAR), New Delhi, India
| | - Kumar Paritosh
- Centre for Genetic Manipulation of Crop Plants, New Delhi, India
| | - Doina Caragea
- Department of Computer Science, Kansas State University, Manhattan, KS, United States
| | - Sanjay Kapoor
- Department of Plant Molecular Biology, University of Delhi, New Delhi, India
| | - Girish Chandel
- Department of Plant Molecular Biology and Biotechnology, Indira Gandhi Krishi Vishwavidyalaya, Chattisgarh, India
| | - Anil Grover
- Department of Plant Molecular Biology, University of Delhi, New Delhi, India
| | | | | | - Manu Agarwal
- Department of Botany, University of Delhi, Delhi, India
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10
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Zhong V, Archibald BN, Brophy JAN. Transcriptional and post-transcriptional controls for tuning gene expression in plants. CURRENT OPINION IN PLANT BIOLOGY 2023; 71:102315. [PMID: 36462457 DOI: 10.1016/j.pbi.2022.102315] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/22/2022] [Accepted: 10/27/2022] [Indexed: 06/17/2023]
Abstract
Plant biotechnologists seek to modify plants through genetic reprogramming, but our ability to precisely control gene expression in plants is still limited. Here, we review transcription and translation in the model plants Arabidopsis thaliana and Nicotiana benthamiana with an eye toward control points that may be used to predictably modify gene expression. We highlight differences in gene expression requirements between these plants and other species, and discuss the ways in which our understanding of gene expression has been used to engineer plants. This review is intended to serve as a resource for plant scientists looking to achieve precise control over gene expression.
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Affiliation(s)
- Vivian Zhong
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Bella N Archibald
- Department of Bioengineering, Stanford University, Stanford, CA, USA
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11
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Gao XR, Zhang H, Li X, Bai YW, Peng K, Wang Z, Dai ZR, Bian XF, Zhang Q, Jia LC, Li Y, Liu QC, Zhai H, Gao SP, Zhao N, He SZ. The B-box transcription factor IbBBX29 regulates leaf development and flavonoid biosynthesis in sweet potato. PLANT PHYSIOLOGY 2023; 191:496-514. [PMID: 36377782 PMCID: PMC9806656 DOI: 10.1093/plphys/kiac516] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 09/23/2022] [Indexed: 06/01/2023]
Abstract
Plant flavonoids are valuable natural antioxidants. Sweet potato (Ipomoea batatas) leaves are rich in flavonoids, regenerate rapidly, and can adapt to harsh environments, making them an ideal material for flavonoid biofortification. Here, we demonstrate that the B-box (BBX) family transcription factor IbBBX29 regulates the flavonoid contents and development of sweet potato leaves. IbBBX29 was highly expressed in sweet potato leaves and significantly induced by auxin (IAA). Overexpression of IbBBX29 contributed to a 21.37%-70.94% increase in leaf biomass, a 12.08%-21.85% increase in IAA levels, and a 31.33%-63.03% increase in flavonoid accumulation in sweet potato, whereas silencing this gene produced opposite effects. Heterologous expression of IbBBX29 in Arabidopsis (Arabidopsis thaliana) led to a dwarfed phenotype, along with enhanced IAA and flavonoid accumulation. RNA-seq analysis revealed that IbBBX29 modulates the expression of genes involved in the IAA signaling and flavonoid biosynthesis pathways. Chromatin immunoprecipitation-quantitative polymerase chain reaction and electrophoretic mobility shift assay indicated that IbBBX29 targets key genes of IAA signaling and flavonoid biosynthesis to activate their expression by binding to specific T/G-boxes in their promoters, especially those adjacent to the transcription start site. Moreover, IbBBX29 physically interacted with developmental and phenylpropanoid biosynthesis-related proteins, such as AGAMOUS-LIKE 21 protein IbAGL21 and MYB308-like protein IbMYB308L. Finally, overexpressing IbBBX29 also increased flavonoid contents in sweet potato storage roots. These findings indicate that IbBBX29 plays a pivotal role in regulating IAA-mediated leaf development and flavonoid biosynthesis in sweet potato and Arabidopsis, providing a candidate gene for flavonoid biofortification in plants.
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Affiliation(s)
- Xiao-ru Gao
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Huan Zhang
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
- Sanya Institute of China Agricultural University, Hainan 572025, China
| | - Xu Li
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
- Sanya Institute of China Agricultural University, Hainan 572025, China
| | - Yi-wei Bai
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Kui Peng
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Zhen Wang
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Zhuo-ru Dai
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Xiao-feng Bian
- Provincial Key Laboratory of Agrobiology, Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210000, China
| | - Qian Zhang
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
- Provincial Key Laboratory of Agrobiology, Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210000, China
| | - Li-cong Jia
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
- Institute of Grain and Oil Crops, Yantai Academy of Agricultural Sciences, Yantai 265500, China
| | - Yan Li
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Qing-chang Liu
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Hong Zhai
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Shao-pei Gao
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Ning Zhao
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Shao-zhen He
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
- Sanya Institute of China Agricultural University, Hainan 572025, China
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12
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Jameel A, Ketehouli T, Wang Y, Wang F, Li X, Li H. Detection and validation of cis-regulatory motifs in osmotic stress-inducible synthetic gene switches via computational and experimental approaches. FUNCTIONAL PLANT BIOLOGY : FPB 2022; 49:1043-1054. [PMID: 35940614 DOI: 10.1071/fp21314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
Synthetic cis -regulatory modules can improve our understanding of gene regulatory networks. We applied an ensemble approach for de novo cis motif discovery among the promoters of 181 drought inducible differentially expressed soybean (Glycine max L.) genes. A total of 43 cis motifs were identified in promoter regions of all gene sets using the binding site estimation suite of tools (BEST). Comparative analysis of these motifs revealed similarities with known cis -elements found in PLACE database and led to the discovery of cis -regulatory motifs that were not yet implicated in drought response. Compiled with the proposed synthetic promoter design rationale, three synthetic assemblies were constructed by concatenating multiple copies of drought-inducible cis motifs in a specific order with inter-motif spacing using random bases and placed upstream of 35s minimal core promoter. Each synthetic module substituted 35S promoter in pBI121 and pCAMBIA3301 to drive glucuronidase expression in soybean hairy roots and Arabidopsis thaliana L. Chimeric soybean seedlings and 3-week-old transgenic Arabidopsis plants were treated with simulated with different levels of osmotic stress. Histochemical staining of transgenic soybean hairy roots and Arabidopsis displayed drought-inducible GUS activity of synthetic promoters. Fluorometric assay and expression analysis revealed that SP2 is the better manual combination of cis -elements for stress-inducible expression. qRT-PCR results further demonstrated that designed synthetic promoters are not tissue-specific and thus active in different parts upon treatment with osmotic stress in Arabidopsis plants. This study provides tools for transcriptional upgradation of valuable crops against drought stress and adds to the current knowledge of synthetic biology.
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Affiliation(s)
- Aysha Jameel
- College of Life Sciences, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun 130118, China
| | - Toi Ketehouli
- College of Life Sciences, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun 130118, China
| | - Yifan Wang
- College of Life Sciences, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun 130118, China
| | - Fawei Wang
- College of Life Sciences, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun 130118, China
| | - Xiaowei Li
- College of Life Sciences, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun 130118, China
| | - Haiyan Li
- College of Tropical Crops, Hainan University, 570228, Haikou, China
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13
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He L, Cheng L, Wang J, Liu J, Cheng J, Yang Z, Cao R, Han Y, Li H, Zhang B. Carotenoid Cleavage Dioxygenase 1 Catalyzes Lutein Degradation To Influence Carotenoid Accumulation and Color Development in Foxtail Millet Grains. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:9283-9294. [PMID: 35876162 DOI: 10.1021/acs.jafc.2c01951] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Foxtail millet is a minor but economically important crop in certain regions of the world. Millet color is often used to judge grain quality, yet the molecular determinants of millet coloration remain unclear. Here, we explored the relationship between SiCCD1 and millet coloration in yellow and white millet varieties. Carotenoid levels declined with grain maturation and were negatively correlated with SiCCD1 expression, which was significantly higher in white millet as compared to yellow millet during the color development stage. Cloning of the SiCCD1 promoter and CDS sequences from these different millet varieties revealed the presence of two additional cis-regulatory elements within the SiCCD1 promoter in white millet varieties, including an enhancer-like GC motif element associated with anoxic specific inducibility and a GCN4-motif element associated with endosperm expression. Dual-luciferase reporter assays confirmed that SiCCD1 promoter fragments containing these additional cis-acting elements derived from white millet varieties were significantly more active than those from yellow millet varieties, consistent with the observed SiCCD1 expression patterns. Further in vitro enzyme detection assays confirmed that SiCCD1 primarily targets and degrades lutein. Together, these data suggest that SiCCD1 promoter variation was a key factor associated with the observed differences in SiCCD1 expression, which in turn led to the difference in millet coloration.
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Affiliation(s)
- Lu He
- College of Agriculture, Shanxi Agricultural University, Taigu 030801, China
- Maize Research Institute, Shanxi Agricultural University, Xinzhou 034000, China
| | - Lu Cheng
- College of Agriculture, Shanxi Agricultural University, Taigu 030801, China
| | - Junjie Wang
- College of Agriculture, Shanxi Agricultural University, Taigu 030801, China
| | - Jing Liu
- College of Agriculture, Shanxi Agricultural University, Taigu 030801, China
| | - Jinjin Cheng
- College of Agriculture, Shanxi Agricultural University, Taigu 030801, China
| | - Zhirong Yang
- Department of Foundation, Shanxi Agricultural University, Taigu 030801, China
| | - Rui Cao
- Shanxi Biological Research Institute Co., Ltd, Taiyuan 030000, China
| | - Yuanhuai Han
- College of Agriculture, Shanxi Agricultural University, Taigu 030801, China
- Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu 030801, China
- Ministerial and Provincial Co-Innovation Centre for Endemic Crops Production with High-quality and Efficiency in Loess Plateau, Shanxi Agricultural University, Taigu 030801, China
| | - Hongying Li
- College of Agriculture, Shanxi Agricultural University, Taigu 030801, China
- Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu 030801, China
| | - Bin Zhang
- College of Agriculture, Shanxi Agricultural University, Taigu 030801, China
- Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu 030801, China
- Ministerial and Provincial Co-Innovation Centre for Endemic Crops Production with High-quality and Efficiency in Loess Plateau, Shanxi Agricultural University, Taigu 030801, China
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14
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Liu J, Wu MW, Liu CM. Cereal Endosperms: Development and Storage Product Accumulation. ANNUAL REVIEW OF PLANT BIOLOGY 2022; 73:255-291. [PMID: 35226815 DOI: 10.1146/annurev-arplant-070221-024405] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The persistent triploid endosperms of cereal crops are the most important source of human food and animal feed. The development of cereal endosperms progresses through coenocytic nuclear division, cellularization, aleurone and starchy endosperm differentiation, and storage product accumulation. In the past few decades, the cell biological processes involved in endosperm formation in most cereals have been described. Molecular genetic studies performed in recent years led to the identification of the genes underlying endosperm differentiation, regulatory network governing storage product accumulation, and epigenetic mechanism underlying imprinted gene expression. In this article, we outline recent progress in this area and propose hypothetical models to illustrate machineries that control aleurone and starchy endosperm differentiation, sugar loading, and storage product accumulations. A future challenge in this area is to decipher the molecular mechanisms underlying coenocytic nuclear division, endosperm cellularization, and programmed cell death.
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Affiliation(s)
- Jinxin Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China;
| | - Ming-Wei Wu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China;
| | - Chun-Ming Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China;
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- School of Advanced Agricultural Sciences, Peking University, Beijing, China
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15
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Abstract
Endosperm of cereal crops is the main component of its grain. Improvement of endosperm traits will bolster grain yield and quality. Functional analysis of endosperm trait-related genes often requires the use of an endosperm cell system. Here, we describe a protocol for the isolation and transfection of maize endosperm cell protoplast. The endosperm protoplast system can be used for several molecular studies including protein subcellular localization, protein-protein interaction by bimolecular fluorescence complementation (BiFC), protein immunoblotting, transient gene expression, and regulatory analyses by qRT-PCR.
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Affiliation(s)
- Yufeng Hu
- College of Agronomy, Sichuan Agricultural University, Chengdu, People's Republic of China
| | - Yubi Huang
- College of Agronomy, Sichuan Agricultural University, Chengdu, People's Republic of China.
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16
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He W, Wang L, Lin Q, Yu F. Rice seed storage proteins: Biosynthetic pathways and the effects of environmental factors. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:1999-2019. [PMID: 34581486 DOI: 10.1111/jipb.13176] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/27/2021] [Indexed: 05/02/2023]
Abstract
Rice (Oryza sativa L.) is the most important food crop for at least half of the world's population. Due to improved living standards, the cultivation of high-quality rice for different purposes and markets has become a major goal. Rice quality is determined by the presence of many nutritional components, including seed storage proteins (SSPs), which are the second most abundant nutrient components of rice grains after starch. Rice SSP biosynthesis requires the participation of multiple organelles and is influenced by the external environment, making it challenging to understand the molecular details of SSP biosynthesis and improve rice protein quality. In this review, we highlight the current knowledge of rice SSP biosynthesis, including a detailed description of the key molecules involved in rice SSP biosynthetic processes and the major environmental factors affecting SSP biosynthesis. The effects of these factors on SSP accumulation and their contribution to rice quality are also discussed based on recent findings. This recent knowledge suggests not only new research directions for exploring rice SSP biosynthesis but also innovative strategies for breeding high-quality rice varieties.
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Affiliation(s)
- Wei He
- National Engineering Laboratory for Rice and By-product Deep Processing, Central South University of Forestry and Technology, Changsha, 410004, China
- College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, and Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, 410082, China
| | - Long Wang
- College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, and Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, 410082, China
| | - Qinlu Lin
- National Engineering Laboratory for Rice and By-product Deep Processing, Central South University of Forestry and Technology, Changsha, 410004, China
| | - Feng Yu
- College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, and Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, 410082, China
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17
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Construction of a Porcine Skeletal Muscle-Specific Promoter by Inducing the Seed Region of miR-208a. Mol Biotechnol 2021; 64:473-481. [PMID: 34822105 DOI: 10.1007/s12033-021-00428-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 11/17/2021] [Indexed: 10/19/2022]
Abstract
Transgenic promoter systems are of great interest for their potential use in gene therapy or production due to their high activity, long term, and cell specificity. Here, in order to obtain promoters with high activity and expressed specifically in skeletal muscle, the MYOD1, MYF5, and MCK were selected as the candidate genes. The truncated promoters were amplified and their activity was verified through dual-luciferase reporter gene test. We used genetic engineering techniques to improve promoter activity by tandemly linking enhancers and promoters or two promoters. Furthermore, synthetic promoter was the most active when two eMCK enhancers and pMCK promoter were cascaded. To improve the tissue specificity of the promoter, the seed region of translational repressor miR-208a was inserted into the downstream of the promoter (pGL3-2eMCK-pMCK-T208-mCherry-EGFP). The results showed that the expression level of target genes decreased significantly (P < 0.05) in myocardium rather than in skeletal muscle. The results of in vivo transfection indicated that tandem transcriptional regulatory elements can increase promoter activity in mice. This work laid the foundation for future research on genetically modified pigs.
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18
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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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19
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Arya H, Singh MB, Bhalla PL. Overexpression of
PIF4
affects plant morphology and accelerates reproductive phase transitions in soybean. Food Energy Secur 2021. [DOI: 10.1002/fes3.291] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Affiliation(s)
- Hina Arya
- Plant Molecular Biology and Biotechnology Laboratory School of Agriculture and Food Faculty of Veterinary and Agricultural Sciences The University of Melbourne Victoria Australia
| | - Mohan B. Singh
- Plant Molecular Biology and Biotechnology Laboratory School of Agriculture and Food Faculty of Veterinary and Agricultural Sciences The University of Melbourne Victoria Australia
| | - Prem L. Bhalla
- Plant Molecular Biology and Biotechnology Laboratory School of Agriculture and Food Faculty of Veterinary and Agricultural Sciences The University of Melbourne Victoria Australia
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21
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Gahlaut V, Samtani H, Khurana P. Genome-wide identification and expression profiling of cytosine-5 DNA methyltransferases during drought and heat stress in wheat (Triticum aestivum). Genomics 2020; 112:4796-4807. [PMID: 32890700 DOI: 10.1016/j.ygeno.2020.08.031] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/17/2020] [Accepted: 08/25/2020] [Indexed: 01/25/2023]
Abstract
DNA methylation is a potential epigenetic mechanism that regulates genome stability, development, and stress mitigation in plants. It is mediated by cytosine-5 DNA methyltransferases (C5-MTases). We identified 52 wheat C5-MTases; and based on domain structure and phylogenetics, these 52 C5-MTases were classified into four sub-families including MET, CMT, DRM and DNMT2; and were distributed on 18 chromosomes. Cis-acting regulatory elements analysis identified abiotic stress-responsive, phytohormone-responsive, development-related and light-related elements in the promoters of TaC5-MTases. We also examined the transcript abundance of TaC5-MTases in different tissues, developmental stages and under abiotic stresses. Notably, most of the TaC5-MTases (TaCMT2, TaCMT3b, TaCMT3c, TaMET1, TaDRM10, TaDNMT2) showed differential regulation of their transcript abundance during drought and heat stress. Overall, the above results provide significant insights into the expression and the probable functions of TaC5-MTases and will also expedite future research programs to explore the mechanisms of epigenetic regulation in wheat.
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Affiliation(s)
- Vijay Gahlaut
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India.
| | - Harsha Samtani
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - Paramjit Khurana
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
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Yang Y, Chai Y, Zhang X, Lu S, Zhao Z, Wei D, Chen L, Hu YG. Multi-Locus GWAS of Quality Traits in Bread Wheat: Mining More Candidate Genes and Possible Regulatory Network. FRONTIERS IN PLANT SCIENCE 2020; 11:1091. [PMID: 32849679 PMCID: PMC7411135 DOI: 10.3389/fpls.2020.01091] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 07/02/2020] [Indexed: 05/20/2023]
Abstract
In wheat breeding, improved quality traits, including grain quality and dough rheological properties, have long been a critical goal. To understand the genetic basis of key quality traits of wheat, two single-locus and five multi-locus GWAS models were performed for six grain quality traits and three dough rheological properties based on 19, 254 SNPs in 267 bread wheat accessions. As a result, 299 quantitative trait nucleotides (QTNs) within 105 regions were identified to be associated with these quality traits in four environments. Of which, 40 core QTN regions were stably detected in at least three environments, 19 of which were novel. Compared with the previous studies, these novel QTN regions explained smaller phenotypic variation, which verified the advantages of the multi-locus GWAS models in detecting important small effect QTNs associated with complex traits. After characterization of the function and expression in-depth, 67 core candidate genes involved in protein/sugar synthesis, histone modification and the regulation of transcription factor were observed to be associated with the formation of grain quality, which showed that multi-level regulations influenced wheat grain quality. Finally, a preliminary network of gene regulation that may affect wheat quality formation was inferred. This study verified the power and reliability of multi-locus GWAS methods in wheat quality trait research, and increased the understanding of wheat quality formation mechanisms. The detected QTN regions and candidate genes in this study could be further used for gene cloning and marker-assisted selection in high-quality breeding of bread wheat.
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Affiliation(s)
- Yang Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Yongmao Chai
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Xuan Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Shan Lu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Zhangchen Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Di Wei
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Liang Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Yin-Gang Hu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
- Institute of Water Saving Agriculture in Arid Regions of China, Northwest A&F University, Yangling, China
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Zhang D, Yang H, Wang X, Qiu Y, Tian L, Qi X, Qu LQ. Cytochrome P450 family member CYP96B5 hydroxylates alkanes to primary alcohols and is involved in rice leaf cuticular wax synthesis. THE NEW PHYTOLOGIST 2020; 225:2094-2107. [PMID: 31618451 DOI: 10.1111/nph.16267] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 10/09/2019] [Indexed: 05/24/2023]
Abstract
Odd-numbered primary alcohols are components of plant cuticular wax, but their biosynthesis remains unknown. We isolated a rice wax crystal-sparse leaf 5 (WSL5) gene using a map-based cloning strategy. The function of WSL5 was illustrated by overexpression and knockout in rice, heterologous expression in Arabidopsis and transient expression in tobacco leaves. WSL5 is predicted to encode a cytochrome P450 family member CYP96B5. The wsl5 mutant lacked crystalloid platelets on the surface of cuticle membrane, and its cuticle membrane was thicker than that of the wild-type. The wsl5 mutant is more tolerant to drought stress. The load of C23 -C33 alkanes increased, whereas the C29 primary alcohol reduced significantly in wsl5 mutant and WSL5 knockout transgenic plants. Overexpression of WSL5 increased the C29 primary alcohol and decreased alkanes in rice leaves. Heterologous expression of WSL5 increased the C29 primary alcohol and decreased alkanes, secondary alcohol, and ketone in Arabidopsis stem wax. Transient expression of WSL5 in tobacco leaves also increased the production C29 primary alcohol. WSL5 catalyzes the terminal hydroxylation of alkanes, yielding odd-numbered primary alcohols, and is involved in the formation of epidermal wax crystals on rice leaf, affecting drought sensitivity.
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Affiliation(s)
- Du Zhang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100093, China
| | - Huifang Yang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100093, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaochen Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yijian Qiu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100093, China
| | - Lihong Tian
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100093, China
| | - Xiaoquan Qi
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100093, China
| | - Le Qing Qu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100093, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China
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The DOF Transcription Factors in Seed and Seedling Development. PLANTS 2020; 9:plants9020218. [PMID: 32046332 PMCID: PMC7076670 DOI: 10.3390/plants9020218] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 02/05/2020] [Accepted: 02/06/2020] [Indexed: 01/28/2023]
Abstract
The DOF (DNA binding with one finger) family of plant-specific transcription factors (TF) was first identified in maize in 1995. Since then, DOF proteins have been shown to be present in the whole plant kingdom, including the unicellular alga Chlamydomonas reinhardtii. The DOF TF family is characterised by a highly conserved DNA binding domain (DOF domain), consisting of a CX2C-X21-CX2C motif, which is able to form a zinc finger structure. Early in the study of DOF proteins, their relevance for seed biology became clear. Indeed, the PROLAMIN BINDING FACTOR (PBF), one of the first DOF proteins characterised, controls the endosperm-specific expression of the zein genes in maize. Subsequently, several DOF proteins from both monocots and dicots have been shown to be primarily involved in seed development, dormancy and germination, as well as in seedling development and other light-mediated processes. In the last two decades, the molecular network underlying these processes have been outlined, and the main molecular players and their interactions have been identified. In this review, we will focus on the DOF TFs involved in these molecular networks, and on their interaction with other proteins.
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Khan MS, Joyia FA, Mustafa G. Seeds as Economical Production Platform for Recombinant Proteins. Protein Pept Lett 2020; 27:89-104. [DOI: 10.2174/0929866526666191014151237] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 05/13/2019] [Accepted: 08/02/2019] [Indexed: 11/22/2022]
Abstract
:
The cost-effective production of high-quality and biologically active recombinant
molecules especially proteins is extremely desirable. Seed-based recombinant protein production
platforms are considered as superior choice owing to lack of human/animal pathogenic organisms,
lack of cold chain requirements for transportation and long-term storage, easy scalability and
development of edible biopharmaceuticals in plants with objective to be used in purified or partially
processed form is desirable. This review article summarizes the exceptional features of seed-based
biopharming and highlights the needs of exploiting it for commercial purposes. Plant seeds offer a
perfect production platform for high-value molecules of industrial as well as therapeutic nature
owing to lower water contents, high protein storage capacity, weak protease activity and long-term
storage ability at ambient temperature. Exploiting extraordinarily high protein accumulation
potential, vaccine antigens, antibodies and other therapeutic proteins can be stored without effecting
their stability and functionality up to years in seeds. Moreover, ability of direct oral consumption
and post-harvest stabilizing effect of seeds offer unique feature of oral delivery of pharmaceutical
proteins and vaccine antigens for immunization and disease treatment through mucosal as well as
oral route.
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Affiliation(s)
- Muhammad Sarwar Khan
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, Pakistan
| | - Faiz Ahmad Joyia
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, Pakistan
| | - Ghulam Mustafa
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, Pakistan
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Duan L, Han S, Wang K, Jiang P, Gu Y, Chen L, Mu J, Ye X, Li Y, Yan Y, Li X. Analyzing the action of evolutionarily conserved modules on HMW-GS 1Ax1 promoter activity. PLANT MOLECULAR BIOLOGY 2020; 102:225-237. [PMID: 31820284 DOI: 10.1007/s11103-019-00943-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 12/04/2019] [Indexed: 06/10/2023]
Abstract
The specific and high-level expression of 1Ax1 is determined by different promoter regions. HMW-GS synthesis occurs in aleurone layer cells. Heterologous proteins can be stored in protein bodies. High-molecular-weight glutenin subunit (HMW-GS) is highly expressed in the endosperm of wheat and relative species, where their expression level and allelic variation affect the bread-making quality and nutrient quality of flour. However, the mechanism regulating HMW-GS expression remains elusive. In this study, we analyzed the distribution of cis-acting elements in the 2659-bp promoter region of the HMW-GS gene 1Ax1, which can be divided into five element-enriched regions. Fragments derived from progressive 5' deletions were used to drive GUS gene expression in transgenic wheat, which was confirmed in aleurone layer cells, inner starchy endosperm cells, starchy endosperm transfer cells, and aleurone transfer cells by histochemical staining. The promoter region ranging from - 297 to - 1 was responsible for tissue-specific expression, while fragments from - 1724 to - 618 and from - 618 to - 297 were responsible for high-level expression. Under the control of the 1Ax1 promoter, heterologous protein could be stored in the form of protein bodies in inner starchy endosperm cells, even without a special location signal. Our findings not only deepen our understanding of glutenin expression regulation, trafficking, and accumulation but also provide a strategy for the utilization of wheat endosperm as a bioreactor for the production of nutrients and metabolic products.
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Affiliation(s)
- Luning Duan
- Key Laboratory of Genetics and Biotechnology, College of Life Science, Capital Normal University, Beijing, 100048, China
| | - Shichen Han
- Key Laboratory of Genetics and Biotechnology, College of Life Science, Capital Normal University, Beijing, 100048, China
| | - Ke Wang
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Peihong Jiang
- Key Laboratory of Genetics and Biotechnology, College of Life Science, Capital Normal University, Beijing, 100048, China
| | - Yunsong Gu
- Key Laboratory of Genetics and Biotechnology, College of Life Science, Capital Normal University, Beijing, 100048, China
| | - Lin Chen
- Key Laboratory of Genetics and Biotechnology, College of Life Science, Capital Normal University, Beijing, 100048, China
| | - Junyi Mu
- Key Laboratory of Genetics and Biotechnology, College of Life Science, Capital Normal University, Beijing, 100048, China
| | - Xingguo Ye
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yaxuan Li
- Key Laboratory of Genetics and Biotechnology, College of Life Science, Capital Normal University, Beijing, 100048, China
| | - Yueming Yan
- Key Laboratory of Genetics and Biotechnology, College of Life Science, Capital Normal University, Beijing, 100048, China
| | - Xiaohui Li
- Key Laboratory of Genetics and Biotechnology, College of Life Science, Capital Normal University, Beijing, 100048, China.
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Kumari K, Rai MP, Bansal N, Rama Prashat G, Kumari S, Krishnan V, Srivathsa R, Dahuja A, Sachdev A, Praveen S, Vinutha T. Analysis of γ-Tocopherol methyl transferase3 promoter activity and study of methylation patterns of the promoter and its gene body. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 144:375-385. [PMID: 31622940 DOI: 10.1016/j.plaphy.2019.09.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 09/11/2019] [Accepted: 09/26/2019] [Indexed: 06/10/2023]
Abstract
Soybeans are known for its good source of protein (40%), oil (20%) and also serve as a source of nutraceutical compounds including tocopherols (toc). To know the molecular basis of differential α-toc accumulation in two contrasting soybean genotypes: DS74 (low α-toc - 1.36 μg/g and total-toc -29.72 μg/g) and Bragg (high α-toc - 10.48 μg/g and total-toc 178.91 μg/g), the analysis of γ-TMT3 promoter activity and its methylation patterns were carried out. The sequencing results revealed nucleotide variation between Bragg:γ-TMT3-P and DS74:γ-TMT3-P, however none of the variations were found in core-promoter region or in cis-elements. The histochemical GUS assay revealed higher promoter activity of Bragg:γ-TMT3-P than that of DS74:γ-TMT3-P and correlated with significantly higher and lower (P < 0.05) expression of γ-TMT3 gene respectively. To know the molecular basis of differential accumulation of α-toc in these contrasting soybean genotypes, the DNA methylation pattern of γ-TMT3 gene body and its promoter was studied in both varieties. The results showed higher percentage (62.5%) of methylation in DS74:γ-TMT3-P than in Bragg:γ-TMT3-P (50%). Out of all the methylation sites in the promoter region, one of methylation site was found at CAAT box (-190 bp) of DS74:γ-TMT3-P. Further gene body methylation patterns revealed lowest % (40%) of CG methylation in DS74:γ-TMT3 gene as compared to Bragg:γ-TMT3 (64.2%). Thus our study revealed that, expression of γ-TMT3 gene was influenced by its promoter activity and methylation patterns in cis-elements of γ-TMT3 promoter and gene body. This study will help us to understand the possible role of methylation and promoter activity in determining the α-toc content in soybean seeds.
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Affiliation(s)
- Khushboo Kumari
- Division of Biochemistry, IARI, New Delhi, 110012, India; Amity University, Noida, Uttar Pradesh, 201313, India
| | | | - Navita Bansal
- Division of Biochemistry, IARI, New Delhi, 110012, India; Amity University, Noida, Uttar Pradesh, 201313, India
| | | | - Sweta Kumari
- Division of Biochemistry, IARI, New Delhi, 110012, India
| | - Veda Krishnan
- Division of Biochemistry, IARI, New Delhi, 110012, India
| | - Rohini Srivathsa
- National Research Centre for Plant Biotechnology, Pusa, New Delhi, 110012, India
| | - Anil Dahuja
- Division of Biochemistry, IARI, New Delhi, 110012, India
| | | | - Shelly Praveen
- Division of Biochemistry, IARI, New Delhi, 110012, India.
| | - T Vinutha
- Division of Biochemistry, IARI, New Delhi, 110012, India.
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Gong P, Wei R, Li Y, Wang R, Tang Y, Wang L, Zhu H, Wang Y, Zhang C. Molecular cloning and functional characterization of a seed-specific VvβVPE gene promoter from Vitis vinifera. PLANTA 2019; 250:657-665. [PMID: 31147828 DOI: 10.1007/s00425-019-03197-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 05/24/2019] [Indexed: 06/09/2023]
Abstract
The grapevine VvβVPE promoter is specifically expressed in the seed. The - 1306~- 1045 bp core region restricts expression in other tissues and organs. Vacuolar processing enzyme (VPE) is a cysteine proteinase regulating vacuolar protein maturation and executing programmed cell death (PCD) in plants. Vitis vinifera (Vv)βVPE is a β-type VPE showing seed-specific expression that processes seed proteins during ovule development. However, the regulation of the seed-specific gene expression is far from understood. In this study, we characterize VvβVPE promoter (pVvβVPE) from 12 seeded and seedless grape genotypes. 94.56% of the pVvβVPE coding sequence is consistent. Two βVPE promoters were constructed and transformed into Arabidopsis thaliana via β-glucuronidase (GUS) fused expression vectors, using cv. Pinot Noir and cv. Thompson as seed and seedless candidates. GUS staining in different tissues and organs revealed that VvβVPE expresses specifically in the embryo, including the cotyledon, hypocotyl and suspensor, but not in the leaf, stem, root or flowers of the seedling. Using promoter deletion analysis, we created four incomplete VvβVPE promoters and found each pVvβVPE deletion could drive GUS gene to express in seeds. Interestingly, seed specificity disappeared when the promoter missed the core - 1306~- 1045 bp region. All deletion promoters presenting various quantified GUS activities indicate that the region - 1704~- 1306 bp inhibits, and the region - 705~- 861 bp promotes gene expression of VvβVPE. Our results demonstrate that pVvβVPE is a seed-specific promoter in both seeded and seedless grapes. Moreover, the core region of pVvβVPE (- 1306~- 1045 bp) is the key one responsible for seed-specific expression.
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Affiliation(s)
- Peijie Gong
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northwest Region), Ministry of Agriculture, Yangling, Shaanxi, 712100, China
| | - Rong Wei
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northwest Region), Ministry of Agriculture, Yangling, Shaanxi, 712100, China
| | - Yan Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Ruipu Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yujin Tang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northwest Region), Ministry of Agriculture, Yangling, Shaanxi, 712100, China
| | - Ling Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northwest Region), Ministry of Agriculture, Yangling, Shaanxi, 712100, China
| | - Huijun Zhu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yuejin Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northwest Region), Ministry of Agriculture, Yangling, Shaanxi, 712100, China
| | - Chaohong Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China.
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northwest Region), Ministry of Agriculture, Yangling, Shaanxi, 712100, China.
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Wang P, Wang Y, Ren F. Genome-wide identification of the CLAVATA3/EMBRYO SURROUNDING REGION (CLE) family in grape (Vitis vinifera L.). BMC Genomics 2019; 20:553. [PMID: 31277568 PMCID: PMC6612224 DOI: 10.1186/s12864-019-5944-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 06/30/2019] [Indexed: 12/14/2022] Open
Abstract
Background CLE genes play various biological roles in plant growth and development, as well as in responses to environmental stimuli. Results In the present study, we identified nine CLE genes in the grape genome using an effective identification method. We analyzed the expression profiles of grape CLE genes in different tissues and under environmental different stimuli. VvCLE3 was expressed in shoot apical meristem (SAM) enriched regions, and VvCLE6 was expressed in shoot tissue without SAM. When grapes were infected with bois noir, VvCLE2 was up-regulated. Under ABA treatment, VvCLE3 was down-regulated. VvCLE6 was up-regulated under high temperature stress. We found that VvCLE6 and VvCLE1 were highly expressed in root tissue. In addition, we compared the characteristics of CLEs from grape and other plant species. The CLE family in Sphagnum fallax underwent positive selection, while the CLE family in grape underwent purifying selection. The frequency of optimal codons and codon adaptation index of rice and grape CLE family members were positively correlated with GC content at the third site of synonymous codons, indicating that the dominant evolutionary pressure acting on rice and grape CLE genes was mutation pressure. We also found that closely related species had higher levels of similarity in relative synonymous codon usage in CLE genes. The rice CLE family was biased toward C and G nucleotides at third codon positions. Gene duplication and loss events were also found in grape CLE genes. Conclusion These results demonstrate an effective identification method for CLE motifs and increase the understanding of grape CLEs. Future research on CLE genes may have applications for grape breeding and cultivation to better understand root and nodulation development. Electronic supplementary material The online version of this article (10.1186/s12864-019-5944-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pengfei Wang
- Shandong Academy of Grape; Shandong Engineering Research Center for Grape Cultivation and Deep-Processing, Jinan, 250100, People's Republic of China.
| | - Yongmei Wang
- Shandong Academy of Grape; Shandong Engineering Research Center for Grape Cultivation and Deep-Processing, Jinan, 250100, People's Republic of China.
| | - Fengshan Ren
- Shandong Academy of Grape; Shandong Engineering Research Center for Grape Cultivation and Deep-Processing, Jinan, 250100, People's Republic of China.
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Koul A, Sharma D, Kaul S, Dhar MK. Identification and in silico characterization of cis-acting elements of genes involved in carotenoid biosynthesis in tomato. 3 Biotech 2019; 9:287. [PMID: 31297303 DOI: 10.1007/s13205-019-1798-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 06/06/2019] [Indexed: 02/06/2023] Open
Abstract
Carotenoids, the widespread and structurally diverse class of pigments, accumulate in the fruits of tomato plants in a tissue specific manner. The carotenoid biosynthetic pathway genes have been cloned and characterized in tomato and other plants, however, its regulation is still obscure. We collected and analyzed forty different accessions of tomato for the present study. HPLC analysis revealed differential accumulation of major carotenoids (lycopene and ß-carotene) in the ripe fruit tissue. In order to understand the underlying regulatory mechanisms in carotenoid biosynthesis and accumulation, we sequenced the cis-acting elements i.e. promoter, 5' and 3' untranslated regions of the carotenoid pathway genes, in all accessions, followed by their in silico validation. Major differences observed in the CAAT Box, Opaque-2 Box and L-box in the promoters of carotenoid isomerase and lycopene-beta cyclase genes, respectively, along with the variations in musashi binding element of 5' untranslated regions of the carotenoid isomerase gene, suggest their differential role in regulating the carotenogenesis process in tomato. The binding sites for various transcription factors namely RIN, AGAMOUS, CRY, RAP2.2 and PIF1 on the promoters of important carotenoid pathway genes were predicted in silico. We propose that expression of carotenoid genes and also the formation of protein product in ripe tomato fruits, is regulated efficiently by the binding of these transcription factors at selected sites in the promoter region. Finally, the differential expression of the above-mentioned genes in different developmental tissues supports the possible involvement of promoters and untranslated regions in carotenoid biosynthesis and accumulation process. The present study has generated significant information concerning regulatory players involved in the carotenoid biosynthesis in tomato.
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31
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Takahashi K, Kohno H, Kanabayashi T, Okuda M. Glutelin subtype-dependent protein localization in rice grain evidenced by immunodetection analyses. PLANT MOLECULAR BIOLOGY 2019; 100:231-246. [PMID: 30911876 PMCID: PMC6542783 DOI: 10.1007/s11103-019-00855-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 03/14/2019] [Indexed: 05/29/2023]
Abstract
GluA and GluB-4/5 glutelin subfamilies are mainly localized to outer region of the endosperm, particularly in its ventral side, in rice grain, but GluC is localized to throughout the endosperm. The major seed storage protein in rice (Oryza sativa) is glutelin, which forms a vacuole-derived protein body type-II. Glutelins are encoded by multiple genes, and generally comprise four protein subfamilies, namely, GluA, GluB, GluC, and GluD: however, the localization pattern of glutelin in rice grains remains obscure. In this study, we investigated the localization pattern of five subtypes of the glutelin protein in rice grains using glutelin-subtype specific antibodies. Immunoblot analysis against sequentially polished rice flour fractions from three crop years and seven japonica rice varieties revealed that GluA was strongly localized in the outer region of the endosperm, including the subaleurone layer, whereas GluC was distributed throughout the endosperm. Among the glutelin subtypes, GluA was mostly found in the outer region of the rice grain, followed by GluB-4/5, GluB-1, GluD, and GluC. Immunofluorescence labeling microscopy analysis using immature rice seeds clearly revealed that the localization pattern of GluC and GluD was completely different from that of GluA and GluB. Expression levels of all glutelins, particularly GluA, GluB-1, and GluB-4/5, were stronger on the ventral than dorsal side in rice grains. These results provide strong and consistent evidence that glutelins localize to the rice grain in a subfamily-dependent manner.
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Affiliation(s)
- Kei Takahashi
- National Research Institute of Brewing, 3-7-1 Kagamiyama, Higashi-hiroshima, Hiroshima, 739-0046, Japan.
| | - Hiromi Kohno
- National Research Institute of Brewing, 3-7-1 Kagamiyama, Higashi-hiroshima, Hiroshima, 739-0046, Japan
| | - Tomomichi Kanabayashi
- Biopathology Institute Co., Ltd, 1200-2, Ohara Kunisakicho, Kunisaki-city, Oita, 873-0511, Japan
| | - Masaki Okuda
- National Research Institute of Brewing, 3-7-1 Kagamiyama, Higashi-hiroshima, Hiroshima, 739-0046, Japan
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Li J, Wang K, Li G, Li Y, Zhang Y, Liu Z, Ye X, Xia X, He Z, Cao S. Dissecting conserved cis-regulatory modules of Glu-1 promoters which confer the highly active endosperm-specific expression via stable wheat transformation. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.cj.2018.08.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Liu C, Zhang TZ. Functional diversifications of GhERF1 duplicate genes after the formation of allotetraploid cotton. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:60-74. [PMID: 30578593 DOI: 10.1111/jipb.12764] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 12/17/2018] [Indexed: 06/09/2023]
Abstract
Whole genome duplication, a prevalent force of evolution in plants, results in massive genome restructuring in different organisms. Roles of the resultant duplicated genes are poorly understood, both functionally and evolutionarily. In the present study, differentially expressed ethylene responsive factors (GhERF1s), anchored on Chr-A07 and Chr-D07, were isolated from a high-yielding cotton hybrid (XZM2) and its parents. The GhERF1 was located in the B3 subgroup of the ethylene responsive factors subfamily involved in conferring tolerance to abiotic stress. Nucleotide sequence analysis of 524 diverse accessions, together with quantitative real-time polymerase chain reaction analysis, elucidated that de-functionalization of GhERF1-7A occurred due to one base insertion following formation of the allotetraploid cotton. Our quantitative trait loci and association mapping analyses highlighted a role for GhERF1-7A in conferring high boll number per plant in modern cotton cultivars. Overexpression of GhERF1-7A in transgenic Arabidopsis resulted in a substantial increase in the number of siliques and total seed yield. Neo-functionalization of GhERF1-7A was also observed in modern cultivars rather than in races and/or landraces, further supporting its role in the development of high-yielding cotton cultivars. Both de- and neo-functionalization occurred in one of the duplicate genes, thus providing new genomic insight into the evolution of allotetraploid cotton species.
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Affiliation(s)
- Chunxiao Liu
- National Key Laboratory of Crop Genetics & Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, Nanjing 210095, China
| | - Tian Zhen Zhang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, Nanjing 210095, China
- Crop Science Institute, Agronomy Department, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310029, China
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Liu X, Li S, Yang W, Mu B, Jiao Y, Zhou X, Zhang C, Fan Y, Chen R. Synthesis of Seed-Specific Bidirectional Promoters for Metabolic Engineering of Anthocyanin-Rich Maize. PLANT & CELL PHYSIOLOGY 2018; 59:1942-1955. [PMID: 29917151 DOI: 10.1093/pcp/pcy110] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 06/05/2018] [Indexed: 05/03/2023]
Abstract
Tissue-specific promoters play an important role in plant molecular farming. Here, we describe a strategy to modify the tissue specificity of a maize embryo-specific bidirectional promoter PZmBD1. Six types of cis-elements, i.e. RY repeats (R), GCN4 (G), the prolamin box (P), Skn-1 (S), and the ACGT and AACA (A) motifs, were collected and fused to PZmBD1 to generate eight chimeric putative bidirectional promoters. Qualitative and quantitative analysis of reporter genes driven by the promoters showed that two promoters exhibited high seed-specific bidirectional activity in maize transient and stable transformed systems. The stronger one was chosen and fused to the intergenic region of two gene clusters consisting of four anthocyanin biosynthesis-related genes (ZmBz1, ZmBz2, ZmC1 and ZmR2) and seven reporter genes, resulting in the first embryo and endosperm anthocyanin-rich purple maize. Anthocyanin analysis showed that the total anthocyanin content reaches 2,910 mg kg-1 DW in transgenic maize and cyanidin is the major anthocyanin in transgenic maize, as in natural varieties. The expression profile analysis of endogenous genes showed that the anthocyanin biosynthesis pathway was activated by two transgenic transcription factor genes ZmC1 and ZmR2. Our results indicate that both the modification strategy and these functionally characterized tissue-specific bidirectional promoters generated could be used for genetic research and development of plant biotechnology products. The anthocyanin-rich purple maize could provide economic natural colorants for the food and beverage industry, and valuable germplasm for developing anthocyanin-rich fresh corn.
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Affiliation(s)
- Xiaoqing Liu
- Department of Crop Genomics & Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 ZhongGuanCun South Street, Beijing, China
| | - Suzhen Li
- Department of Crop Genomics & Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 ZhongGuanCun South Street, Beijing, China
| | - Wenzhu Yang
- Department of Crop Genomics & Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 ZhongGuanCun South Street, Beijing, China
| | - Bona Mu
- Department of Crop Genomics & Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 ZhongGuanCun South Street, Beijing, China
| | - Yong Jiao
- Department of Crop Genomics & Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 ZhongGuanCun South Street, Beijing, China
- Key Laboratory of Crop Biology of Anhui Province, Anhui Agricultural University, Hefei, China
| | - Xiaojin Zhou
- Department of Crop Genomics & Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 ZhongGuanCun South Street, Beijing, China
| | - Chunyi Zhang
- Department of Crop Genomics & Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 ZhongGuanCun South Street, Beijing, China
| | - Yunliu Fan
- Department of Crop Genomics & Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 ZhongGuanCun South Street, Beijing, China
| | - Rumei Chen
- Department of Crop Genomics & Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 ZhongGuanCun South Street, Beijing, China
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Li H, Li J, Xu R, Qin R, Song F, Li L, Wei P, Yang J. Isolation of five rice nonendosperm tissue-expressed promoters and evaluation of their activities in transgenic rice. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:1138-1147. [PMID: 29105251 PMCID: PMC5978396 DOI: 10.1111/pbi.12858] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 10/17/2017] [Accepted: 10/28/2017] [Indexed: 06/07/2023]
Abstract
Using promoters expressed in nonendosperm tissues to activate target genes in specific plant tissues or organs with very limited expression in the endosperm is an attractive approach in crop transgenic engineering. In this article, five putative nonendosperm tissue-expressed promoters were cloned from the rice genome and designated POsNETE1 , POsNETE2 , POsNETE3 , POsNETE4 and POsNETE5 . By qualitatively and quantitatively examining GUSplus reporter gene expression in transgenic rice plants, POsNETE1 -POsNETE5 were all found to be active in the roots, leaves, stems, sheaths and panicles but not in the endosperm of plants at different developmental stages. In addition, POsNETE2 , POsNETE4 and POsNETE5 were also inactive in rice embryos. Among these promoters, POsNETE4 and POsNETE5 exhibited higher activities in all of the tested tissues, and their activities in stems, leaves, roots and sheaths were higher than or comparable to those of the rice Actin1 promoter. We also progressively monitored the activities of POsNETE1 -POsNETE5 in two generations of single-copy lines and found that these promoters were stably expressed between generations. Transgenic rice was produced using POsNETE4 and POsNETE5 to drive a modified Bt gene, mCry1Ab. Bt protein expressed in the tested plants ranged from 1769.4 to 4428.8 ng/g fresh leaves, whereas Bt protein was barely detected in the endosperm. Overall, our study identified five novel nonendosperm tissue-expressed promoters that might be suitable for rice genetic engineering and might reduce potential social concern regarding the safety of GMO crops.
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Affiliation(s)
- Hao Li
- Key Laboratory of Rice Genetic Breeding of Anhui ProvinceRice Research InstituteAnhui Academy of Agricultural SciencesHefeiChina
| | - Juan Li
- Key Laboratory of Rice Genetic Breeding of Anhui ProvinceRice Research InstituteAnhui Academy of Agricultural SciencesHefeiChina
| | - Rongfang Xu
- Key Laboratory of Rice Genetic Breeding of Anhui ProvinceRice Research InstituteAnhui Academy of Agricultural SciencesHefeiChina
| | - Ruiying Qin
- Key Laboratory of Rice Genetic Breeding of Anhui ProvinceRice Research InstituteAnhui Academy of Agricultural SciencesHefeiChina
| | - Fengshun Song
- Key Laboratory of Rice Genetic Breeding of Anhui ProvinceRice Research InstituteAnhui Academy of Agricultural SciencesHefeiChina
| | - Li Li
- Key Laboratory of Rice Genetic Breeding of Anhui ProvinceRice Research InstituteAnhui Academy of Agricultural SciencesHefeiChina
| | - Pengcheng Wei
- Key Laboratory of Rice Genetic Breeding of Anhui ProvinceRice Research InstituteAnhui Academy of Agricultural SciencesHefeiChina
| | - Jianbo Yang
- Key Laboratory of Rice Genetic Breeding of Anhui ProvinceRice Research InstituteAnhui Academy of Agricultural SciencesHefeiChina
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Minhas AP, Tuli R, Puri S. Pathway Editing Targets for Thiamine Biofortification in Rice Grains. FRONTIERS IN PLANT SCIENCE 2018; 9:975. [PMID: 30042775 PMCID: PMC6048418 DOI: 10.3389/fpls.2018.00975] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Accepted: 06/15/2018] [Indexed: 05/21/2023]
Abstract
Thiamine deficiency is common in populations consuming polished rice as a major source of carbohydrates. Thiamine is required to synthesize thiamine pyrophosphate (TPP), an essential cofactor of enzymes of central metabolism. Its biosynthesis pathway has been partially elucidated and the effect of overexpression of a few genes such as thi1 and thiC, on thiamine accumulation in rice has been reported. Based on current knowledge, this review focuses on the potential of gene editing in metabolic engineering of thiamine biosynthesis pathway to improve thiamine in rice grains. Candidate genes, suitable for modification of the structural part to evolve more efficient versions of enzymes in the pathway, are discussed. For example, adjacent cysteine residues may be introduced in the catalytic domain of thi4 to improve the turn over activity of thiamine thiazole synthase 2. Motif specific editing to modify promoter regulatory regions of genes is discussed to modulate gene expression. Editing cis acting regulatory elements in promoter region can shift the expression of transporters and thiamine binding proteins to endosperm. This can enhance dietary availability of thiamine from rice grains. Differential transcriptomics on rice varieties with contrasting grain thiamine and functional genomic studies will identify more strategic targets for editing in future. Developing functionally enhanced foods by biofortification is a sustainable approach to make diets wholesome.
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Holme IB, Wendt T, Gil-Humanes J, Deleuran LC, Starker CG, Voytas DF, Brinch-Pedersen H. Evaluation of the mature grain phytase candidate HvPAPhy_a gene in barley (Hordeum vulgare L.) using CRISPR/Cas9 and TALENs. PLANT MOLECULAR BIOLOGY 2017; 95:111-121. [PMID: 28755320 DOI: 10.1007/s11103-017-0640-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Accepted: 07/20/2017] [Indexed: 05/05/2023]
Abstract
In the present study, we utilized TALEN- and CRISPR/Cas9-induced mutations to analyze the promoter of the barley phytase gene HvPAPhy_a. The purpose of the study was dual, validation of the PAPhy_a enzyme as the main contributor of the mature grain phytase activity (MGPA), as well as validating the importance of a specific promoter region of the PAPhy_a gene which contains three overlapping cis-acting regulatory elements (GCN4, Skn1 and the RY-element) known to be involved in gene expression during grain filling. The results confirm that the barley PAPhy_a enzyme is the main contributor to the MGPA as grains of knock-out lines show very low MGPA. Additionally, the analysis of the HvPAPhy_a promoter region containing the GCN4/Skn1/RY motif highlights its importance for HvPAPhy_a expression as the MGPA in grains of plant lines with mutations within this motif is significantly reduced. Interestingly, lines with deletions located downstream of the motif show even lower MGPA levels, indicating that the GCN4/SKn1/RY motif is not the only element responsible for the level of PAPhy_a expression during grain maturation. Mutant grains with very low MPGA showed delayed germination as compared to grains of wild type barley. As grains with high levels of preformed phytases would provide more readily available phosphorous needed for a fast germination, this indicates that faster germination may be implicated in the positive selection of the ancient PAPhy gene duplication that lead to the creation of the PAPhy_a gene.
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Affiliation(s)
- Inger B Holme
- Department of Molecular Biology and Genetics, Research Centre Flakkebjerg, Aarhus University, Slagelse, Denmark.
| | - Toni Wendt
- Department of Molecular Biology and Genetics, Research Centre Flakkebjerg, Aarhus University, Slagelse, Denmark
| | - Javier Gil-Humanes
- Department of Genetics, Cell Biology and Development and Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
- Calyxt Inc., New Brighton, MN, USA
| | - Lise C Deleuran
- Department of Agroecology, Research Centre Flakkebjerg, Aarhus University, Slagelse, Denmark
| | - Colby G Starker
- Department of Genetics, Cell Biology and Development and Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Daniel F Voytas
- Department of Genetics, Cell Biology and Development and Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Henrik Brinch-Pedersen
- Department of Molecular Biology and Genetics, Research Centre Flakkebjerg, Aarhus University, Slagelse, Denmark
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Chen Z, Kong L, Zhou Y, Chen Z, Tian D, Lin Y, Wang F, Chen S. Endosperm-specific OsPYL8 and OsPYL9 act as positive regulators of the ABA signaling pathway in rice seed germination. FUNCTIONAL PLANT BIOLOGY : FPB 2017; 44:635-645. [PMID: 32480594 DOI: 10.1071/fp16314] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 03/09/2017] [Indexed: 05/25/2023]
Abstract
Pyrabactin resistance-like (PYL) proteins were identified as receptors of the plant hormone ABA. The PYL family consists of multiple members that are differently expressed in various tissues, exhibit distinct biochemical properties and have diverse biological functions. In the present study, we explored the expression patterns of the rice (Oryza sativa L.) OsPYL family genes and determined that OsPYL8 and OsPYL9 are specifically expressed in the endosperms. Sequence analysis and deletion experiments revealed that the OsPYL8 and OsPYL9 promoters contain multiple motifs involved in endosperm-specific expression. Transgenic rice plants overexpressing OsPYL8 or OsPYL9 showed hypersensitivity to ABA during seed germination, suggesting that both OsPYL8 and OsPYL9 act as positive regulators of the ABA signalling pathway in the seed. OsPYL8 and OsPYL9 interact with OsPP2C51 and OsPP2C68, whose expression is induced in the endosperms by ABA. Our results provided a foundation for future studies on OsPYL8- and OsPYL9-mediated ABA signalling in the rice endosperms.
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Affiliation(s)
- Ziqiang Chen
- Biotechnology Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350003, China
| | - Lan Kong
- Biotechnology Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350003, China
| | - Yun Zhou
- Biotechnology Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350003, China
| | - Zaijie Chen
- Biotechnology Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350003, China
| | - Dagang Tian
- Biotechnology Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350003, China
| | - Yan Lin
- Biotechnology Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350003, China
| | - Feng Wang
- Biotechnology Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350003, China
| | - Songbiao Chen
- Biotechnology Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350003, China
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Exploring the Functions of 9-Lipoxygenase (DkLOX3) in Ultrastructural Changes and Hormonal Stress Response during Persimmon Fruit Storage. Int J Mol Sci 2017; 18:ijms18030589. [PMID: 28294971 PMCID: PMC5372605 DOI: 10.3390/ijms18030589] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Revised: 02/21/2017] [Accepted: 02/27/2017] [Indexed: 12/28/2022] Open
Abstract
Lipoxygenase (LOX) initiates the hydroperoxidation of polyunsaturated fatty acids and is involved in multiple physiological processes. In this study, investigation of various microscopic techniques showed that the fruit peel cellular microstructure of the two persimmon cultivars differed after 12 days of storage, resulting in fruit weight loss and an increased number and depth of microcracks. Analysis of subcellular localization revealed that greater amounts of DkLOX3-immunolabelled gold particles accumulated in “Fupingjianshi” than in “Ganmaokui” during storage. In addition, the expression of DkLOX3 was positively up-regulated by abscisic acid (ABA), concomitant with the promotion of ethylene synthesis and loss of firmness, and was suppressed by salicylic acid (SA), concomitant with the maintenance of fruit firmness, inhibition of ethylene production and weight loss. In particular, the expression of DkLOX3 differed from the ethylene trajectory after methyl jasmonate (MeJA) treatment. Furthermore, we isolated a 1105 bp 5′ flanking region of DkLOX3 and the activity of promoter deletion derivatives was induced through various hormonal treatments. Promoter sequence cis-regulatory elements were analysed, and two conserved hormone-responsive elements were found to be essential for responsiveness to hormonal stress. Overall, these results will provide us with new clues for exploring the functions of DkLOX3 in fruit ripening and hormonal stress response.
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40
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Montesinos L, Bundó M, Badosa E, San Segundo B, Coca M, Montesinos E. Production of BP178, a derivative of the synthetic antibacterial peptide BP100, in the rice seed endosperm. BMC PLANT BIOLOGY 2017; 17:63. [PMID: 28292258 PMCID: PMC5351061 DOI: 10.1186/s12870-017-1011-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 03/06/2017] [Indexed: 05/20/2023]
Abstract
BACKGROUND BP178 peptide is a synthetic BP100-magainin derivative possessing strong inhibitory activity against plant pathogenic bacteria, offering a great potential for future applications in plant protection and other fields. Here we report the production and recovery of a bioactive BP178 peptide using rice seeds as biofactories. RESULTS A synthetic gene encoding the BP178 peptide was prepared and introduced in rice plants. The gene was efficiently expressed in transgenic rice under the control of an endosperm-specific promoter. Among the three endosperm-specific rice promoters (Glutelin B1, Glutelin B4 or Globulin 1), best results were obtained when using the Globulin 1 promoter. The BP178 peptide accumulated in the seed endosperm and was easily recovered from rice seeds using a simple procedure with a yield of 21 μg/g. The transgene was stably inherited for at least three generations, and peptide accumulation remained stable during long term storage of transgenic seeds. The purified peptide showed in vitro activity against the bacterial plant pathogen Dickeya sp., the causal agent of the dark brown sheath rot of rice. Seedlings of transgenic events showed enhanced resistance to the fungal pathogen Fusarium verticillioides, supporting that the in planta produced peptide was biologically active. CONCLUSIONS The strategy developed in this work for the sustainable production of BP178 peptide using rice seeds as biofactories represents a promising system for future production of peptides for plant protection and possibly in other fields.
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Affiliation(s)
- Laura Montesinos
- Institute of Food and Agricultural Technology-CIDSAV-XaRTA, University of Girona, Girona, 17071 Spain
| | - Mireia Bundó
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB. Edifici CRAG, Campus de la UAB, 08193 Bellaterra, Barcelona Spain
| | - Esther Badosa
- Institute of Food and Agricultural Technology-CIDSAV-XaRTA, University of Girona, Girona, 17071 Spain
| | - Blanca San Segundo
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB. Edifici CRAG, Campus de la UAB, 08193 Bellaterra, Barcelona Spain
| | - María Coca
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB. Edifici CRAG, Campus de la UAB, 08193 Bellaterra, Barcelona Spain
| | - Emilio Montesinos
- Institute of Food and Agricultural Technology-CIDSAV-XaRTA, University of Girona, Girona, 17071 Spain
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41
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Passricha N, Saifi S, Ansari MW, Tuteja N. Prediction and validation of cis-regulatory elements in 5' upstream regulatory regions of lectin receptor-like kinase gene family in rice. PROTOPLASMA 2017; 254:669-684. [PMID: 27193099 DOI: 10.1007/s00709-016-0979-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 04/29/2016] [Indexed: 05/10/2023]
Abstract
Lectin receptor-like kinases (LecRLKs) play crucial roles in regulating plant growth and developmental processes in response to stress. In transcriptional gene regulation for normal cellular functions, cis-acting regulatory elements (CREs) direct the temporal and spatial gene expression with respect to environmental stimuli. A complete insightful of the transcriptional gene regulation system relies on effective functional analysis of CREs. Here, we analyzed the potential putative CREs present in the promoters of rice LecRLKs genes by using PlantCARE database. The CREs in LecRLKs promoters are associated with plant growth/development, light response, plant hormonal regulation processes, various stress responses, hormonal response like ABA, root-specific expression responsive, drought responsive, and cell and organ specific regulatory elements. The effect of methylation on these cis-regulatory elements was also analyzed. Real-time analysis of rice seedling under various stress conditions showed the expression levels of selected LecRLK genes superimposing the number of different CREs present in 5' upstream region. The overall results showed that the possible CREs function in the selective expression/regulation of LecRLKs gene family and during rice plant development under stress.
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MESH Headings
- Base Sequence
- Computer Simulation
- CpG Islands/genetics
- Databases, Genetic
- Gene Expression Profiling
- Gene Expression Regulation, Plant/radiation effects
- Genes, Plant
- Light
- Models, Biological
- Multigene Family
- Oligonucleotide Array Sequence Analysis
- Oryza/drug effects
- Oryza/enzymology
- Oryza/genetics
- Oryza/radiation effects
- Plant Development/drug effects
- Plant Development/genetics
- Plant Development/radiation effects
- Plant Growth Regulators/pharmacology
- Plant Proteins/genetics
- Plant Proteins/metabolism
- Promoter Regions, Genetic
- Protein Kinases/genetics
- Protein Kinases/metabolism
- Receptors, Mitogen/genetics
- Receptors, Mitogen/metabolism
- Regulatory Sequences, Nucleic Acid/genetics
- Reproducibility of Results
- Stress, Physiological/drug effects
- Stress, Physiological/genetics
- Stress, Physiological/radiation effects
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Affiliation(s)
- Nishat Passricha
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, ArunaAsaf Ali Marg, New Delhi, 110067, India
| | - Shabnam Saifi
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, ArunaAsaf Ali Marg, New Delhi, 110067, India
| | - Mohammad W Ansari
- Zakir Husain Delhi College, University of Delhi, Jawahar Lal Nehru Marg, New Delhi, 110002, India
| | - Narendra Tuteja
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, ArunaAsaf Ali Marg, New Delhi, 110067, India.
- Amity Institute of Microbial Technology, Amity University, Noida, 201313, India.
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42
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Kaur G, Pati PK. Analysis of cis-acting regulatory elements of Respiratory burst oxidase homolog (Rboh) gene families in Arabidopsis and rice provides clues for their diverse functions. Comput Biol Chem 2016; 62:104-18. [PMID: 27111707 DOI: 10.1016/j.compbiolchem.2016.04.002] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 03/30/2016] [Accepted: 04/02/2016] [Indexed: 12/17/2022]
Abstract
NADPH oxidase (NOX) is a critical enzyme in the production of reactive oxygen species (ROS). It catalyzes the production of apoplastic superoxide (O2(-)), that regulates a wide array of biological functions in different organisms. Plant Noxes are homologs of catalytic subunit of mammalian NADPH oxidase and are well-known as Respiratory burst oxidase homologs (Rbohs). In recent years, there has been growing interest to study plant Noxes due to their versatile roles in plant systems. In the present work, comprehensive analysis on upstream regions from 10 Rbohs from Arabidopsis thaliana and 9 from Oryza sativa japonica was conducted. The distribution of various cis-elements, CpG islands and tandem repeats were analyzed to uncover the 5' regulatory region in wide array of functions from Rbohs. Information retrieved from cis-elements analysis was also correlated with the microarray data. Present study which involves uncovering transcription regulatory elements provided vital clues for diverse functions of plant Rbohs.
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Affiliation(s)
- Gurpreet Kaur
- Department of Biotechnology, Guru Nanak Dev University (GNDU), Amritsar, 143005, Punjab, India.
| | - Pratap Kumar Pati
- Department of Biotechnology, Guru Nanak Dev University (GNDU), Amritsar, 143005, Punjab, India.
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Liu W, Stewart CN. Plant synthetic promoters and transcription factors. Curr Opin Biotechnol 2016; 37:36-44. [DOI: 10.1016/j.copbio.2015.10.001] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 10/06/2015] [Indexed: 10/22/2022]
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Geng Y, Pang B, Hao C, Tang S, Zhang X, Li T. Expression of wheat high molecular weight glutenin subunit 1Bx is affected by large insertions and deletions located in the upstream flanking sequences. PLoS One 2014; 9:e105363. [PMID: 25133580 PMCID: PMC4136844 DOI: 10.1371/journal.pone.0105363] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2014] [Accepted: 07/20/2014] [Indexed: 11/18/2022] Open
Abstract
To better understand the transcriptional regulation of high molecular weight glutenin subunit (HMW-GS) expression, we isolated four Glu-1Bx promoters from six wheat cultivars exhibiting diverse protein expression levels. The activities of the diverse Glu-1Bx promoters were tested and compared with β-glucuronidase (GUS) reporter fusions. Although all the full-length Glu-1Bx promoters showed endosperm-specific activities, the strongest GUS activity was observed with the 1Bx7OE promoter in both transient expression assays and stable transgenic rice lines. A 43 bp insertion in the 1Bx7OE promoter, which is absent in the 1Bx7 promoter, led to enhanced expression. Analysis of promoter deletion constructs confirmed that a 185 bp MITE (miniature inverted-repeat transposable element) in the 1Bx14 promoter had a weak positive effect on Glu-1Bx expression, and a 54 bp deletion in the 1Bx13 promoter reduced endosperm-specific activity. To investigate the effect of the 43 bp insertion in the 1Bx7OE promoter, a functional marker was developed to screen 505 Chinese varieties and 160 European varieties, and only 1Bx7-type varieties harboring the 43 bp insertion in their promoters showed similar overexpression patterns. Hence, the 1Bx7OE promoter should be important tool in crop genetic engineering as well as in molecular assisted breeding.
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Affiliation(s)
- Yuke Geng
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Biological sciences, China Agricultural University, Beijing, China
| | - Binshuang Pang
- Beijing Engineering and Technique Research Center of Hybrid Wheat, Beijing Academy of Agricultural and Forestry Sciences, Beijing, China
| | - Chenyang Hao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Saijun Tang
- College of Biological sciences, China Agricultural University, Beijing, China
| | - Xueyong Zhang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- * E-mail: (XZ); (TL)
| | - Tian Li
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- * E-mail: (XZ); (TL)
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Tao YB, Luo L, He LL, Ni J, Xu ZF. A promoter analysis of MOTHER OF FT AND TFL1 1 (JcMFT1), a seed-preferential gene from the biofuel plant Jatropha curcas. JOURNAL OF PLANT RESEARCH 2014; 127:513-24. [PMID: 24879400 DOI: 10.1007/s10265-014-0639-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 03/07/2014] [Indexed: 05/06/2023]
Abstract
MOTHER OF FT AND TFL1 (MFT)-like genes belong to the phosphatidylethanoamine-binding protein (PEBP) gene family in plants. In contrast to their homologs FLOWERING LOCUS T (FT)-like and TERMINAL FLOWER 1 (TFL1)-like genes, which are involved in the regulation of the flowering time pathway, MFT-like genes function mainly during seed development and germination. In this study, a full-length cDNA of the MFT-like gene JcMFT1 from the biodiesel plant Jatropha curcas (L.) was isolated and found to be highly expressed in seeds. The promoter of JcMFT1 was cloned and characterized in transgenic Arabidopsis. A histochemical β-glucuronidase (GUS) assay indicated that the JcMFT1 promoter was predominantly expressed in both embryos and endosperms of transgenic Arabidopsis seeds. Fluorometric GUS analysis revealed that the JcMFT1 promoter was highly active at the mid to late stages of seed development. After seed germination, the JcMFT1 promoter activity decreased gradually. In addition, both the JcMFT1 expression in germinating Jatropha embryos and its promoter activity in germinating Arabidopsis embryos were induced by abscisic acid (ABA), possibly due to two ABA-responsive elements, a G-box and an RY repeat, in the JcMFT1 promoter region. These results show that the JcMFT1 promoter is seed-preferential and can be used to control transgene expression in the seeds of Jatropha and other transgenic plants.
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Affiliation(s)
- Yan-Bin Tao
- Key Laboratory of Tropical Plant Resource and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, 666303, China,
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Chen Y, Sun A, Wang M, Zhu Z, Ouwerkerk PBF. Functions of the CCCH type zinc finger protein OsGZF1 in regulation of the seed storage protein GluB-1 from rice. PLANT MOLECULAR BIOLOGY 2014; 84:621-34. [PMID: 24282069 DOI: 10.1007/s11103-013-0158-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Accepted: 11/20/2013] [Indexed: 05/19/2023]
Abstract
Glutelins are the most abundant storage proteins in rice grain and can make up to 80 % of total protein content. The promoter region of GluB-1, one of the glutelin genes in rice, has been intensively used as a model to understand regulation of seed-storage protein accumulation. In this study, we describe a zinc finger gene of the Cys3His1 (CCCH or C3H) class, named OsGZF1, which was identified in a yeast one-hybrid screening using the core promoter region of GluB-1 as bait and cDNA expression libraries prepared from developing rice panicles and grains as prey. The OsGZF1 protein binds specifically to the bait sequence in yeast and this interaction was confirmed in vitro. OsGZF1 is predominantly expressed in a confined domain surrounding the scutellum of the developing embryo and is localised in the nucleus. Transient expression experiments demonstrated that OsGZF1 can down-regulate a GluB-1-GUS (β-glucuronidase) reporter and OsGZF1 was also able to significantly reduce activation conferred by RISBZ1 which is a known strong GluB-1 activator. Furthermore, down-regulation of OsGZF1 by an RNAi approach increased grain nitrogen concentration. We propose that OsGZF1 has a function in regulating the GluB-1 promoter and controls accumulation of glutelins during grain development.
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Affiliation(s)
- Yi Chen
- Sylvius Laboratory, Institute of Biology (IBL), Leiden University, Sylviusweg 72, 2333 BE, PO Box 9505, 2300 RA, Leiden, The Netherlands
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Sunkara S, Bhatnagar-Mathur P, Sharma KK. Isolation and functional characterization of a novel seed-specific promoter region from peanut. Appl Biochem Biotechnol 2014; 172:325-39. [PMID: 24078220 DOI: 10.1007/s12010-013-0482-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2013] [Accepted: 08/26/2013] [Indexed: 10/26/2022]
Abstract
The importance of using tissue-specific promoters in the genetic transformation of plants has been emphasized increasingly. Here, we report the isolation of a novel seed-specific promoter region from peanut and its validation in Arabidopsis and tobacco seeds. The reported promoter region referred to as groundnut seed promoter (GSP) confers seed-specific expression in heterologous systems, which include putative promoter regions of the peanut (Arachis hypogaea L.) gene 8A4R19G1. This region was isolated, sequenced, and characterized using gel shift assays. Tobacco transgenics obtained using binary vectors carrying uidA reporter gene driven by GSP and/or cauliflower mosaic virus 35S promoters were confirmed through polymerase chain reaction (PCR), RT-PCR, and computational analysis of motifs which revealed the presence of TATA, CAAT boxes, and ATG signals. This seed-specific promoter region successfully targeted the reporter uidA gene to seed tissues in both Arabidopsis and tobacco model systems, where its expression was confirmed by histochemical analysis of the transgenic seeds. This promoter region is routinely being used in the genetic engineering studies in legumes aimed at targeting novel transgenes to the seeds, especially those involved in micronutrient enhancement, fungal resistance, and molecular pharming.
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Li J, Liang D, Li M, Ma F. Light and abiotic stresses regulate the expression of GDP-L-galactose phosphorylase and levels of ascorbic acid in two kiwifruit genotypes via light-responsive and stress-inducible cis-elements in their promoters. PLANTA 2013; 238:535-47. [PMID: 23775440 DOI: 10.1007/s00425-013-1915-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Accepted: 06/06/2013] [Indexed: 05/03/2023]
Abstract
Ascorbic acid (AsA) plays an essential role in plants by protecting cells against oxidative damage. GDP-L-galactose phosphorylase (GGP) is the first committed gene for AsA synthesis. Our research examined AsA levels, regulation of GGP gene expression, and how these are related to abiotic stresses in two species of Actinidia (kiwifruit). When leaves were subjected to continuous darkness or light, ABA or MeJA, heat, or a hypoxic environment, we found some correlation between the relative levels of GGP mRNA and AsA concentrations. In transformed tobacco plants, activity of the GGP promoter was induced by all of these treatments. However, the degree of inducibility in the two kiwifruit species differed among the GGP promoter deletions. We deduced that the G-box motif, a light-responsive element, may have an important function in regulating GGP transcripts under various light conditions in both A. deliciosa and A. eriantha. Other elements such as ABRE, the CGTCA motif, and HSE might also control the promoter activities of GGP in kiwifruit. Altogether, these data suggest that GGP expression in the two kiwifruit species is regulated by light or abiotic stress via the relative cis-elements in their promoters. Furthermore, GGP has a critical role in modulating AsA concentrations in kiwifruit species under abiotic stresses.
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Affiliation(s)
- Juan Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
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Wang K, Zhang X, Zhao Y, Chen F, Xia G. Structure, variation and expression analysis of glutenin gene promoters from Triticum aestivum cultivar Chinese Spring shows the distal region of promoter 1Bx7 is key regulatory sequence. Gene 2013; 527:484-90. [PMID: 23850729 DOI: 10.1016/j.gene.2013.06.068] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Revised: 06/19/2013] [Accepted: 06/20/2013] [Indexed: 10/26/2022]
Abstract
In this study, ten glutenin gene promoters were isolated from model wheat (Triticum aestivum L. cv. Chinese Spring) using a genomic PCR strategy with gene-specific primers. Six belonged to high-molecular-weight glutenin subunit (HMW-GS) gene promoters, and four to low-molecular-weight glutenin subunit (LMW-GS). Sequence lengths varied from 1361 to 2,554 bp. We show that the glutenin gene promoter motifs are conserved in diverse sequences in this study, with HMW-GS and LMW-GS gene promoters characterized by distinct conserved motif combinations. Our findings show that HMW-GS promoters contain more functional motifs in the distal region of the glutenin gene promoter (> -700 bp) compared with LMW-GS. The y-type HMW-GS gene promoters possess unique motifs including RY repeat and as-2 box compared to the x-type. We also identified important motifs in the distal region of HMW-GS gene promoters including the 5'-UTR Py-rich stretch motif and the as-2 box motif. We found that cis-acting elements in the distal region of promoter 1Bx7 enhanced the expression of HMW-GS gene 1Bx7. Taken together, these data support efforts in designing molecular breeding strategies aiming to improve wheat quality. Our results offer insight into the regulatory mechanisms of glutenin gene expression.
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Affiliation(s)
- Kai Wang
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, Jinan 250100, PR China
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Greenham T, Altosaar I. Molecular strategies to engineer transgenic rice seed compartments for large-scale production of plant-made pharmaceuticals. Methods Mol Biol 2013; 956:311-26. [PMID: 23135861 DOI: 10.1007/978-1-62703-194-3_22] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The use of plants as bioreactors for the large-scale production of recombinant proteins has emerged as an exciting area of research. The current shortages in protein therapeutics due to the capacity and economic bottlenecks faced with modern protein production platforms (microbial, yeast, mammalian) has driven considerable attention towards molecular pharming. Utilizing plants for the large-scale production of recombinant proteins is estimated to be 2-10% the cost of microbial platforms, and up to 1,000-fold more cost effective than mammalian platforms (Twyman et al. Trends Biotechnol 21:570-578, 2003; Sharma and Sharma, Biotechnol Adv 27:811-832, 2009). In order to achieve an economically feasible plant production host, protein expression and accumulation must be optimized. The seed, and more specifically the rice seed has emerged as an ideal candidate in molecular pharming due to its low protease activity, low water content, stable protein storage environment, relatively high biomass, and the molecular tools available for manipulation (Lau and Sun, Biotechnol Adv 27:1015-1022, 2009).
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Affiliation(s)
- Trevor Greenham
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
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