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Yang Y, Chaffin TA, Shao Y, Balasubramanian VK, Markillie M, Mitchell H, Rubio‐Wilhelmi MM, Ahkami AH, Blumwald E, Neal Stewart C. Novel synthetic inducible promoters controlling gene expression during water-deficit stress with green tissue specificity in transgenic poplar. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1596-1609. [PMID: 38232002 PMCID: PMC11123411 DOI: 10.1111/pbi.14289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 11/16/2023] [Accepted: 01/03/2024] [Indexed: 01/19/2024]
Abstract
Synthetic promoters may be designed using short cis-regulatory elements (CREs) and core promoter sequences for specific purposes. We identified novel conserved DNA motifs from the promoter sequences of leaf palisade and vascular cell type-specific expressed genes in water-deficit stressed poplar (Populus tremula × Populus alba), collected through low-input RNA-seq analysis using laser capture microdissection. Hexamerized sequences of four conserved 20-base motifs were inserted into each synthetic promoter construct. Two of these synthetic promoters (Syn2 and Syn3) induced GFP in transformed poplar mesophyll protoplasts incubated in 0.5 M mannitol solution. To identify effect of length and sequence from a valuable 20 base motif, 5' and 3' regions from a basic sequence (GTTAACTTCAGGGCCTGTGG) of Syn3 were hexamerized to generate two shorter synthetic promoters, Syn3-10b-1 (5': GTTAACTTCA) and Syn3-10b-2 (3': GGGCCTGTGG). These promoters' activities were compared with Syn3 in plants. Syn3 and Syn3-10b-1 were specifically induced in transient agroinfiltrated Nicotiana benthamiana leaves in water cessation for 3 days. In stable transgenic poplar, Syn3 presented as a constitutive promoter but had the highest activity in leaves. Syn3-10b-1 had stronger induction in green tissues under water-deficit stress conditions than mock control. Therefore, a synthetic promoter containing the 5' sequence of Syn3 endowed both tissue-specificity and water-deficit inducibility in transgenic poplar, whereas the 3' sequence did not. Consequently, we have added two new synthetic promoters to the poplar engineering toolkit: Syn3-10b-1, a green tissue-specific and water-deficit stress-induced promoter, and Syn3, a green tissue-preferential constitutive promoter.
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Affiliation(s)
- Yongil Yang
- Center for Agricultural Synthetic BiologyUniversity of Tennessee Institute of AgricultureKnoxvilleTennesseeUSA
| | - Timothy A. Chaffin
- Center for Agricultural Synthetic BiologyUniversity of Tennessee Institute of AgricultureKnoxvilleTennesseeUSA
| | - Yuanhua Shao
- Center for Agricultural Synthetic BiologyUniversity of Tennessee Institute of AgricultureKnoxvilleTennesseeUSA
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTennesseeUSA
| | | | - Meng Markillie
- Environmental Molecular Sciences Laboratory, Pacific Northwest National LaboratoryRichlandWAUSA
| | - Hugh Mitchell
- Environmental Molecular Sciences Laboratory, Pacific Northwest National LaboratoryRichlandWAUSA
| | | | - Amir H. Ahkami
- Environmental Molecular Sciences Laboratory, Pacific Northwest National LaboratoryRichlandWAUSA
| | - Eduardo Blumwald
- Department of Plant SciencesUniversity of CaliforniaDavisCaliforniaUSA
| | - C. Neal Stewart
- Center for Agricultural Synthetic BiologyUniversity of Tennessee Institute of AgricultureKnoxvilleTennesseeUSA
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTennesseeUSA
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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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Hajib A, El Harkaoui S, Choukri H, Khouchlaa A, Aourabi S, El Menyiy N, Bouyahya A, Matthaeus B. Apiaceae Family an Important Source of Petroselinic Fatty Acid: Abundance, Biosynthesis, Chemistry, and Biological Proprieties. Biomolecules 2023; 13:1675. [PMID: 38002357 PMCID: PMC10669383 DOI: 10.3390/biom13111675] [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: 03/01/2023] [Revised: 03/30/2023] [Accepted: 04/26/2023] [Indexed: 11/26/2023] Open
Abstract
Petroselinic fatty acid (PeFA) is considered a rare fatty acid and one of the most important fatty acids in the Apiaceae family. Its content varies depending on plant species, geographical origin, extraction method, ripeness, etc. Indeed, reported levels of petroselinic fatty acid range from 10.4 to 75.6% (in anise seed oil), 1 to 81.9% (in coriander seed oil), 28.5 to 57.6% (in caraway seed oil), 49.4 to 75.6% (in celery seed oil), 41.3 to 61.8% (in caraway seed oil), 79.9 to 87.2% (in dill seed oil), 43.1 to 81.9% (in fennel seed oil), and 35 to 75.1% (parsley seed oil). In this review, we also show current knowledge about genes encoding biosynthesis, from the desaturation of 16:0-ACP to petroselinic acid stored in triacylglycerol in the seeds. Furthermore, petroselinic acid is not related to the synthesis of ABA. PeFA was successfully isolated from Apiaceae family plant seeds in order to study their reactivity and biological activities. Several investigations showed that this fatty acid has a wide range of biological potentials, including antidiabetic, antibacterial, and antifungal activities. In cosmetics, PeFA alone or in association with other active compounds has interesting applications as an anti-inflammatory agent for the treatment of skin, hair, and nail disorders.
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Affiliation(s)
- Ahmed Hajib
- Laboratory of Bioactive and Molecules of Interest, National Agency of Medicinal and Aromatic Plants (NAMAP), Taounate 34000, Morocco
| | - Said El Harkaoui
- Department of Safety and Quality of Cereals, Max Rubner-Institut, Federal Research Insitute for Nutrition and Food, Schützenberg 12, D-32756 Detmold, Germany
| | - Hasnae Choukri
- International Center for Agricultural Research in the Dry Areas, Rabat 10000, Morocco
| | - Aya Khouchlaa
- Laboratory of Biochemistry, National Agency of Medicinal and Aromatic Plants (NAMAP), Taounate 34000, Morocco
| | - Sarra Aourabi
- Laboratory of Bioactive and Molecules of Interest, National Agency of Medicinal and Aromatic Plants (NAMAP), Taounate 34000, Morocco
| | - Naoual El Menyiy
- Laboratory of Pharmacology, National Agency of Medicinal and Aromatic Plants (NAMAP), Taounate 34000, Morocco
| | - Abdelhakim Bouyahya
- Laboratory of Human Pathologies Biology, Faculty of Sciences, Mohammed V University in Rabat, Rabat 10106, Morocco
| | - Bertrand Matthaeus
- Department of Safety and Quality of Cereals, Max Rubner-Institut, Federal Research Insitute for Nutrition and Food, Schützenberg 12, D-32756 Detmold, Germany
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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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Yang P, Ling XY, Zhou XF, Chen YX, Wang TT, Lin XJ, Zhao YY, Ye YS, Huang LX, Sun YW, Qi YX, Ma DM, Zhan RT, Huang XS, Yang JF. Comparing genomes of Fructus Amomi-producing species reveals genetic basis of volatile terpenoid divergence. PLANT PHYSIOLOGY 2023; 193:1244-1262. [PMID: 37427874 DOI: 10.1093/plphys/kiad400] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/25/2023] [Accepted: 06/13/2023] [Indexed: 07/11/2023]
Abstract
Wurfbainia longiligularis and Wurfbainia villosa are both rich in volatile terpenoids and are 2 primary plant sources of Fructus Amomi used for curing gastrointestinal diseases. Metabolomic profiling has demonstrated that bornyl diphosphate (BPP)-related terpenoids are more abundant in the W. villosa seeds and have a wider tissue distribution in W. longiligularis. To explore the genetic mechanisms underlying the volatile terpenoid divergence, a high-quality chromosome-level genome of W. longiligularis (2.29 Gb, contig N50 of 80.39 Mb) was assembled. Functional characterization of 17 terpene synthases (WlTPSs) revealed that WlBPPS, along with WlTPS 24/26/28 with bornyl diphosphate synthase (BPPS) activity, contributes to the wider tissue distribution of BPP-related terpenoids in W. longiligularis compared to W. villosa. Furthermore, transgenic Nicotiana tabacum showed that the GCN4-motif element positively regulates seed expression of WvBPPS and thus promotes the enrichment of BPP-related terpenoids in W. villosa seeds. Systematic identification and analysis of candidate TPS in 29 monocot plants from 16 families indicated that substantial expansion of TPS-a and TPS-b subfamily genes in Zingiberaceae may have driven increased diversity and production of volatile terpenoids. Evolutionary analysis and functional identification of BPPS genes showed that BPP-related terpenoids may be distributed only in the Zingiberaceae of monocot plants. This research provides valuable genomic resources for breeding and improving Fructus Amomi with medicinal and edible value and sheds light on the evolution of terpenoid biosynthesis in Zingiberaceae.
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Affiliation(s)
- Peng Yang
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
- Hunan Provincial Key Laboratory for Synthetic Biology of Traditional Chinese Medicine, School of Pharmaceutical Sciences, Hunan University of Medicine, Huaihua 418000, China
| | - Xu-Yi Ling
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Xiao-Fan Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
| | - Yuan-Xia Chen
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Tian-Tian Wang
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Xiao-Jing Lin
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Yuan-Yuan Zhao
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Yu-Shi Ye
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Lin-Xuan Huang
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Ye-Wen Sun
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Yu-Xin Qi
- Hunan Provincial Key Laboratory for Synthetic Biology of Traditional Chinese Medicine, School of Pharmaceutical Sciences, Hunan University of Medicine, Huaihua 418000, China
| | - Dong-Ming Ma
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Ruo-Ting Zhan
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Xue-Shuang Huang
- Hunan Provincial Key Laboratory for Synthetic Biology of Traditional Chinese Medicine, School of Pharmaceutical Sciences, Hunan University of Medicine, Huaihua 418000, China
| | - Jin-Fen Yang
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
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6
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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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Khan A, Pudhuvai B, Shrestha A, Mishra AK, Shah MP, Koul B, Dey N. CRISPR-mediated iron and folate biofortification in crops: advances and perspectives. Biotechnol Genet Eng Rev 2023:1-31. [PMID: 37092872 DOI: 10.1080/02648725.2023.2205202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Micronutrient deficiency conditions, such as anemia, are the most prevalent global health problem due to inadequate iron and folate in dietary sources. Biofortification advancements can propel the rapid amelioration of nutritionally beneficial components in crops that are required to combat the adverse effects of micronutrient deficiencies on human health. To date, several strategies have been proposed to increase micronutrients in plants to improve food quality, but very few approaches have intrigued `clustered regularly interspaced short palindromic repeats' (CRISPR) modules for the enhancement of iron and folate concentration in the edible parts of plants. In this review, we discuss two important approaches to simultaneously enhance the bioavailability of iron and folate concentrations in rice endosperms by utilizing advanced CRISPR-Cas9-based technology. This includes the 'tuning of cis-elements' and 'enhancer re-shuffling' in the regulatory components of genes that play a vital role in iron and folate biosynthesis/transportation pathways. In particular, base-editing and enhancer re-installation in native promoters of selected genes can lead to enhanced accumulation of iron and folate levels in the rice endosperm. The re-distribution of micronutrients in specific plant organs can be made possible using the above-mentioned contemporary approaches. Overall, the present review discusses the possible approaches for synchronized iron and folate biofortification through modification in regulatory gene circuits employing CRISPR-Cas9 technology.
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Affiliation(s)
- Ahamed Khan
- Biology Centre of the Czech Academy of Sciences, Institute of Plant Molecular Biology, České Budějovice, Czech Republic
| | - Baveesh Pudhuvai
- Department of Genetics and Biotechnology, Faculty of Agriculture and Technology, University of South Bohemia in České Budějovice, České Budějovice, Czech Republic
| | - Ankita Shrestha
- Division of Microbial and Plant Biotechnology, Department of Biotechnology, Government of India, Institute of Life Sciences, Bhubaneswar, Odisha, India
| | - Ajay Kumar Mishra
- Khalifa Centre for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Maulin P Shah
- Division of Applied and Environmental Microbiology, Enviro Technology Ltd, Ankleshwar, Gujarat, India
| | - Bhupendra Koul
- Department of Biotechnology, Lovely Professional University, Phagwara, Punjab, India
| | - Nrisingha Dey
- Division of Microbial and Plant Biotechnology, Department of Biotechnology, Government of India, Institute of Life Sciences, Bhubaneswar, Odisha, India
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Liu S, Lei J, Zhang J, Liu H, Ye Z, Yang J, Lu Q, Liu P, Chen J, Yang J. Genome-wide identification and analysis of wheat LRR-RLK family genes following Chinese wheat mosaic virus infection. FRONTIERS IN PLANT SCIENCE 2023; 13:1109845. [PMID: 36733595 PMCID: PMC9887201 DOI: 10.3389/fpls.2022.1109845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 12/28/2022] [Indexed: 06/18/2023]
Abstract
BACKGROUND As the largest plant receptor-like protein kinase (RLK) superfamily, the 21 leucine-rich repeat receptor-like kinases (LRR-RLKs) family are involved in plant 22 growth, development, and stress responses. However, the functions of LRR-RLKs in 23 wheat immunity remain unknown. RESULTS In the current study, 929 LRR-RLKs were identified in Triticum aestivum 25 genome database using the BLAST and hidden Markov models (HMM) approach and 26 divided into 14 clades. Chromosomal localization and synteny analysis revealed that 27 TaLRR-RLKs were randomly distributed on all chromosomes with 921 collinear 28 events. Through the cis-acting elements analysis, we observed that TaLRR-RLKs 29 participated in hormone response, light response, development, metabolism, and 30 response to environmental stress. The transcript level of 14 random selected 31 TaLRR-RLKs from each subfamily was regulated by plant hormone treatment and 32 Chinese wheat mosaic virus (CWMV) infection. The function of TaLRR-RLKs in 33 wheat resistance to CWMV infection was further investigated by virus-induced gene 34 silencing assay. Additionally, the accumulation of MeJA response genes, as well as 35 CWMV RNA were not changed in the TaLRR-RLK silencing plants under MeJA 36 treatment. CONCLUSIONS Our results demonstrated that TaLRR-RLKs play an important role in 38 wheat resistance to viral infection via hormone signals and lay the groundwork for the 39 functional study of TaLRR-RLKs in wheat.
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Affiliation(s)
- Shuang Liu
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Jiajia Lei
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Juan Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Hanhong Liu
- Junan County Bureau of Agriculture and Country, Linyi, China
| | - Zhuangxin Ye
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Jin Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Qiseng Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Peng Liu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Jianping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Jian Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
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Yang T, Wu X, Wang W, Wu Y. Regulation of seed storage protein synthesis in monocot and dicot plants: A comparative review. MOLECULAR PLANT 2023; 16:145-167. [PMID: 36495013 DOI: 10.1016/j.molp.2022.12.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/27/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023]
Abstract
Seeds are a major source of nutrients for humans and animal livestock worldwide. With improved living standards, high nutritional quality has become one of the main targets for breeding. Storage protein content in seeds, which is highly variable depending on plant species, serves as a pivotal criterion of seed nutritional quality. In the last few decades, our understanding of the molecular genetics and regulatory mechanisms of storage protein synthesis has greatly advanced. Here, we systematically and comprehensively summarize breakthroughs on the conservation and divergence of storage protein synthesis in dicot and monocot plants. With regard to storage protein accumulation, we discuss evolutionary origins, developmental processes, characteristics of main storage protein fractions, regulatory networks, and genetic modifications. In addition, we discuss potential breeding strategies to improve storage protein accumulation and provide perspectives on some key unanswered problems that need to be addressed.
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Affiliation(s)
- Tao Yang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Xingguo Wu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200233, China
| | - Wenqin Wang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200233, China
| | - Yongrui Wu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.
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10
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Yan Y, Li C, Liu Z, Zhuang JJ, Kong JR, Yang ZK, Yu J, Shah Alam M, Ruan CC, Zhang HM, Xu JH. A new demethylase gene, OsDML4, is involved in high temperature-increased grain chalkiness in rice. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:7273-7284. [PMID: 36073837 DOI: 10.1093/jxb/erac367] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 09/07/2022] [Indexed: 06/15/2023]
Abstract
High temperature (HT) can affect the accumulation of seed storage materials and cause adverse effects on the yield and quality of rice. DNA methylation plays an important role in plant growth and development. Here, we identified a new demethylase gene OsDML4 and discovered its function in cytosine demethylation to affect endosperm formation. Loss of function of OsDML4 induced chalky endosperm only under HT and dramatically reduced the transcription and accumulation of glutelins and 16 kDa prolamin. The expression of two transcription factor genes RISBZ1 and RPBF was significantly decreased in the osdml4 mutants, which caused adverse effects on the formation of protein bodies (PBs) with greatly decreased PB-II number, and incomplete and abnormally shaped PB-IIs. Whole-genome bisulfite sequencing analysis of seeds at 15 d after pollination revealed much higher global methylation levels of CG, CHG, and CHH contexts in the osdml4 mutants compared with the wild type. Moreover, the RISBZ1 promoter was hypermethylated but the RPBF promoter was almost unchanged under HT. No significant difference was detected between the wild type and osdml4 mutants under normal temperature. Our study demonstrated a novel OsDML4-mediated DNA methylation involved in the formation of chalky endosperm only under HT and provided a new perspective in regulating endosperm development and the accumulation of seed storage proteins in rice.
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Affiliation(s)
- Yan Yan
- Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, China
- Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Chao Li
- Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, China
- Shandong (Linyi) Institute of Modern Agriculture, Zhejiang University, Shandong 276034, China
| | - Zhen Liu
- Hainan Institute, Zhejiang University, Sanya, Hainan 572000, China
| | - Jun-Jie Zhuang
- Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, China
| | - Jia-Rui Kong
- Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, China
| | - Zhen-Kun Yang
- Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, China
| | - Jie Yu
- Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, China
- Hainan Institute, Zhejiang University, Sanya, Hainan 572000, China
| | - Mohammad Shah Alam
- Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, China
| | - Cheng-Cheng Ruan
- Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, China
| | - Heng-Mu Zhang
- Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Jian-Hong Xu
- Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, China
- Shandong (Linyi) Institute of Modern Agriculture, Zhejiang University, Shandong 276034, China
- Hainan Institute, Zhejiang University, Sanya, Hainan 572000, China
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11
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Wheat genomic study for genetic improvement of traits in China. SCIENCE CHINA. LIFE SCIENCES 2022; 65:1718-1775. [PMID: 36018491 DOI: 10.1007/s11427-022-2178-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/10/2022] [Indexed: 01/17/2023]
Abstract
Bread wheat (Triticum aestivum L.) is a major crop that feeds 40% of the world's population. Over the past several decades, advances in genomics have led to tremendous achievements in understanding the origin and domestication of wheat, and the genetic basis of agronomically important traits, which promote the breeding of elite varieties. In this review, we focus on progress that has been made in genomic research and genetic improvement of traits such as grain yield, end-use traits, flowering regulation, nutrient use efficiency, and biotic and abiotic stress responses, and various breeding strategies that contributed mainly by Chinese scientists. Functional genomic research in wheat is entering a new era with the availability of multiple reference wheat genome assemblies and the development of cutting-edge technologies such as precise genome editing tools, high-throughput phenotyping platforms, sequencing-based cloning strategies, high-efficiency genetic transformation systems, and speed-breeding facilities. These insights will further extend our understanding of the molecular mechanisms and regulatory networks underlying agronomic traits and facilitate the breeding process, ultimately contributing to more sustainable agriculture in China and throughout the world.
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12
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Aslam N, Sameeullah M, Yildirim M, Baloglu MC, Yucesan B, Lössl AG, Waheed MT, Gurel E. Isolation of the 3β-HSD promoter from Digitalis ferruginea subsp. ferruginea and its functional characterization in Arabidopsis thaliana. Mol Biol Rep 2022; 49:7173-7183. [PMID: 35733064 DOI: 10.1007/s11033-022-07634-4] [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: 11/03/2021] [Revised: 05/06/2022] [Accepted: 05/24/2022] [Indexed: 12/01/2022]
Abstract
BACKGROUND Although members of the SDR gene family (short chain dehydrogenase) are distributed in kingdom of life, they have diverse roles in stress tolerance mechanism or secondary metabolite biosynthesis. Nevertheless, their precise roles in gene expression or regulation under stress are yet to be understood. METHODS As a case study, we isolated, sequenced and functionally characterized the 3β-HSD promoter from Digitalis ferruginea subsp. ferruginea in Arabidopsis thaliana. RESULTS The promoter fragment contained light and stress response elements such as Box-4, G-Box, TCT-motif, LAMP element, ABRE, ARE, WUN-motif, MYB, MYC, W box, STRE and Box S. The functional analysis of the 3β-HSD promoter in transgenic Arabidopsis seedlings showed that the promoter was expressed in cotyledon and root elongation zone in 2 days' seedlings. However, this expression was extended to hypocotyl and complete root in 6 days' seedlings. In 20 days-old seedlings, promoter expression was distributed to the whole seedling including hydathodes aperture, vascular bundle, shoot apical meristem, trichomes, midrib, leaf primordia, hypocotyl and xylem tissues. Further, expression of the promoter was enhanced or remained stable under the different abiotic stress conditions like osmotic, heat, cold, cadmium or low pH. In addition, the promoter also showed response to methyl jasmonate (MeJA) application. The expression could not be induced in wounded cotyledon most likely due to lack of interacting elements in the promoter fragment. CONCLUSIONS Taken together, the 3β-HSD promoter could be a candidate for the development of transgenic plants especially under changing environmental conditions.
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Affiliation(s)
- Noreen Aslam
- Department of Biology, Faculty of Science and Literature, Bolu Abant Izzet Baysal University, 14030, Bolu, Turkey
| | - Muhammad Sameeullah
- Department of Biology, Faculty of Science and Literature, Bolu Abant Izzet Baysal University, 14030, Bolu, Turkey.,Center for Innovative Food Technologies Development, Application and Research, Bolu Abant Izzet Baysal University, 14030, Bolu, Turkey
| | - Muhammet Yildirim
- Department of Chemistry, Faculty of Science and Literature, Bolu Abant Izzet Baysal University, 14030, Bolu, Turkey
| | - Mehmet Cengiz Baloglu
- Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Kastamonu University, 37100, Kastamonu, Turkey
| | - Buhara Yucesan
- Department of Seed Science and Technology, Faculty of Agriculture, Bolu Abant Izzet Baysal University, 14030, Bolu, Turkey
| | - Andreas G Lössl
- Department of Applied Plant Sciences and Plant Biotechnology (DAPP), University of Natural Resources and Applied Life Sciences (BOKU), Vienna, Austria
| | - Mohammad Tahir Waheed
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Ekrem Gurel
- Department of Biology, Faculty of Science and Literature, Bolu Abant Izzet Baysal University, 14030, Bolu, Turkey.
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13
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Chenarani N, Emamjomeh A, Rahnama H, Zamani K, Solouki M. Characterization of sucrose binding protein as a seed-specific promoter in transgenic tobacco Nicotiana tabacum L. PLoS One 2022; 17:e0268036. [PMID: 35657906 PMCID: PMC9165846 DOI: 10.1371/journal.pone.0268036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 04/20/2022] [Indexed: 11/24/2022] Open
Abstract
Seed-specific expression using appropriate promoters is a recommended strategy for the efficiently producing valuable metabolites in transgenic plants. In the present study, we investigated the sequence of sucrose binding protein (SBP) as a seed-specific promoter to find the cis-acting elements specific to gene expression in seeds. The 1860 bp SBP sequence was analyzed using Plant Care and PLACE databases to find cis-acting elements, which resulted in a finding of 22 cis-acting elements required for seed expression. In addition, we have discovered cis- acting elements that are indirectly involved in triacylglycerol synthesis (GATABOX, DOFCOREZM, CACGTGMOTIF). The seed specificity of SBP was analyzed by generating a stable transgenic tobacco plant harboring β-glucuronidase (GUS) reporter gene under the control of the SBP promoter. Histochemical analysis of these transgenic tobacco plants indicated decreasing GUS activity in the leaves during the vegetative stage. However, the mature seeds of transgenic plants showed GUS activity. Moreover, the SBP promoter function in the seed oil content was evaluated by the expression of DGAT1. The expression analysis of DGAT1 in SBP-DGAT1 transgenic tobacco seeds using quantitative real-time PCR revealed a 7.8-fold increase in DGAT1 than in non-transgenic plants. Moreover, oil content increased up to 2.19 times more than in non-transgenic plants. And the oil content of the SBP-DGAT1 transgenic tobacco leaves did not change compared to the control plant. Therefore, we suggested that the SBP promoter could be used as a seed-specific promoter for targeted expression of desired genes in the metabolite engineering of oilseed crops.
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Affiliation(s)
- Nasibeh Chenarani
- Department of Plant Breeding and Biotechnology (PBB), Faculty of Agriculture, University of Zabol, Zabol, Iran
| | - Abbasali Emamjomeh
- Department of Plant Breeding and Biotechnology (PBB), Faculty of Agriculture, University of Zabol, Zabol, Iran
- Department of Bioinformatics, Laboratory of Computational Biotechnology and Bioinformatics (CBB Lab), University of Zabol, Zabol, Iran
| | - Hassan Rahnama
- Department of Genetic Engineering & Biosafety, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran
| | - Katayoun Zamani
- Department of Genetic Engineering & Biosafety, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran
| | - Mahmoud Solouki
- Department of Plant Breeding and Biotechnology (PBB), Faculty of Agriculture, University of Zabol, Zabol, Iran
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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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Wang L, Dai W, Shi Y, Wang Y, Zhang C. Cloning and activity analysis of the highly expressed gene VviABCG20 promoter in seed and its activity is negatively regulated by the transcription factor VviDof14. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 315:111152. [PMID: 35067313 DOI: 10.1016/j.plantsci.2021.111152] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 12/09/2021] [Accepted: 12/11/2021] [Indexed: 06/14/2023]
Abstract
Half-size ATP binding cassette G (ABCG) transporters participate in the growth and development of plants by transporting substrates. The VviABCG20 gene is highly expressed in seed and plays an important role in seed development/abortion. However, little is known about the function of the VviABCG20 promoter (pVviABCG20) and its regulatory factors. In our study, we obtained pVviABCG20s from 15 seeded and seedless grape varieties and there were two types of 'a' and 'b' with 41 bp non-deletion or deletion, respectively. The pVviABCG20 activity was higher in seeds, siliques, flowers and roots of pVviABCG20-GUS Arabidopsis. The GUS activity analysis revealed that the activities of P4 (-586 bp) to P7 (-155 bp) were becoming increasingly weaker, and the P7 activity almost disappears compared with the pVviABCG20 (P0, -1604). Yeast one-hybrid and GUS activity analysis indicated that VviDof14 binds to the AAAG element in the P7' (-586 bp) fragment of the pVviABCG20 and regulated the activity negatively. The quantitative real-time PCR analysis suggested that the expression of VviDof14 in Thompson seedless seeds was higher than that in Pinot noir. Our study laid the foundation for further analysis of the functions of the pVviABCG20 and its regulator VviDof14 in grape seed development/abortion.
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Affiliation(s)
- Ling Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northwest Region), Ministry of Agriculture, P.R. China, Yangling, Shaanxi, China
| | - Weina Dai
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northwest Region), Ministry of Agriculture, P.R. China, Yangling, Shaanxi, China
| | - Yuanyuan Shi
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northwest Region), Ministry of Agriculture, P.R. China, Yangling, Shaanxi, China
| | - Yuejin Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northwest Region), Ministry of Agriculture, P.R. China, Yangling, Shaanxi, China
| | - Chaohong Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northwest Region), Ministry of Agriculture, P.R. China, Yangling, Shaanxi, China.
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16
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Singh A, Mathan J, Yadav A, K. Goyal A, Chaudhury A. Molecular and Transcriptional Regulation of Seed Development in Cereals: Present Status and Future Prospects. CEREAL GRAINS - VOLUME 1 2021. [DOI: 10.5772/intechopen.99318] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/19/2023]
Abstract
Cereals are a rich source of vitamins, minerals, carbohydrates, fats, oils and protein, making them the world’s most important source of nutrition. The influence of rising global population, as well as the emergence and spread of disease, has the major impact on cereal production. To meet the demand, there is a pressing need to increase cereal production. Optimal seed development is a key agronomical trait that contributes to crop yield. The seed development and maturation is a complex process that includes not only embryo and endosperm development, but also accompanied by huge physiological, biochemical, metabolic, molecular and transcriptional changes. This chapter discusses the growth of cereal seed and highlights the novel biological insights, with a focus on transgenic and new molecular breeding, as well as biotechnological intervention strategies that have improved crop yield in two major cereal crops, primarily wheat and rice, over the last 21 years (2000–2021).
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17
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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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18
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Li Y, Ma S, Zhao Q, Lv D, Wang B, Xiao K, Zhu J, Li S, Yang W, Liu X, Wang H, Zhou X, Chen R. ZmGRAS11, transactivated by Opaque2, positively regulates kernel size in maize. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:2031-2037. [PMID: 34850567 DOI: 10.1111/jipb.13198] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 11/30/2021] [Indexed: 06/13/2023]
Abstract
Although the genetic basis for endosperm development in maize (Zea mays) has been well studied, the mechanism for coordinating grain filling with increasing kernel size remains elusive. Here, we report that increased kernel size was selected during modern breeding and identify a novel DELLA-like transcriptional regulator, ZmGRAS11, which positively regulates kernel size and kernel weight in maize. We find that Opaque2, a core transcription factor for zein protein and starch accumulation, transactivates the expression of ZmGRAS11. Our data suggest that the Opaque2-ZmGRAS11 module mediates synergistic endosperm enlargement with grain filling.
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Affiliation(s)
- Ye Li
- Crop Functional Genome Research Center, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Key Laboratory of Agricultural Products Chemical and Biological Processing Technology, Zhejiang University of Science and Technology, Hangzhou, 310023, China
| | - Shuai Ma
- Crop Functional Genome Research Center, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Qianqian Zhao
- Crop Functional Genome Research Center, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Di Lv
- Crop Functional Genome Research Center, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Baobao Wang
- Crop Functional Genome Research Center, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ke Xiao
- Crop Functional Genome Research Center, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, 100193, China
| | - Jiameng Zhu
- Crop Functional Genome Research Center, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei, 230036, China
| | - Suzhen Li
- Crop Functional Genome Research Center, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Wenzhu Yang
- Crop Functional Genome Research Center, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaoqing Liu
- Crop Functional Genome Research Center, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Haiyang Wang
- College of Life Sciences, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Xiaojin Zhou
- Crop Functional Genome Research Center, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Rumei Chen
- Crop Functional Genome Research Center, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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Genome-Wide Identification of LRR-RLK Family in Saccharum and Expression Analysis in Response to Biotic and Abiotic Stress. Curr Issues Mol Biol 2021; 43:1632-1651. [PMID: 34698114 PMCID: PMC8929030 DOI: 10.3390/cimb43030116] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/05/2021] [Accepted: 10/07/2021] [Indexed: 12/17/2022] Open
Abstract
The leucine-rich repeat receptor-like protein kinase (LRR-RLK) gene family is the largest family of the receptor-like protein kinases (RLKs) superfamily in higher plants, which is involved in regulating the plant growth and development, stress responses, signal transduction and so on. However, no comprehensive analyses of LRR-RLKs have been reported in sugarcane. Here, we performed a comprehensive analysis of the LRR-RLK gene family in sugarcane ancestor species Saccharum spontaneum. A total of 437 LRR-RLK genes were identified and categorized into 14 groups based on a maximum likelihood phylogenetic tree. The chromosome location showed an uneven distribution on all 32 chromosomes in sugarcane. Subsequently, the exon-intron organization structure and conserved motif arrangement were relatively conserved among the same groups or subgroups and between Arabidopsis and S. spontaneum genomes. Furthermore, the promoter sequences analyses showed that sugarcane LRR-RLK genes (SsLRR-RLKs) were strongly regulated by various environmental stimuli, phytohormonal factors and transcription factors (TFs). Eventually, the expression profiles of SsLRR-RLK genes at different stresses were analyzed based on RNA-seq data, suggesting their potential roles in the regulation of sugarcane responses to diverse abiotic and biotic stress. Overall, the findings provide insight into the potential functional roles and lay the foundation for further functional study.
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20
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Mulat MW, Sinha VB. Distribution and abundance of CREs in the promoters depicts crosstalk by WRKYs in Tef [Eragrostis tef (Zucc.) Troetter]. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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21
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Ram H, Singh A, Katoch M, Kaur R, Sardar S, Palia S, Satyam R, Sonah H, Deshmukh R, Pandey AK, Gupta I, Sharma TR. Dissecting the nutrient partitioning mechanism in rice grain using spatially resolved gene expression profiling. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:2212-2230. [PMID: 33197257 DOI: 10.1093/jxb/eraa536] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 11/12/2020] [Indexed: 06/11/2023]
Abstract
Rice, a staple food worldwide, contains varying amounts of nutrients in different grain tissues. The underlying molecular mechanism of such distinct nutrient partitioning remains poorly investigated. Here, an optimized rapid laser capture microdissection (LCM) approach was used to individually collect pericarp, aleurone, embryo and endosperm from grains 10 days after fertilization. Subsequent RNA-Seq analysis in these tissues identified 7760 differentially expressed genes. Analysis of promoter sequences of tissue-specific genes identified many known and novel cis-elements important for grain filling and seed development. Using the identified differentially expressed genes, comprehensive spatial gene expression pathways were built for accumulation of starch, proteins, lipids, and iron. The extensive transcriptomic analysis provided novel insights about nutrient partitioning mechanisms; for example, it revealed a gradient in seed storage protein accumulation across the four tissue types analysed. The analysis also revealed that the partitioning of various minerals, such as iron, is most likely regulated through transcriptional control of their transporters. We present the extensive analysis from this study as an interactive online tool that provides a much-needed resource for future functional genomics studies aimed to improve grain quality and seed development.
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Affiliation(s)
- Hasthi Ram
- National Agri-Food Biotechnology Institute (NABI), S.A.S. Nagar, Mohali, Punjab, India
| | - Anmol Singh
- National Agri-Food Biotechnology Institute (NABI), S.A.S. Nagar, Mohali, Punjab, India
| | - Megha Katoch
- National Agri-Food Biotechnology Institute (NABI), S.A.S. Nagar, Mohali, Punjab, India
| | - Ravneet Kaur
- National Agri-Food Biotechnology Institute (NABI), S.A.S. Nagar, Mohali, Punjab, India
| | - Shaswati Sardar
- National Agri-Food Biotechnology Institute (NABI), S.A.S. Nagar, Mohali, Punjab, India
| | - Shubham Palia
- Department of Biochemical Engineering and Biotechnology, Block I, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India
| | - Rohit Satyam
- Department of Biochemical Engineering and Biotechnology, Block I, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India
| | - Humira Sonah
- National Agri-Food Biotechnology Institute (NABI), S.A.S. Nagar, Mohali, Punjab, India
| | - Rupesh Deshmukh
- National Agri-Food Biotechnology Institute (NABI), S.A.S. Nagar, Mohali, Punjab, India
| | - Ajay Kumar Pandey
- National Agri-Food Biotechnology Institute (NABI), S.A.S. Nagar, Mohali, Punjab, India
| | - Ishaan Gupta
- Department of Biochemical Engineering and Biotechnology, Block I, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India
| | - Tilak Raj Sharma
- National Agri-Food Biotechnology Institute (NABI), S.A.S. Nagar, Mohali, Punjab, India
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New insights on the function of plant acyl carrier proteins from comparative and evolutionary analysis. Genomics 2020; 113:1155-1165. [PMID: 33221517 DOI: 10.1016/j.ygeno.2020.11.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 10/02/2020] [Accepted: 11/16/2020] [Indexed: 11/20/2022]
Abstract
Acyl carrier proteins (ACPs) play a central role in both plastidial and mitochondrial Type II fatty acid synthesis in plant cells. However, a large proportion of plant ACPs remain functionally uncharacterized, and their evolutionary history remains elusive. In present study, 97 putative ACPs were identified from ten angiosperm species examined. Based on phylogenetic analysis, ACP genes were grouped into plastidial (cpACP: ACP1/2/3/4/5) and mitochondrial (mtACP: mtACP1/mtACP2/mtACP3) ACPs. Protein sequence (motifs and length), tertiary structure, and gene structure (exon number, average intron length, and intron phase) were highly conserved in different ACP subclades. The differentiation of ACPs into distinct types occurred 85-98 and 45-57 million years ago. A limited proportion of ACP genes experience tandem or segmental duplication, corresponding to two rounds of whole genome duplication. Ka/Ks ratios revealed that duplicated ACP genes underwent a purifying selection. Regarding expression patterns, most ACPs were expressed constitutively and tissue-specifically. Notably, the average expression levels of ACP1, mtACP3, and mtACP1 were positively correlated with those of ACP3, ACP4, and mtACP2, respectively. Analysis of cis-elements showed that seven motifs (CACTFTPPCA1, DOFCOREZM, GT1CONSENSUS, CAATBOX1, ARR1AT, POLLEN1LELAT52, and GATABOX) related to tissue-specific, ABA, and light-mediated gene regulation were ubiquitous in all ACPs investigated, which shed new light on the regulation patterns of these central enzymatic partners of the FAS system. This study presents a thorough overview of angiosperm ACP gene families and provides informative clues for the functional characterization of plant ACPs in the future.
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Kumar A, Daware A, Kumar A, Kumar V, Gopala Krishnan S, Mondal S, Patra BC, Singh AK, Tyagi AK, Parida SK, Thakur JK. Genome-wide analysis of polymorphisms identified domestication-associated long low-diversity region carrying important rice grain size/weight quantitative trait loci. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:1525-1547. [PMID: 32432802 DOI: 10.1111/tpj.14845] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 05/01/2020] [Accepted: 05/12/2020] [Indexed: 05/02/2023]
Abstract
Rice grain size and weight are major determinants of grain quality and yield and so have been under rigorous selection since domestication. However, the genetic basis for contrasting grain size/weight trait among Indian germplasms and their association with domestication-driven evolution is not well understood. In this study, two long (LGG) and two short grain (SGG) genotypes were resequenced. LGG (LGR and PB 1121) differentiated from SGG (Sonasal and Bindli) by 504 439 single nucleotide polymorphisms (SNPs) and 78 166 insertion-and-deletion polymorphisms. The LRK gene cluster was different and a truncation mutation in the LRK8 kinase domain was associated with LGG. Phylogeny with 3000 diverse rice accessions revealed that the four sequenced genotypes belonged to the japonica group and were at the edge of the clades indicating them to be the potential source of genetic diversity available in Indian rice germplasm. Six SNPs were significantly associated with grain size/weight and the top four of these could be validated in mapping a population, suggesting this study as a valuable resource for high-throughput genotyping. A contiguous long low-diversity region (LDR) of approximately 6 Mb carrying a major grain weight quantitative trait loci (harbouring OsTOR gene) was identified on Chromosome 5. This LDR was identified as an evolutionary important site with significant positive selection and multiple selection sweeps, and showed association with many domestication-related traits, including grain size/weight. The aus population retained more allelic variations in the LDR than the japonica and indica populations, suggesting it to be one of the divergence loci. All the data and analyses can be accessed from the RiceSzWtBase database.
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Affiliation(s)
- Angad Kumar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Anurag Daware
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Arvind Kumar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Vinay Kumar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - S Gopala Krishnan
- Division of Genetics, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi, 110012, India
| | - Subhasish Mondal
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Bhaskar C Patra
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, 753006, India
| | - Ashok K Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi, 110012, India
| | - Akhilesh K Tyagi
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Swarup K Parida
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Jitendra K Thakur
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
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Nonhebel HM, Griffin K. Production and roles of IAA and ABA during development of superior and inferior rice grains. FUNCTIONAL PLANT BIOLOGY : FPB 2020; 47:716-726. [PMID: 32438973 DOI: 10.1071/fp19291] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 02/10/2020] [Indexed: 06/11/2023]
Abstract
Current understanding of the role of plant hormones during cereal grain filling is confounded by contradictory reports on hormone production that is based on poor methodology. We report here on the accurate measurement of indole-3-acetic acid (IAA) and abscisic acid (ABA) by combined liquid chromatography-tandem mass spectrometry in multiple reaction-monitoring mode with heavy isotope labelled internal standards. ABA and IAA contents of superior versus inferior rice grains (ABA maxima 159 ng g-1 FW and 109 ng g-1 FW, IAA maxima 2 µg g-1 FW and 1.7 µg g-1 FW respectively) correlated with the expression of biosynthetic genes and with grain fill. Results confirm that grain ABA is produced primarily by OsNCED2(5), but suggest that ABA import and metabolism also play important roles in ABA regulation. The IAA content of grains is primarily influenced by OsYUC9 and OsYUC11. However, the distinct expression profile of OsYUC12 suggests a specific role for IAA produced by this enzyme. Co-expression of OsYUC12 with OsIAA29 indicates their involvement in a common signalling pathway. Co-expression and cis-element analysis identified several aleurone-specific transcriptional regulators as well as glutelin as strong candidates for detailed investigation for direct regulation by the auxin-signalling pathway.
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Affiliation(s)
- Heather M Nonhebel
- School of Science and Technology, University of New England, Armidale, NSW 2351, Australia; and Corresponding author.
| | - Karina Griffin
- School of Science and Technology, University of New England, Armidale, NSW 2351, Australia; and Present address: Macadamia Processing Company, 2 Cowlong Road, Lindendale NSW 2480, Australia
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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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Tang L, Zhang F, Liu A, Sun J, Mei S, Wang X, Liu Z, Liu W, Lu Q, Chen S. Genome-Wide Association Analysis Dissects the Genetic Basis of the Grain Carbon and Nitrogen Contents in Milled Rice. RICE (NEW YORK, N.Y.) 2019; 12:101. [PMID: 31889226 PMCID: PMC6937365 DOI: 10.1186/s12284-019-0362-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 12/20/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND Carbon (C) and nitrogen (N) are two fundamental components of starch and protein, which are important determinants of grain yield and quality. The food preferences of consumers and the expected end-use of grains in different rice-growing regions require diverse varieties that differ in terms of the grain N content (GNC) and grain C content (GCC) of milled rice. Thus, it is important that quantitative trait loci (QTLs)/genes with large effects on the variation of GNC and GCC are identified in breeding programs. RESULTS To dissect the genetic basis of the variation of GNC and GCC in rice, the Dumas combustion method was used to analyze 751 diverse accessions regarding the GNC, GCC, and C/N ratio of the milled grains. The GCC and GNC differed significantly among the rice subgroups, especially between Xian/Indica (XI) and Geng/Japonica (GJ). Interestingly, in the GJ subgroup, the GNC was significantly lower in modern varieties (MV) than in landraces (LAN). In the XI subgroup, the GCC was significantly higher in MV than in LAN. One, six, and nine QTLs, with 55 suggestively associated single nucleotide polymorphisms, were detected for the GNC, GCC, and C/N ratio in three panels during a single-locus genome-wide association study (GWAS). Three of these QTLs were also identified in a multi-locus GWAS. We screened 113 candidate genes in the 16 QTLs in gene-based haplotype analyses. Among these candidate genes, LOC_Os01g06240 at qNC-1.1, LOC_Os05g33300 at qCC-5.1, LOC_Os01g04360 at qCN-1.1, and LOC_Os05g43880 at qCN-5.2 may partially explain the significant differences between the LAN and MV. These candidate genes should be cloned and may be useful for molecular breeding to rapidly improve the GNC, GCC, and C/N ratio of rice. CONCLUSIONS Our findings represent valuable information regarding the genetic basis of the GNC and GCC and may be relevant for enhancing the application of favorable haplotypes of candidate genes for the molecular breeding of new rice varieties with specific grain N and C contents.
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Affiliation(s)
- Liang Tang
- Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866, China.
| | - Fan Zhang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Haidian District, Beijing, 100081, China.
| | - Anjin Liu
- Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866, China
| | - Jian Sun
- Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866, China
| | - Song Mei
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Haidian District, Beijing, 100081, China
| | - Xin Wang
- Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866, China
| | - Zhongyuan Liu
- Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866, China
| | - Wanying Liu
- Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866, China
| | - Qing Lu
- Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866, China
| | - Shuangjie Chen
- Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866, China
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Xiong Y, Ren Y, Li W, Wu F, Yang W, Huang X, Yao J. NF-YC12 is a key multi-functional regulator of accumulation of seed storage substances in rice. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:3765-3780. [PMID: 31211389 PMCID: PMC6685661 DOI: 10.1093/jxb/erz168] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 03/27/2019] [Indexed: 05/02/2023]
Abstract
Starch and storage proteins, the primary storage substances of cereal endosperm, are a major source of food for humans. However, the transcriptional regulatory networks of the synthesis and accumulation of storage substances remain largely unknown. Here, we identified a rice endosperm-specific gene, NF-YC12, that encodes a putative nuclear factor-Y transcription factor subunit C. NF-YC12 is expressed in the aleurone layer and starchy endosperm during grain development. Knockout of NF-YC12 significantly decreased grain weight as well as altering starch and protein accumulation and starch granule formation. RNA-sequencing analysis revealed that in the nf-yc12 mutant genes related to starch biosynthesis and the metabolism of energy reserves were enriched in the down-regulated category. In addition, starch and protein contents in seeds differed between NF-YC12-overexpression lines and the wild-type. NF-YC12 was found to interact with NF-YB1. ChIP-qPCR and yeast one-hybrid assays showed that NF-YC12 regulated the rice sucrose transporter OsSUT1 in coordination with NF-YB1 in the aleurone layer. In addition, NF-YC12 was directly bound to the promoters of FLO6 (FLOURY ENDOSPERM6) and OsGS1;3 (glutamine synthetase1) in developing endosperm. This study demonstrates a transcriptional regulatory network involving NF-YC12, which coordinates multiple pathways to regulate endosperm development and the accumulation of storage substances in rice seeds.
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Affiliation(s)
- Yufei Xiong
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ye Ren
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Wang Li
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Fengsheng Wu
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Wenjie Yang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xiaolong Huang
- The Key Laboratory of Plant Physiology and Development Regulation, School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Jialing Yao
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
- Correspondence:
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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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Jin X, Bai C, Bassie L, Nogareda C, Romagosa I, Twyman RM, Christou P, Zhu C. ZmPBF and ZmGAMYB transcription factors independently transactivate the promoter of the maize (Zea mays) β-carotene hydroxylase 2 gene. THE NEW PHYTOLOGIST 2019; 222:793-804. [PMID: 30489637 DOI: 10.1111/nph.15614] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 11/21/2018] [Indexed: 05/26/2023]
Abstract
The maize (Zea mays) enzyme β-carotene hydroxylase 2 (ZmBCH2) controls key steps in the conversion of β-carotene to zeaxanthin in the endosperm. The ZmBCH2 gene has an endosperm-preferred and developmentally regulated expression profile, but the detailed regulatory mechanism is unknown. To gain insight into the regulation of ZmBCH2, we isolated 2036 bp of the 5'-flanking region containing the 263 bp 5'-untranslated region (5'-UTR) including the first intron. We linked this to the β-glucuronidase reporter gene gusA. We found that high-level expression of gusA in rice seeds requires the 5'-UTR for enhanced activation. Truncated variants of the ZmBCH2 promoter retained their seed-preferred expression profile as long as a prolamin box and AACA motif were present. We identified candidate genes encoding the corresponding transcription factors (ZmPBF and ZmGAMYB) and confirmed that their spatiotemporal expression profiles are similar to ZmBCH2. Both ZmPBF and ZmGAMYB can transactivate ZmBCH2 expression in maize endosperm. To eliminate potential confounding effects in maize, we characterized the regulation of the minimal promoter region of ZmBCH2 in transgenic rice. This revealed that ZmPBF and ZmGAMYB independently transactivate the ZmBCH2 promoter. The mechanism that underpins our data provides an exciting new strategy for the control of target gene expression in engineered plants.
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Affiliation(s)
- Xin Jin
- Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio Center, Av. Alcalde Rovira Roure, 191, Lleida, 25198, Spain
| | - Chao Bai
- Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio Center, Av. Alcalde Rovira Roure, 191, Lleida, 25198, Spain
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 10081, China
| | - Ludovic Bassie
- Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio Center, Av. Alcalde Rovira Roure, 191, Lleida, 25198, Spain
| | - Carmina Nogareda
- Department of Animal Science, ETSEA, University of Lleida-Agrotecnio Center, Lleida, 25198, Spain
| | - Ignacio Romagosa
- Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio Center, Av. Alcalde Rovira Roure, 191, Lleida, 25198, Spain
| | | | - Paul Christou
- Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio Center, Av. Alcalde Rovira Roure, 191, Lleida, 25198, Spain
- ICREA, Catalan Institute for Research and Advanced Studies, Passeig Lluís Companys 23, Barcelona, 08010, Spain
| | - Changfu Zhu
- Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio Center, Av. Alcalde Rovira Roure, 191, Lleida, 25198, Spain
- School of Life Sciences, Changchun Normal University, Changchun, 130032, China
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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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Analysis of genes encoding seed storage proteins (SSPs) in chickpea (Cicer arietinum L.) reveals co-expressing transcription factors and a seed-specific promoter. Funct Integr Genomics 2018; 19:373-390. [PMID: 30560463 DOI: 10.1007/s10142-018-0650-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 11/22/2018] [Accepted: 11/26/2018] [Indexed: 12/27/2022]
Abstract
Improvement of the quality and quantity of chickpea seed protein can be greatly facilitated by an understanding of the genic organization and the genetic architecture of the genes encoding seed storage proteins (SSPs). The aim of this study was to provide a comprehensive analysis of the chickpea SSP genes, putative co-expressing transcription factors (TFs), and to identify a seed-specific SSP gene promoter. A genome-wide identification of SSP genes in chickpea led to the identification of 21 non-redundant SSP encoding genes located on 6 chromosomes. Phylogenetic analysis grouped SSP genes into 3 subgroups where members within the same clade demonstrated similar motif composition and intron-exon organization. Tandem duplications were identified to be the major contributors to the expansion of the SSP gene family in chickpea. Co-expression analysis revealed 14 TFs having expression profiles similar to the SSP genes that included members of important TF families that are known to regulate seed development. Expression analysis of SSP genes and TFs revealed significantly higher expression in late stages of seed development as well as in high seed protein content (HPC) genotypes. In silico analysis of the promoter regions of the SSP encoding genes revealed several seed-specific cis-regulatory elements such as RY repeats, ACGT motifs, CAANTG, and GCN4. A candidate promoter was analyzed for seed specificity by generating stable transgenics in Arabidopsis. Overall, this study provides a useful resource to explore the regulatory networks involved in SSP synthesis and/or accumulation for utilization in developing nutritionally improved chickpea genotypes.
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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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Sharma N, Dang TM, Singh N, Ruzicic S, Mueller-Roeber B, Baumann U, Heuer S. Allelic variants of OsSUB1A cause differential expression of transcription factor genes in response to submergence in rice. RICE (NEW YORK, N.Y.) 2018; 11:2. [PMID: 29313187 PMCID: PMC5758481 DOI: 10.1186/s12284-017-0192-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 12/12/2017] [Indexed: 05/21/2023]
Abstract
BACKGROUND Flooding during seasonal monsoons affects millions of hectares of rice-cultivated areas across Asia. Submerged rice plants die within a week due to lack of oxygen, light and excessive elongation growth to escape the water. Submergence tolerance was first reported in an aus-type rice landrace, FR13A, and the ethylene-responsive transcription factor (TF) gene SUB1A-1 was identified as the major tolerance gene. Intolerant rice varieties generally lack the SUB1A gene but some intermediate tolerant varieties, such as IR64, carry the allelic variant SUB1A-2. Differential effects of the two alleles have so far not been addressed. As a first step, we have therefore quantified and compared the expression of nearly 2500 rice TF genes between IR64 and its derived tolerant near isogenic line IR64-Sub1, which carries the SUB1A-1 allele. Gene expression was studied in internodes, where the main difference in expression between the two alleles was previously shown. RESULTS Nineteen and twenty-six TF genes were identified that responded to submergence in IR64 and IR64-Sub1, respectively. Only one gene was found to be submergence-responsive in both, suggesting different regulatory pathways under submergence in the two genotypes. These differentially expressed genes (DEGs) mainly included MYB, NAC, TIFY and Zn-finger TFs, and most genes were downregulated upon submergence. In IR64, but not in IR64-Sub1, SUB1B and SUB1C, which are also present in the Sub1 locus, were identified as submergence responsive. Four TFs were not submergence responsive but exhibited constitutive, genotype-specific differential expression. Most of the identified submergence responsive DEGs are associated with regulatory hormonal pathways, i.e. gibberellins (GA), abscisic acid (ABA), and jasmonic acid (JA), apart from ethylene. An in-silico promoter analysis of the two genotypes revealed the presence of allele-specific single nucleotide polymorphisms, giving rise to ABRE, DRE/CRT, CARE and Site II cis-elements, which can partly explain the observed differential TF gene expression. CONCLUSION This study identified new gene targets with the potential to further enhance submergence tolerance in rice and provides insights into novel aspects of SUB1A-mediated tolerance.
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Affiliation(s)
- Niharika Sharma
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Plant Genomics Centre, Hartley Grove, Urrbrae, Adelaide, South Australia, 5064, Australia
| | - Trang Minh Dang
- International Rice Research Institute (IRRI), Los Banos, Philippines
- Intrexon Corp, California, USA
| | - Namrata Singh
- International Rice Research Institute (IRRI), Los Banos, Philippines
- Section of Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | | | | | - Ute Baumann
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Plant Genomics Centre, Hartley Grove, Urrbrae, Adelaide, South Australia, 5064, Australia
| | - Sigrid Heuer
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Plant Genomics Centre, Hartley Grove, Urrbrae, Adelaide, South Australia, 5064, Australia.
- International Rice Research Institute (IRRI), Los Banos, Philippines.
- Rothamsted Research, Plant Science Department, Hertfordshire, Harpenden, AL5 2JQ, UK.
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Kim JS, Chae S, Jun KM, Pahk YM, Lee TH, Chung PJ, Kim YK, Nahm BH. Genome-wide identification of grain filling genes regulated by the OsSMF1 transcription factor in rice. RICE (NEW YORK, N.Y.) 2017; 10:16. [PMID: 28444616 PMCID: PMC5405039 DOI: 10.1186/s12284-017-0155-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 04/13/2017] [Indexed: 05/05/2023]
Abstract
BACKGROUND Spatial- and temporal-specific expression patterns are primarily regulated at the transcriptional level by gene promoters. Therefore, it is important to identify the binding motifs of transcription factors to better understand the networks associated with embryogenesis. RESULTS Here, we used a protein-binding microarray (PBM) to identify the binding motifs of OsSMF1, which is a basic leucine zipper transcription factor involved in the regulation of rice seed maturation. OsSMF1 (previously called RISBZ1 or OsbZIP58) is known to interact with GCN4 motifs (TGA(G/C)TCA) to regulate seed storage protein synthesis, and it functions as a key regulator of starch synthesis. Quadruple 9-mer-based PBM analysis and electrophoretic mobility shift assay revealed that OsSMF1 bound to the GCN4 (TGA(G/C)TCA), ACGT (CCACGT(C/G)), and ATGA (GGATGAC) motifs with three different affinities. We predicted 44 putative OsSMF1 target genes using data obtained from both the PBM and RiceArrayNet. Among these putative target genes, 18, 21, and 13 genes contained GCN4, ACGT, and ATGA motifs within their 1-kb promoter regions, respectively. Among them, six genes encoding major grain filling proteins and transcription factors were chosen to confirm the activation of their expression in vivo. OsSMF1 was shown to bind directly to the promoters of Os03g0168500 (GCN4 motif), patatin-like gene (GCN4 motif), α-globulin (ACGT motif), rice prolamin box-binding factor (RPBF) (ATGA motif), and ONAC024 (GCN4 and ACGT motifs) and to regulate their expression. CONCLUSIONS The results of this study suggest that OsSMF1 is one of the key transcription factors that functions in a wide range of seed developmental processes with different specific binding affinities for the three DNA-binding motifs.
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Affiliation(s)
- Joung Sug Kim
- Division of Bioscience and Bioinformatics, Myongji University, Yongin, Kyonggido, 449-728, Republic of Korea
| | - Songhwa Chae
- Division of Bioscience and Bioinformatics, Myongji University, Yongin, Kyonggido, 449-728, Republic of Korea
| | - Kyong Mi Jun
- Genomics Genetics Institute, GreenGene BioTech Inc., Yongin, Kyonggido, 449-728, Republic of Korea
| | - Yoon-Mok Pahk
- Genomics Genetics Institute, GreenGene BioTech Inc., Yongin, Kyonggido, 449-728, Republic of Korea
| | - Tae-Ho Lee
- Department of Agricultural Biotechnology, National Institute of Agricultural Science, 370 Nongsaengmyeong-ro, Wansan-gu, Jeonju, North Jeolla Province, 54874, Republic of Korea
| | - Pil Joong Chung
- Crop Biotechnology Institute, GreenBio Science and Technology, Seoul National University, Pyeongchang, 25354, Republic of Korea
| | - Yeon-Ki Kim
- Division of Bioscience and Bioinformatics, Myongji University, Yongin, Kyonggido, 449-728, Republic of Korea
| | - Baek Hie Nahm
- Division of Bioscience and Bioinformatics, Myongji University, Yongin, Kyonggido, 449-728, Republic of Korea.
- Genomics Genetics Institute, GreenGene BioTech Inc., Yongin, Kyonggido, 449-728, Republic of Korea.
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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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Kim S, Lee SB, Han CS, Lim MN, Lee SE, Yoon IS, Hwang YS. Dissection of cis-regulatory element architecture of the rice oleosin gene promoters to assess abscisic acid responsiveness in suspension-cultured rice cells. JOURNAL OF PLANT PHYSIOLOGY 2017; 215:20-29. [PMID: 28527335 DOI: 10.1016/j.jplph.2017.04.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 04/26/2017] [Accepted: 04/26/2017] [Indexed: 06/07/2023]
Abstract
Oleosins are the most abundant proteins in the monolipid layer surrounding neutral storage lipids that form oil bodies in plants. Several lines of evidence indicate that they are physiologically important for the maintenance of oil body structure and for mobilization of the lipids stored inside. Rice has six oleosin genes in its genome, the expression of all of which was found to be responsive to abscisic acid (ABA) in our examination of mature embryo and aleurone tissues. The 5'-flanking region of OsOle5 was initially characterized for its responsiveness to ABA through a transient expression assay system using the protoplasts from suspension-cultured rice cells. A series of successive deletions and site-directed mutations identified five regions critical for the hormonal induction of its promoter activity. A search for cis-acting elements in these regions deposited in a public database revealed that they contain various promoter elements previously reported to be involved in the ABA response of various genes. A gain-of-function experiment indicated that multiple copies of all five regions were sufficient to provide the minimal promoter with a distinct ABA responsiveness. Comparative sequence analysis of the short, but still ABA-responsive, promoters of OsOle genes revealed no common modular architecture shared by them, indicating that various distinct promoter elements and independent trans-acting factors are involved in the ABA responsiveness of rice oleosin multigenes.
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Affiliation(s)
- Sol Kim
- Department of Systems Biotechnology, Konkuk University, Seoul 143-701, Korea
| | - Soo-Bin Lee
- Department of Systems Biotechnology, Konkuk University, Seoul 143-701, Korea
| | - Chae-Seong Han
- Department of Systems Biotechnology, Konkuk University, Seoul 143-701, Korea
| | - Mi-Na Lim
- Department of Systems Biotechnology, Konkuk University, Seoul 143-701, Korea
| | - Sung-Eun Lee
- Department of Systems Biotechnology, Konkuk University, Seoul 143-701, Korea
| | - In Sun Yoon
- Molecular Breeding Division, Natural Academy of Agricultural Science, Rural, Development Adminstration, Suwon 441-857, Korea
| | - Yong-Sic Hwang
- Department of Systems Biotechnology, Konkuk University, Seoul 143-701, Korea.
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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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Sun F, Liu X, Wei Q, Liu J, Yang T, Jia L, Wang Y, Yang G, He G. Functional Characterization of TaFUSCA3, a B3-Superfamily Transcription Factor Gene in the Wheat. FRONTIERS IN PLANT SCIENCE 2017; 8:1133. [PMID: 28702045 PMCID: PMC5487486 DOI: 10.3389/fpls.2017.01133] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 06/13/2017] [Indexed: 05/19/2023]
Abstract
The end-use quality of wheat, including its unique rheology and viscoelastic properties, is predominantly determined by the composition and concentration of gluten proteins. While, the mechanism regulating expression of the seed storage protein (SSP) genes and other related genes in wheat remains unclear. In this study, we report on the cloning and functional identification of TaFUSCA3, a B3-superfamily transcription factor (TF) gene in wheat. Sequence alignment indicated that wheat and barley FUSCA3 genes are highly conserved. Quantitative reverse-transcription (qRT)-PCR analysis showed that the transcript of TaFUSCA3 was accumulated mostly in the stamens and the endosperms of immature wheat seeds. Yeast-one-hybrid results proved that the full-length TaFUSCA3 and its C-terminal region had transcriptional activities. Yeast-two-hybrid and bimolecular fluorescence complementation assays indicated that TaFUSCA3 could activate the expression of the high molecular weight glutenin subunit gene Glu-1Bx7 and interact with the seed-specific bZIP protein TaSPA. DNA-protein-interaction enzyme-linked immunosorbent assay demonstrated that TaFUSCA3 specifically recognizes the RY-box of the Glu-1Bx7 promoter region. Transient expression results showed that TaFUSCA3 could trans-activate the Glu-1Bx7 promoter, which contains eight RY-box sequences. TaFUSCA3 was unable to activate the downstream transcription when the RY-box was fully mutated. TaFUSCA3 could activate the transcription of the At2S3 gene promoter in a complementation of loss-of-function experiment using the Arabidopsis thaliana line fus3-3, which is a FUSCA3 mutant, demonstrating the evolutionary conservation of the TaFUSCA3 gene. In conclusion, the wheat B3-type TF, TaFUSCA3, is functional conserved between monocot and dicot, and could regulate SSP gene expression by interacting specifically with TaSPA.
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Pandurangan S, Diapari M, Yin F, Munholland S, Perry GE, Chapman BP, Huang S, Sparvoli F, Bollini R, Crosby WL, Pauls KP, Marsolais F. Genomic Analysis of Storage Protein Deficiency in Genetically Related Lines of Common Bean (Phaseolus vulgaris). FRONTIERS IN PLANT SCIENCE 2016; 7:389. [PMID: 27066039 PMCID: PMC4814446 DOI: 10.3389/fpls.2016.00389] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 03/14/2016] [Indexed: 05/06/2023]
Abstract
A series of genetically related lines of common bean (Phaseolus vulgaris L.) integrate a progressive deficiency in major storage proteins, the 7S globulin phaseolin and lectins. SARC1 integrates a lectin-like protein, arcelin-1 from a wild common bean accession. SMARC1N-PN1 is deficient in major lectins, including erythroagglutinating phytohemagglutinin (PHA-E) but not α-amylase inhibitor, and incorporates also a deficiency in phaseolin. SMARC1-PN1 is intermediate and shares the phaseolin deficiency. Sanilac is the parental background. To understand the genomic basis for variations in protein profiles previously determined by proteomics, the genotypes were submitted to short-fragment genome sequencing using an Illumina HiSeq 2000/2500 platform. Reads were aligned to reference sequences and subjected to de novo assembly. The results of the analyses identified polymorphisms responsible for the lack of specific storage proteins, as well as those associated with large differences in storage protein expression. SMARC1N-PN1 lacks the lectin genes pha-E and lec4-B17, and has the pseudogene pdlec1 in place of the functional pha-L gene. While the α-phaseolin gene appears absent, an approximately 20-fold decrease in β-phaseolin accumulation is associated with a single nucleotide polymorphism converting a G-box to an ACGT motif in the proximal promoter. Among residual lectins compensating for storage protein deficiency, mannose lectin FRIL and α-amylase inhibitor 1 genes are uniquely present in SMARC1N-PN1. An approximately 50-fold increase in α-amylase inhibitor like protein accumulation is associated with multiple polymorphisms introducing up to eight potential positive cis-regulatory elements in the proximal promoter specific to SMARC1N-PN1. An approximately 7-fold increase in accumulation of 11S globulin legumin is not associated with variation in proximal promoter sequence, suggesting that the identity of individual proteins involved in proteome rebalancing might also be determined at the translational level.
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Affiliation(s)
- Sudhakar Pandurangan
- Department of Biology, University of Western Ontario, LondonON, Canada
- Genomics and Biotechnology, London Research and Development Centre, Agriculture and Agri-Food Canada, LondonON, Canada
| | - Marwan Diapari
- Genomics and Biotechnology, London Research and Development Centre, Agriculture and Agri-Food Canada, LondonON, Canada
| | - Fuqiang Yin
- Genomics and Biotechnology, London Research and Development Centre, Agriculture and Agri-Food Canada, LondonON, Canada
- Department of Bioscience and Biotechnology, School of Life Sciences, Sun Yat-sen UniversityGuangzhou, China
| | - Seth Munholland
- Department of Biological Sciences, University of Windsor, WindsorON, Canada
| | - Gregory E. Perry
- Department of Plant Agriculture, University of Guelph, GuelphON, Canada
| | - B. Patrick Chapman
- Genomics and Biotechnology, London Research and Development Centre, Agriculture and Agri-Food Canada, LondonON, Canada
| | - Shangzhi Huang
- Department of Bioscience and Biotechnology, School of Life Sciences, Sun Yat-sen UniversityGuangzhou, China
| | - Francesca Sparvoli
- Institute of Agricultural Biology and Biotechnology, National Research CouncilMilan, Italy
| | - Roberto Bollini
- Institute of Agricultural Biology and Biotechnology, National Research CouncilMilan, Italy
| | - William L. Crosby
- Department of Biological Sciences, University of Windsor, WindsorON, Canada
| | - Karl P. Pauls
- Department of Plant Agriculture, University of Guelph, GuelphON, Canada
| | - Frédéric Marsolais
- Department of Biology, University of Western Ontario, LondonON, Canada
- Genomics and Biotechnology, London Research and Development Centre, Agriculture and Agri-Food Canada, LondonON, Canada
- *Correspondence: Frédéric Marsolais,
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Mansilla N, Garcia L, Gonzalez DH, Welchen E. AtCOX10, a protein involved in haem o synthesis during cytochrome c oxidase biogenesis, is essential for plant embryogenesis and modulates the progression of senescence. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:6761-75. [PMID: 26246612 DOI: 10.1093/jxb/erv381] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Cytochrome c oxidase (CcO) biogenesis requires several accessory proteins implicated, among other processes, in copper and haem a insertion. In yeast, the farnesyltransferase Cox10p that catalyses the conversion of haem b to haem o is the limiting factor in haem a biosynthesis and is essential for haem a insertion in CcO. In this work, we characterized AtCOX10, a putative Cox10p homologue from Arabidopsis thaliana. AtCOX10 was localized in mitochondria and was able to restore growth of a yeast Δcox10 null mutant on non-fermentable carbon sources, suggesting that it also participates in haem o synthesis. Plants with T-DNA insertions in the coding region of both copies of AtCOX10 could not be recovered, and heterozygous mutant plants showed seeds with embryos arrested at early developmental stages that lacked CcO activity. Heterozygous mutant plants exhibited lower levels of CcO activity and cyanide-sensitive respiration but normal levels of total respiration at the expense of an increase in alternative respiration. AtCOX10 seems to be implicated in the onset and progression of senescence, since heterozygous mutant plants showed a faster decrease in chlorophyll content and photosynthetic performance than wild-type plants after natural and dark-induced senescence. Furthermore, complementation of mutants by expressing AtCOX10 under its own promoter allowed us to obtain plants with T-DNA insertions in both AtCOX10 copies, which showed phenotypic characteristics comparable to those of wild type. Our results highlight the relevance of haem o synthesis in plants and suggest that this process is a limiting factor that influences CcO activity levels, mitochondrial respiration, and plant senescence.
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Affiliation(s)
- Natanael Mansilla
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Centro Científico Tecnológico Santa Fe - Colectora Ruta Nacional Nº 168 Km 0, Paraje El Pozo, 3000 Santa Fe, Argentina
| | - Lucila Garcia
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Centro Científico Tecnológico Santa Fe - Colectora Ruta Nacional Nº 168 Km 0, Paraje El Pozo, 3000 Santa Fe, Argentina
| | - Daniel H Gonzalez
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Centro Científico Tecnológico Santa Fe - Colectora Ruta Nacional Nº 168 Km 0, Paraje El Pozo, 3000 Santa Fe, Argentina
| | - Elina Welchen
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Centro Científico Tecnológico Santa Fe - Colectora Ruta Nacional Nº 168 Km 0, Paraje El Pozo, 3000 Santa Fe, Argentina
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Guo W, Yang H, Liu Y, Gao Y, Ni Z, Peng H, Xin M, Hu Z, Sun Q, Yao Y. The wheat transcription factor TaGAMyb recruits histone acetyltransferase and activates the expression of a high-molecular-weight glutenin subunit gene. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 84:347-59. [PMID: 26332346 DOI: 10.1111/tpj.13003] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 08/12/2015] [Accepted: 08/25/2015] [Indexed: 05/23/2023]
Abstract
Glutenin proteins in wheat (Triticum aestivum L.) flour confer unique viscoelastic properties to dough products and, therefore, the concentration and composition of the glutenin proteins determine its end-use value. However, the mechanisms governing the glutenin gene expression remain elusive. In this study, we report that wheat TaGAMyb activates the high-molecular-weight glutenin subunit genes (TaGLU) through recruiting the histone acetyltransferase GCN5. By sequencing the promoters of TaGLU-1 genes from 40 modern wheat cultivars, we identified eight types of TaGAMyb binding motifs and verified these by electrophoretic mobility shift assays. The number of TaGAMyb binding motifs in TaGLU-1 genes is correlated with the abundance of glutenin in different cultivars. Chromatin immunoprecipitation plus polymerase chain reaction (ChIP-PCR) analysis reveals that TaGCN5 directly targets the promoters of TaGLU-1 genes in wheat endosperm. We find that TaGAMyb physically interacts with the wheat histone acetyltransferase TaGCN5 and also interacts with Arabidopsis thaliana AtGCN5. TaGAMyb ectopically expressed in Arabidopsis binds to the TaGLU-1Dy promoter on a TaGLU-1Dy transgene and activates its expression. AtGCN5 also targets the TaGLU-1Dy transgene and is involved in the establishment of acetylation at H3K9 and H3K14. These results demonstrate that TaGAMyb plays a dual role in activating expression of glutenin gene by directly binding to the TaGLU promoter and by recruiting GCN5 to modulate histone acetylation during wheat endosperm development.
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Affiliation(s)
- Weiwei Guo
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Hua Yang
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Yongqiang Liu
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Yujiao Gao
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Huiru Peng
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Mingming Xin
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Zhaorong Hu
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Yingyin Yao
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
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Tang G, Xu P, Liu W, Liu Z, Shan L. Cloning and Characterization of 5' Flanking Regulatory Sequences of AhLEC1B Gene from Arachis Hypogaea L. PLoS One 2015; 10:e0139213. [PMID: 26426444 PMCID: PMC4591277 DOI: 10.1371/journal.pone.0139213] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Accepted: 09/09/2015] [Indexed: 11/19/2022] Open
Abstract
LEAFY COTYLEDON1 (LEC1) is a B subunit of Nuclear Factor Y (NF-YB) transcription factor that mainly accumulates during embryo development. We cloned the 5' flanking regulatory sequence of AhLEC1B gene, a homolog of Arabidopsis LEC1, and analyzed its regulatory elements using online software. To identify the crucial regulatory region, we generated a series of GUS expression frameworks driven by different length promoters with 5' terminal and/or 3' terminal deletion. We further characterized the GUS expression patterns in the transgenic Arabidopsis lines. Our results show that both the 65 bp proximal promoter region and the 52 bp 5' UTR of AhLEC1B contain the key motifs required for the essential promoting activity. Moreover, AhLEC1B is preferentially expressed in the embryo and is co-regulated by binding of its upstream genes with both positive and negative corresponding cis-regulatory elements.
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Affiliation(s)
- Guiying Tang
- Bio-Tech Research Centre, Shandong Academy of Agricultural Sciences / Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, China
| | - Pingli Xu
- Bio-Tech Research Centre, Shandong Academy of Agricultural Sciences / Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, China
| | - Wei Liu
- College of Agriculture, Shandong University, Jinan, 250100, China
| | - Zhanji Liu
- Bio-Tech Research Centre, Shandong Academy of Agricultural Sciences / Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, China
| | - Lei Shan
- Bio-Tech Research Centre, Shandong Academy of Agricultural Sciences / Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, China
- College of Agriculture, Shandong University, Jinan, 250100, China
- * E-mail:
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Li Y, Liu X, Li J, Li S, Chen G, Zhou X, Yang W, Chen R. Isolation of a maize ZmCI-1B promoter and characterization of its activity in transgenic maize and tobacco. PLANT CELL REPORTS 2015; 34:1443-57. [PMID: 25941157 DOI: 10.1007/s00299-015-1799-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 04/08/2015] [Accepted: 04/19/2015] [Indexed: 06/04/2023]
Abstract
KEY MESSAGE The 2-kb ZmCI - 1B promoter is active in the root and embryo and induced by wounding in maize and the 220-bp 5'-deleted segment maybe the minimal promoter. The subtilisin-chymotrypsin inhibitor gene, CI-1B of Zea mays (ZmCI-1B), has been suggested to induce the maize defense system to resist insect attack. Real-time RT-PCR showed that ZmCI-1B gene exhibited especially high expression in roots and embryos. The 2-kb full-length promoter of ZmCI-1B gene was isolated from the maize genome and used to drive expression of a beta-glucuronidase (GUS) reporter gene for transient expression and stable expression analysis in maize. The results of GUS histochemical staining in transgenic maize plants revealed that the ZmCI-1B promoter induced GUS expression preferentially in roots and embryos and in response to wounding. A series of 5'-deleted segments of the ZmCI-1B promoter were cloned individually to drive GUS expression for further analysis. Deletion analysis combined with the histochemical staining of transgenic tobacco plants revealed 220-bp segment could drive GUS in a tissue-specific and wounding-induced expression in tobacco; thus, it maybe the minimally active promoter of ZmCI-1B gene. Furthermore, it revealed that the ZmCI-1B promoter contained tissue-specific and wounding-induced elements.
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Affiliation(s)
- Ye Li
- Department of Crop Genomics and Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 ZhongGuanCun South Street, Beijing, 100081, China
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Noma S, Kawaura K, Hayakawa K, Abe C, Tsuge N, Ogihara Y. Comprehensive molecular characterization of the α/β-gliadin multigene family in hexaploid wheat. Mol Genet Genomics 2015; 291:65-77. [DOI: 10.1007/s00438-015-1086-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 06/23/2015] [Indexed: 10/23/2022]
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Gupta S, Garg V, Bhatia S. A new set of ESTs from chickpea (Cicer arietinum L.) embryo reveals two novel F-box genes, CarF-box_PP2 and CarF-box_LysM, with potential roles in seed development. PLoS One 2015; 10:e0121100. [PMID: 25803812 PMCID: PMC4372429 DOI: 10.1371/journal.pone.0121100] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2014] [Accepted: 02/09/2015] [Indexed: 11/18/2022] Open
Abstract
Considering the economic importance of chickpea (C. arietinum L.) seeds, it is important to understand the mechanisms underlying seed development for which a cDNA library was constructed from 6 day old chickpea embryos. A total of 8,186 ESTs were obtained from which 4,048 high quality ESTs were assembled into 1,480 unigenes that majorly encoded genes involved in various metabolic and regulatory pathways. Of these, 95 ESTs were found to be involved in ubiquitination related protein degradation pathways and 12 ESTs coded specifically for putative F-box proteins. Differential transcript accumulation of these putative F-box genes was observed in chickpea tissues as evidenced by quantitative real-time PCR. Further, to explore the role of F-box proteins in chickpea seed development, two F-box genes were selected for molecular characterization. These were named as CarF-box_PP2 and CarF-box_LysM depending on their C-terminal domains, PP2 and LysM, respectively. Their highly conserved structures led us to predict their target substrates. Subcellular localization experiment revealed that CarF-box_PP2 was localized in the cytoplasm and CarF-box_LysM was localized in the nucleus. We demonstrated their physical interactions with SKP1 protein, which validated that they function as F-box proteins in the formation of SCF complexes. Sequence analysis of their promoter regions revealed certain seed specific cis-acting elements that may be regulating their preferential transcript accumulation in the seed. Overall, the study helped in expanding the EST database of chickpea, which was further used to identify two novel F-box genes having a potential role in seed development.
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Affiliation(s)
- Shefali Gupta
- National Institute of Plant Genome Research, New Delhi, India
| | - Vanika Garg
- National Institute of Plant Genome Research, New Delhi, India
| | - Sabhyata Bhatia
- National Institute of Plant Genome Research, New Delhi, India
- * E-mail:
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Pan Y, Ma X, Liang H, Zhao Q, Zhu D, Yu J. Spatial and temporal activity of the foxtail millet (Setaria italica) seed-specific promoter pF128. PLANTA 2015; 241:57-67. [PMID: 25204632 DOI: 10.1007/s00425-014-2164-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 08/22/2014] [Indexed: 05/10/2023]
Abstract
pF128 drives GUS specifically expressed in transgenic seeds of foxtail millet and Zea mays with higher activity than the constitutive CaMV35S promoter and the maize seed-specific 19Z promoter. Foxtail millet (Setaria italica), a member of the Poaceae family, is an important food and fodder crop in arid regions. Foxtail millet is an excellent C4 crop model owing to its small genome (~490 Mb), self-pollination and availability of a complete genome sequence. F128 was isolated from a cDNA library of foxtail millet immature seeds. Real-time PCR analysis revealed that F128 mRNA was specifically expressed in immature and mature seeds. The highest F128 mRNA level was observed 5 days after pollination and gradually decreased as the seed matured. Sequence analysis suggested that the protein encoded by F128 is likely a protease inhibitor/seed storage protein/lipid-transfer protein. The 1,053 bp 5' flanking sequence of F128 (pF128) was isolated and fused to the GUS reporter gene. The corresponding vector was then transformed into Arabidopsis thaliana, foxtail millet and Zea mays. GUS analysis revealed that pF128 drove GUS expression efficiently and specifically in the seeds of transgenic Arabidopsis, foxtail millet and Zea mays. GUS activity was also detected in Arabidopsis cotyledons. Activity of pF128 was higher than that observed for the constitutive CaMV35S promoter and the maize seed-specific 19 Zein (19Z) promoter. These results indicate that pF128 is a seed-specific promoter. Its application is expected to be of considerable value in plant genetic engineering.
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Affiliation(s)
- Yanlin Pan
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
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Jiang SY, Vanitha J, Bai Y, Ramachandran S. Identification and molecular characterization of tissue-preferred rice genes and their upstream regularly sequences on a genome-wide level. BMC PLANT BIOLOGY 2014; 14:331. [PMID: 25428432 PMCID: PMC4248441 DOI: 10.1186/s12870-014-0331-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Accepted: 11/11/2014] [Indexed: 05/08/2023]
Abstract
BACKGROUND Gene upstream regularly sequences (URSs) can be used as one of the tools to annotate the biological functions of corresponding genes. In addition, tissue-preferred URSs are frequently used to drive the transgene expression exclusively in targeted tissues during plant transgenesis. Although many rice URSs have been molecularly characterized, it is still necessary and valuable to identify URSs that will benefit plant transformation and aid in analyzing gene function. RESULTS In this study, we identified and characterized root-, seed-, leaf-, and panicle-preferred genes on a genome-wide level in rice. Subsequently, their expression patterns were confirmed through quantitative real-time RT-PCR (qRT-PCR) by randomly selecting 9candidate tissue-preferred genes. In addition, 5 tissue-preferred URSs were characterized by investigating the URS::GUS transgenic plants. Of these URS::GUS analyses, the transgenic plants harboring LOC_Os03g11350 URS::GUS construct showed the GUS activity only in young pollen. In contrast, when LOC_Os10g22450 URS was used to drive the reporter GUS gene, the GUS activity was detected only in mature pollen. Interestingly, the LOC_Os10g34360 URS was found to be vascular bundle preferred and its activities were restricted only to vascular bundles of leaves, roots and florets. In addition, we have also identified two URSs from genes LOC_Os02G15090 and LOC_Os06g31070 expressed in a seed-preferred manner showing the highest expression levels of GUS activities in mature seeds. CONCLUSION By genome-wide analysis, we have identified tissue-preferred URSs, five of which were further characterized using transgenic plants harboring URS::GUS constructs. These data might provide some evidence for possible functions of the genes and be a valuable resource for tissue-preferred candidate URSs for plant transgenesis.
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Affiliation(s)
- Shu-Ye Jiang
- Rice Functional Genomics Group, Temasek Life Sciences Laboratory, National University of Singapore, Singapore, 117604 Singapore
| | - Jeevanandam Vanitha
- Rice Functional Genomics Group, Temasek Life Sciences Laboratory, National University of Singapore, Singapore, 117604 Singapore
| | - Yanan Bai
- Rice Functional Genomics Group, Temasek Life Sciences Laboratory, National University of Singapore, Singapore, 117604 Singapore
| | - Srinivasan Ramachandran
- Rice Functional Genomics Group, Temasek Life Sciences Laboratory, National University of Singapore, Singapore, 117604 Singapore
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Ravel C, Fiquet S, Boudet J, Dardevet M, Vincent J, Merlino M, Michard R, Martre P. Conserved cis-regulatory modules in promoters of genes encoding wheat high-molecular-weight glutenin subunits. FRONTIERS IN PLANT SCIENCE 2014; 5:621. [PMID: 25429295 PMCID: PMC4228979 DOI: 10.3389/fpls.2014.00621] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 10/21/2014] [Indexed: 05/19/2023]
Abstract
The concentration and composition of the gliadin and glutenin seed storage proteins (SSPs) in wheat flour are the most important determinants of its end-use value. In cereals, the synthesis of SSPs is predominantly regulated at the transcriptional level by a complex network involving at least five cis-elements in gene promoters. The high-molecular-weight glutenin subunits (HMW-GS) are encoded by two tightly linked genes located on the long arms of group 1 chromosomes. Here, we sequenced and annotated the HMW-GS gene promoters of 22 electrophoretic wheat alleles to identify putative cis-regulatory motifs. We focused on 24 motifs known to be involved in SSP gene regulation. Most of them were identified in at least one HMW-GS gene promoter sequence. A common regulatory framework was observed in all the HMW-GS gene promoters, as they shared conserved cis-regulatory modules (CCRMs) including all the five motifs known to regulate the transcription of SSP genes. This common regulatory framework comprises a composite box made of the GATA motifs and GCN4-like Motifs (GLMs) and was shown to be functional as the GLMs are able to bind a bZIP transcriptional factor SPA (Storage Protein Activator). In addition to this regulatory framework, each HMW-GS gene promoter had additional motifs organized differently. The promoters of most highly expressed x-type HMW-GS genes contain an additional box predicted to bind R2R3-MYB transcriptional factors. However, the differences in annotation between promoter alleles could not be related to their level of expression. In summary, we identified a common modular organization of HMW-GS gene promoters but the lack of correlation between the cis-motifs of each HMW-GS gene promoter and their level of expression suggests that other cis-elements or other mechanisms regulate HMW-GS gene expression.
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Affiliation(s)
- Catherine Ravel
- Institut National de la Recherche Agronomique, UMR1095, Genetics, Diversity and Ecophysiology of Cereals Clermont-Ferrand, France ; UMR1095, Genetics, Diversity and Ecophysiology of Cereals, Department of Biology, Blaise Pascal University Aubière, France
| | - Samuel Fiquet
- Institut National de la Recherche Agronomique, UMR1095, Genetics, Diversity and Ecophysiology of Cereals Clermont-Ferrand, France ; UMR1095, Genetics, Diversity and Ecophysiology of Cereals, Department of Biology, Blaise Pascal University Aubière, France
| | - Julie Boudet
- Institut National de la Recherche Agronomique, UMR1095, Genetics, Diversity and Ecophysiology of Cereals Clermont-Ferrand, France ; UMR1095, Genetics, Diversity and Ecophysiology of Cereals, Department of Biology, Blaise Pascal University Aubière, France
| | - Mireille Dardevet
- Institut National de la Recherche Agronomique, UMR1095, Genetics, Diversity and Ecophysiology of Cereals Clermont-Ferrand, France ; UMR1095, Genetics, Diversity and Ecophysiology of Cereals, Department of Biology, Blaise Pascal University Aubière, France
| | - Jonathan Vincent
- Institut National de la Recherche Agronomique, UMR1095, Genetics, Diversity and Ecophysiology of Cereals Clermont-Ferrand, France ; UMR1095, Genetics, Diversity and Ecophysiology of Cereals, Department of Biology, Blaise Pascal University Aubière, France
| | - Marielle Merlino
- Institut National de la Recherche Agronomique, UMR1095, Genetics, Diversity and Ecophysiology of Cereals Clermont-Ferrand, France ; UMR1095, Genetics, Diversity and Ecophysiology of Cereals, Department of Biology, Blaise Pascal University Aubière, France
| | - Robin Michard
- Institut National de la Recherche Agronomique, UMR1095, Genetics, Diversity and Ecophysiology of Cereals Clermont-Ferrand, France ; UMR1095, Genetics, Diversity and Ecophysiology of Cereals, Department of Biology, Blaise Pascal University Aubière, France
| | - Pierre Martre
- Institut National de la Recherche Agronomique, UMR1095, Genetics, Diversity and Ecophysiology of Cereals Clermont-Ferrand, France ; UMR1095, Genetics, Diversity and Ecophysiology of Cereals, Department of Biology, Blaise Pascal University Aubière, France
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Zhang Y, Yang S, Song Y, Wang J. Genome-wide characterization, expression and functional analysis of CLV3/ESR gene family in tomato. BMC Genomics 2014; 15:827. [PMID: 25266499 PMCID: PMC4195864 DOI: 10.1186/1471-2164-15-827] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 09/23/2014] [Indexed: 11/29/2022] Open
Abstract
Background By encoding a group of small secretory peptides, the members of the CLAVATA3/EMBRYO-SURROUNDING REGION (CLE) family play important roles in cell-to-cell communication to control the balance between stem cell proliferation and differentiation in plant development. Despite recent identification and characterization of members of this gene family in several plant species, little is known about its functional role in plants with fleshy fruits. Results In total, fifteen CLE genes (SlCLE1-15) were identified from tomato (Solanum lycopersicum cv. ‘Heinz-1706’) genome and their multiple characters including phylogeny, gene structures, chromosome locations, conserved motifs and cis-elements in the promoter sequences, were analyzed. Real-time PCR analysis showed that 13 out of 15 identified SlCLE genes are transcribed and exhibit remarkably unique expression patterns among tissues and organs. In particular, SlCLE12, the homologue of Arabidopsis CLE41/44 gene, appears to be the dominant CLE gene in most of tested tissues with its maximum expression found in vascular tissues. Meanwhile, SlCLE1, 10, 13 exhibit specific but distinct expression in flower bud, root and shoot apex, respectively. More notably, several SlCLEs are dramatically regulated in their transcriptional levels during fruit development and ripening, indicating significant role these genes may potentially play in the critical physiological process. Upon the treatment with synthetic peptides corresponding to the 12-aa CLE domains of SlCLE 10, 12 and 13, tomato seedlings exhibit a clear reduction in root length to varying degrees. Conclusions This study provides a comprehensive genomic analysis of CLE gene family in tomato, a crop species with fleshy fruit. Differential expression patterns of various SlCLEs provide important insights into the functional divergence of CLE signaling cascade in Solanaceae species, especially their potential involvements in the regulation of fruit development and ripening. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-827) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | - Jiehua Wang
- School of Environmental Science and Engineering, Tianjin University, Weijin Rd, 92#, Nankai District, Tianjin 300072, China.
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50
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Yin G, Xu H, Liu J, Gao C, Sun J, Yan Y, Hu Y. Screening and identification of soybean seed-specific genes by using integrated bioinformatics of digital differential display, microarray, and RNA-seq data. Gene 2014; 546:177-86. [PMID: 24929124 DOI: 10.1016/j.gene.2014.06.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 05/16/2014] [Accepted: 06/10/2014] [Indexed: 01/09/2023]
Abstract
Soybean is one of the most economically important crops in the world. Soybean seeds have abundant protein and lipid content and very high economic value. In this study, a total of 184 seed-specific genes were obtained using online microarray databases, DDD, and RNA-seq data. The reported seed-specific genes in soybean and the 184 seed-specific genes analyzed in this paper were compared. Of the screened genes, 26 were common to both previous reports and the current screening. Meanwhile, 90 of the 184 genes have homologous counterparts in Arabidopsis, among which 24 have seed-specific expression, as indicated by microarray data for Arabidopsis. Furthermore, promoter analysis showed that almost all seed-specific genes contain at least one seed specific-related element. Seed-specific element Skn-1 motif exists in most, if not all, of the seed-specific genes screened. Five genes were randomly selected from 184 soybean seed specific gene pool and their expressions were quantified using quantitative real time polymerase chain reaction (qRT-PCR) to further confirm the specificity of the screened genes. The results indicated that all five genes showed seed-specific expression. Moreover, the identification of genes with seed-specific expression screened in this study provides information valuable to the in-depth study of soybean.
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Affiliation(s)
- Guangjun Yin
- College of Life Sciences, Capital Normal University, Beijing 100048, China.
| | - Hongliang Xu
- Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Jingyi Liu
- College of Life Sciences, Capital Normal University, Beijing 100048, China.
| | - Cong Gao
- College of Life Sciences, Capital Normal University, Beijing 100048, China.
| | - Jinyue Sun
- Plant Biotechnology Institute, National Research Council Canada, Saskatoon S7N 0W9, Canada.
| | - Yueming Yan
- College of Life Sciences, Capital Normal University, Beijing 100048, China.
| | - Yingkao Hu
- College of Life Sciences, Capital Normal University, Beijing 100048, China.
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