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Chen L, Chen K, Xi X, Du X, Zou X, Ma Y, Song Y, Luo C, Weining S. The Evolution, Expression Patterns, and Domestication Selection Analysis of the Annexin Gene Family in the Barley Pan-Genome. Int J Mol Sci 2024; 25:3883. [PMID: 38612691 PMCID: PMC11011394 DOI: 10.3390/ijms25073883] [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: 02/22/2024] [Revised: 03/24/2024] [Accepted: 03/28/2024] [Indexed: 04/14/2024] Open
Abstract
Plant annexins constitute a conserved protein family that plays crucial roles in regulating plant growth and development, as well as in responses to both biotic and abiotic stresses. In this study, a total of 144 annexin genes were identified in the barley pan-genome, comprising 12 reference genomes, including cultivated barley, landraces, and wild barley. Their chromosomal locations, physical-chemical characteristics, gene structures, conserved domains, and subcellular localizations were systematically analyzed to reveal the certain differences between wild and cultivated populations. Through a cis-acting element analysis, co-expression network, and large-scale transcriptome analysis, their involvement in growth, development, and responses to various stressors was highlighted. It is worth noting that HvMOREXann5 is only expressed in pistils and anthers, indicating its crucial role in reproductive development. Based on the resequencing data from 282 barley accessions worldwide, genetic variations in thefamily were investigated, and the results showed that 5 out of the 12 identified HvMOREXanns were affected by selection pressure. Genetic diversity and haplotype frequency showed notable reductions between wild and domesticated barley, suggesting that a genetic bottleneck occurred on the annexin family during the barley domestication process. Finally, qRT-PCR analysis confirmed the up-regulation of HvMOREXann7 under drought stress, along with significant differences between wild accessions and varieties. This study provides some insights into the genome organization and genetic characteristics of the annexin gene family in barley at the pan-genome level, which will contribute to better understanding its evolution and function in barley and other crops.
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Affiliation(s)
- Liqin Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F Univesity, Xianyang 712100, China; (L.C.); (K.C.); (X.X.)
| | - Kunxiang Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F Univesity, Xianyang 712100, China; (L.C.); (K.C.); (X.X.)
| | - Xi Xi
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F Univesity, Xianyang 712100, China; (L.C.); (K.C.); (X.X.)
| | - Xianghong Du
- College of Agronomy, Northwest A&F University, Xianyang 712100, China; (X.D.); (X.Z.)
| | - Xinyi Zou
- College of Agronomy, Northwest A&F University, Xianyang 712100, China; (X.D.); (X.Z.)
| | - Yujia Ma
- College of Landscape Architecture and Art, Northwest A&F University, Xianyang 712100, China;
| | - Yingying Song
- College of Plant Protection, Northwest A&F University, Xianyang 712100, China;
| | - Changquan Luo
- College of Life Sciences, Northwest A&F University, Xianyang 712100, China;
| | - Song Weining
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F Univesity, Xianyang 712100, China; (L.C.); (K.C.); (X.X.)
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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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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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Dhatterwal P, Mehrotra S, Miller AJ, Mehrotra R. Promoter profiling of Arabidopsis amino acid transporters: clues for improving crops. PLANT MOLECULAR BIOLOGY 2021; 107:451-475. [PMID: 34674117 DOI: 10.1007/s11103-021-01193-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 09/16/2021] [Indexed: 06/13/2023]
Abstract
The review describes the importance of amino acid transporters in plant growth, development, stress tolerance, and productivity. The promoter analysis provides valuable insights into their functionality leading to agricultural benefits. Arabidopsis thaliana genome is speculated to possess more than 100 amino acid transporter genes. This large number suggests the functional significance of amino acid transporters in plant growth and development. The current article summarizes the substrate specificity, cellular localization, tissue-specific expression, and expression of the amino acid transporter genes in response to environmental cues. However, till date functionality of a majority of amino acid transporter genes in plant development and stress tolerance is unexplored. Considering, that gene expression is mainly regulated by the regulatory motifs localized in their promoter regions at the transcriptional levels. The promoter regions ( ~ 1-kbp) of these amino acid transporter genes were analysed for the presence of cis-regulatory motifs responsive to developmental and external cues. This analysis can help predict the functionality of known and unexplored amino acid transporters in different tissues, organs, and various growth and development stages and responses to external stimuli. Furthermore, based on the promoter analysis and utilizing the microarray expression data we have attempted to identify plausible candidates (listed below) that might be targeted for agricultural benefits.
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Affiliation(s)
- Pinky Dhatterwal
- Department of Biological Sciences, Birla Institute of Technology & Science Pilani, K.K. Birla Goa Campus, Goa, India
| | - Sandhya Mehrotra
- Department of Biological Sciences, Birla Institute of Technology & Science Pilani, K.K. Birla Goa Campus, Goa, India
| | - Anthony J Miller
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Rajesh Mehrotra
- Department of Biological Sciences, Birla Institute of Technology & Science Pilani, K.K. Birla Goa Campus, Goa, India.
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Islam K, Rawoof A, Ahmad I, Dubey M, Momo J, Ramchiary N. Capsicum chinense MYB Transcription Factor Genes: Identification, Expression Analysis, and Their Conservation and Diversification With Other Solanaceae Genomes. FRONTIERS IN PLANT SCIENCE 2021; 12:721265. [PMID: 34721453 PMCID: PMC8548648 DOI: 10.3389/fpls.2021.721265] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 09/08/2021] [Indexed: 05/27/2023]
Abstract
Myeloblastosis (MYB) genes are important transcriptional regulators of plant growth, development, and secondary metabolic biosynthesis pathways, such as capsaicinoid biosynthesis in Capsicum. Although MYB genes have been identified in Capsicum annuum, no comprehensive study has been conducted on other Capsicum species. We identified a total of 251 and 240 MYB encoding genes in Capsicum chinense MYBs (CcMYBs) and Capsicum baccatum MYBs (CbMYBs). The observation of twenty tandem and 41 segmental duplication events indicated expansion of the MYB gene family in the C. chinense genome. Five CcMYB genes, i.e., CcMYB101, CcMYB46, CcMYB6, CcPHR8, and CcRVE5, and two CaMYBs, i.e., CaMYB3 and CaHHO1, were found within the previously reported capsaicinoid biosynthesis quantitative trait loci. Based on phylogenetic analysis with tomato MYB proteins, the Capsicum MYBs were classified into 24 subgroups supported by conserved amino acid motifs and gene structures. Also, a total of 241 CcMYBs were homologous with 225 C. annuum, 213 C. baccatum, 125 potato, 79 tomato, and 23 Arabidopsis MYBs. Synteny analysis showed that all 251 CcMYBs were collinear with C. annuum, C. baccatum, tomato, potato, and Arabidopsis MYBs spanning over 717 conserved syntenic segments. Using transcriptome data from three fruit developmental stages, a total of 54 CcMYBs and 81 CaMYBs showed significant differential expression patterns. Furthermore, the expression of 24 CcMYBs from the transcriptome data was validated by quantitative real-time (qRT) PCR analysis. Eight out of the 24 CcMYBs validated by the qRT-PCR were highly expressed in fiery hot C. chinense than in the lowly pungent C. annuum. Furthermore, the co-expression analysis revealed several MYB genes clustered with genes from the capsaicinoid, anthocyanin, phenylpropanoid, carotenoid, and flavonoids biosynthesis pathways, and related to determining fruit shape and size. The homology modeling of 126 R2R3 CcMYBs showed high similarity with that of the Arabidopsis R2R3 MYB domain template, suggesting their potential functional similarity at the proteome level. Furthermore, we have identified simple sequence repeat (SSR) motifs in the CcMYB genes, which could be used in Capsicum breeding programs. The functional roles of the identified CcMYBs could be studied further so that they can be manipulated for Capsicum trait improvement.
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Affiliation(s)
- Khushbu Islam
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Abdul Rawoof
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Ilyas Ahmad
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Meenakshi Dubey
- Department of Biotechnology, Delhi Technological University, New Delhi, India
| | - John Momo
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Nirala Ramchiary
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
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Arya H, Singh MB, Bhalla PL. Overexpression of
PIF4
affects plant morphology and accelerates reproductive phase transitions in soybean. Food Energy Secur 2021. [DOI: 10.1002/fes3.291] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Affiliation(s)
- Hina Arya
- Plant Molecular Biology and Biotechnology Laboratory School of Agriculture and Food Faculty of Veterinary and Agricultural Sciences The University of Melbourne Victoria Australia
| | - Mohan B. Singh
- Plant Molecular Biology and Biotechnology Laboratory School of Agriculture and Food Faculty of Veterinary and Agricultural Sciences The University of Melbourne Victoria Australia
| | - Prem L. Bhalla
- Plant Molecular Biology and Biotechnology Laboratory School of Agriculture and Food Faculty of Veterinary and Agricultural Sciences The University of Melbourne Victoria Australia
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7
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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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Kaur A, Pati PK, Pati AM, Nagpal AK. In-silico analysis of cis-acting regulatory elements of pathogenesis-related proteins of Arabidopsis thaliana and Oryza sativa. PLoS One 2017; 12:e0184523. [PMID: 28910327 PMCID: PMC5598985 DOI: 10.1371/journal.pone.0184523] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 08/27/2017] [Indexed: 01/24/2023] Open
Abstract
Pathogenesis related (PR) proteins are low molecular weight family of proteins induced in plants under various biotic and abiotic stresses. They play an important role in plant-defense mechanism. PRs have wide range of functions, acting as hydrolases, peroxidases, chitinases, anti-fungal, protease inhibitors etc. In the present study, an attempt has been made to analyze promoter regions of PR1, PR2, PR5, PR9, PR10 and PR12 of Arabidopsis thaliana and Oryza sativa. Analysis of cis-element distribution revealed the functional multiplicity of PRs and provides insight into the gene regulation. CpG islands are observed only in rice PRs, which indicates that monocot genome contains more GC rich motifs than dicots. Tandem repeats were also observed in 5' UTR of PR genes. Thus, the present study provides an understanding of regulation of PR genes and their versatile roles in plants.
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Affiliation(s)
- Amritpreet Kaur
- Department of Botanical and Environmental sciences, Guru Nanak Dev University, Amritsar, Punjab, India
| | - Pratap Kumar Pati
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, Punjab, India
| | - Aparna Maitra Pati
- Planning Project Monitoring and Evaluation Cell, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Avinash Kaur Nagpal
- Department of Botanical and Environmental sciences, Guru Nanak Dev University, Amritsar, Punjab, India
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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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10
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Chen Y, Sun A, Wang M, Zhu Z, Ouwerkerk PBF. Functions of the CCCH type zinc finger protein OsGZF1 in regulation of the seed storage protein GluB-1 from rice. PLANT MOLECULAR BIOLOGY 2014; 84:621-34. [PMID: 24282069 DOI: 10.1007/s11103-013-0158-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Accepted: 11/20/2013] [Indexed: 05/19/2023]
Abstract
Glutelins are the most abundant storage proteins in rice grain and can make up to 80 % of total protein content. The promoter region of GluB-1, one of the glutelin genes in rice, has been intensively used as a model to understand regulation of seed-storage protein accumulation. In this study, we describe a zinc finger gene of the Cys3His1 (CCCH or C3H) class, named OsGZF1, which was identified in a yeast one-hybrid screening using the core promoter region of GluB-1 as bait and cDNA expression libraries prepared from developing rice panicles and grains as prey. The OsGZF1 protein binds specifically to the bait sequence in yeast and this interaction was confirmed in vitro. OsGZF1 is predominantly expressed in a confined domain surrounding the scutellum of the developing embryo and is localised in the nucleus. Transient expression experiments demonstrated that OsGZF1 can down-regulate a GluB-1-GUS (β-glucuronidase) reporter and OsGZF1 was also able to significantly reduce activation conferred by RISBZ1 which is a known strong GluB-1 activator. Furthermore, down-regulation of OsGZF1 by an RNAi approach increased grain nitrogen concentration. We propose that OsGZF1 has a function in regulating the GluB-1 promoter and controls accumulation of glutelins during grain development.
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Affiliation(s)
- Yi Chen
- Sylvius Laboratory, Institute of Biology (IBL), Leiden University, Sylviusweg 72, 2333 BE, PO Box 9505, 2300 RA, Leiden, The Netherlands
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11
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Sunkara S, Bhatnagar-Mathur P, Sharma KK. Isolation and functional characterization of a novel seed-specific promoter region from peanut. Appl Biochem Biotechnol 2014; 172:325-39. [PMID: 24078220 DOI: 10.1007/s12010-013-0482-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2013] [Accepted: 08/26/2013] [Indexed: 10/26/2022]
Abstract
The importance of using tissue-specific promoters in the genetic transformation of plants has been emphasized increasingly. Here, we report the isolation of a novel seed-specific promoter region from peanut and its validation in Arabidopsis and tobacco seeds. The reported promoter region referred to as groundnut seed promoter (GSP) confers seed-specific expression in heterologous systems, which include putative promoter regions of the peanut (Arachis hypogaea L.) gene 8A4R19G1. This region was isolated, sequenced, and characterized using gel shift assays. Tobacco transgenics obtained using binary vectors carrying uidA reporter gene driven by GSP and/or cauliflower mosaic virus 35S promoters were confirmed through polymerase chain reaction (PCR), RT-PCR, and computational analysis of motifs which revealed the presence of TATA, CAAT boxes, and ATG signals. This seed-specific promoter region successfully targeted the reporter uidA gene to seed tissues in both Arabidopsis and tobacco model systems, where its expression was confirmed by histochemical analysis of the transgenic seeds. This promoter region is routinely being used in the genetic engineering studies in legumes aimed at targeting novel transgenes to the seeds, especially those involved in micronutrient enhancement, fungal resistance, and molecular pharming.
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Nie DM, Ouyang YD, Wang X, Zhou W, Hu CG, Yao J. Genome-wide analysis of endosperm-specific genes in rice. Gene 2013; 530:236-47. [PMID: 23948082 DOI: 10.1016/j.gene.2013.07.088] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Revised: 07/24/2013] [Accepted: 07/26/2013] [Indexed: 12/31/2022]
Abstract
The endosperm of the cereal crop is an important nutrient source for humans. It also acts as a critical integrator of plant seed growth and development. Despite its importance, the comprehensive understanding in regulating of endosperm development in rice remains elusive. Here, we performed a genomic survey comprising the identification and functional characterization of the endosperm-specific genes (OsEnS) in rice using Affymetrix microarray data and Gene Ontology (GO) analysis. A total of 151 endosperm-specific genes were identified, and the expression patterns of 13 selected genes were confirmed by qRT-PCR analysis. Promoter regions of the endosperm-specific expression genes were analyzed by PLACE Signal Scan Search. The results indicated that some motifs were involved in endosperm-specific expression regulation, and some cis-elements were responsible for hormone regulation. The bootstrap analysis indicated that the RY repeat (CATGCA box) was over-represented in promoter regions of endosperm-specific expression genes. GO analysis indicated that these genes could be classified into 12 groups, namely, transcription factor, stress/defense, seed storage protein (SSP), carbohydrate and energy metabolism, seed maturation, protein metabolism, lipid metabolism, transport, cell wall related, hormone related, signal transduction, and one unclassified group. Taken together, our results provide informative clues for further functional characterization of the endosperm-specific genes, which facilitate the understanding of the molecular mechanism in rice endosperm development.
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Affiliation(s)
- Dong-Ming Nie
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
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13
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Hurkman WJ, Tanaka CK, Vensel WH, Thilmony R, Altenbach SB. Comparative proteomic analysis of the effect of temperature and fertilizer on gliadin and glutenin accumulation in the developing endosperm and flour from Triticum aestivum L. cv. Butte 86. Proteome Sci 2013; 11:8. [PMID: 23432757 PMCID: PMC3599944 DOI: 10.1186/1477-5956-11-8] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Accepted: 01/31/2013] [Indexed: 12/04/2022] Open
Abstract
Background Flour quality is largely determined by the gluten proteins, a complex mixture of proteins consisting of high molecular weight-glutenin subunits (HMW-GS), low molecular weight-glutenin subunits (LMW-GS), and α-, γ-, and ω-gliadins. Detailed proteomic analyses of the effects of fertilizer and high temperature on individual gliadin and glutenin protein levels are needed to determine how these environmental factors influence flour quality. Results Wheat plants (Triticum aestivum L. cv. Butte 86) were grown in greenhouses under moderate and high temperature regimens with and without post-anthesis fertilizer. Quantitative two-dimensional gel electrophoresis was used to construct accumulation profiles in developing endosperm for the entire complement of gluten proteins identified previously by tandem mass spectrometry. Amounts of individual gliadins and glutenins were also determined in flour produced under each of the regimens. Under all environmental regimens, most HMW-GS, LMW-GS, γ- and ω-gliadins accumulated rapidly during early stages of grain development and leveled off during middle stages of development. A subset of LMW-GS showed a second distinct profile, accumulating throughout development, while α-gliadins showed a variety of accumulation profiles. In flour, fourteen distinct gluten proteins responded similarly to fertilizer, high temperature, and high temperature plus fertilizer. The majority of HMW-GS and ω-gliadins and some α-gliadins increased while two LMW-GS and a minor γ-gliadin decreased. Fertilizer did not influence gluten protein accumulation under high temperature conditions. Additionally, the effects of fertilizer and high temperature were not additive; very few changes were observed when plants that received fertilizer were subjected to high temperature. Conclusions Although post-anthesis temperature and fertilizer have very different effects on grain development and yield, the two treatments elicit surprisingly similar effects on the accumulation of gluten proteins. The similarity of the responses to the different treatments is likely due to source-sink activities of nitrogen reserves in the wheat plant. Because each protein that showed a response in this study is linked to a gene sequence, the work sets the stage for transgenic studies that will better elucidate the roles of specific proteins in flour quality and in the response to the environment.
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Affiliation(s)
- William J Hurkman
- U,S, Department of Agriculture, Agricultural Research Service, Western Regional Research Center, 800 Buchanan St, Albany, CA, 94710, USA.
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14
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Chen Y, Wang M, Ouwerkerk PBF. Molecular and environmental factors determining grain quality in rice. Food Energy Secur 2012. [DOI: 10.1002/fes3.11] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Affiliation(s)
- Yi Chen
- Sylvius Laboratory Department of Molecular and Developmental Genetics Institute of Biology Leiden University Sylviusweg 72 PO Box 9505 2300 RA Leiden The Netherlands
| | - Mei Wang
- Sylvius Laboratory Department of Molecular and Developmental Genetics Institute of Biology Leiden University Sylviusweg 72 PO Box 9505 2300 RA Leiden The Netherlands
- SU BioMedicine‐TNO Utrechtseweg 48 3704 HE Zeist PO Box 360 3700 AJ Zeist The Netherlands
| | - Pieter B. F. Ouwerkerk
- Sylvius Laboratory Department of Molecular and Developmental Genetics Institute of Biology Leiden University Sylviusweg 72 PO Box 9505 2300 RA Leiden The Netherlands
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Juhász A, Makai S, Sebestyén E, Tamás L, Balázs E. Role of conserved non-coding regulatory elements in LMW glutenin gene expression. PLoS One 2011; 6:e29501. [PMID: 22242127 PMCID: PMC3248431 DOI: 10.1371/journal.pone.0029501] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Accepted: 11/29/2011] [Indexed: 02/02/2023] Open
Abstract
Transcriptional regulation of LMW glutenin genes were investigated in-silico, using publicly available gene sequences and expression data. Genes were grouped into different LMW glutenin types and their promoter profiles were determined using cis-acting regulatory elements databases and published results. The various cis-acting elements belong to some conserved non-coding regulatory regions (CREs) and might act in two different ways. There are elements, such as GCN4 motifs found in the long endosperm box that could serve as key factors in tissue-specific expression. Some other elements, such as the AACA/TA motifs or the individual prolamin box variants, might modulate the level of expression. Based on the promoter sequences and expression characteristic LMW glutenin genes might be transcribed following two different mechanisms. Most of the s- and i-type genes show a continuously increasing expression pattern. The m-type genes, however, demonstrate normal distribution in their expression profiles. Differences observed in their expression could be related to the differences found in their promoter sequences. Polymorphisms in the number and combination of cis-acting elements in their promoter regions can be of crucial importance in the diverse levels of production of single LMW glutenin gene types.
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Affiliation(s)
- Angéla Juhász
- Applied Genomics Department, Agricultural Research Institute of the Hungarian Academy of Sciences, Martonvásár, Hungary.
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16
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Zavallo D, Lopez Bilbao M, Hopp HE, Heinz R. Isolation and functional characterization of two novel seed-specific promoters from sunflower (Helianthus annuus L.). PLANT CELL REPORTS 2010; 29:239-48. [PMID: 20084514 DOI: 10.1007/s00299-010-0816-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2009] [Revised: 12/26/2009] [Accepted: 01/02/2010] [Indexed: 05/14/2023]
Abstract
The promoter region of two sunflower (Helianthus annuus L. HA89 genotype) seed specifically expressed genes, coding for an oleate desaturase (HaFAD2-1) and a lipid transfer protein (HaAP10), were cloned and in silico characterized. The isolated fragments are 867 and 964 bp long, respectively, and contain several seed-specific motifs, such as AACA motif, ACGT element, E-Boxes, SEF binding sites and GCN4 motif. Functional analysis of these promoters in transgenic Arabidopsis plants was investigated after fusing them with the beta-glucuronidase (GUS) reporter gene. None of the promoters triggered GUS activity in any vegetative tissue, with the exception of early seedling cotyledons. HaFAD2-1 and HaAP10 promoters were tested along seed development from globular stage to mature seeds. GUS staining was restricted to embryonic tissue and quantitative fluorometric assays showed high activity values at the later stages of development. In this work we demonstrate that HaFAD2-1 promoter is as strong as 35S promoter even though it is a tissue-specific promoter and its activity derived just from the embryo, thus confirming that it can be considered a strong highly specific seed promoter useful for biotechnology applications.
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Affiliation(s)
- Diego Zavallo
- Instituto de Biotecnología, CNIA, Instituto Nacional de Tecnología Agropecuaria-Castelar, Los Reseros y Nicolas Repeto, 1686 Hurlingham, Buenos Aires Province, Argentina.
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17
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Ravel C, Martre P, Romeuf I, Dardevet M, El-Malki R, Bordes J, Duchateau N, Brunel D, Balfourier F, Charmet G. Nucleotide polymorphism in the wheat transcriptional activator Spa influences its pattern of expression and has pleiotropic effects on grain protein composition, dough viscoelasticity, and grain hardness. PLANT PHYSIOLOGY 2009; 151:2133-44. [PMID: 19828671 PMCID: PMC2785959 DOI: 10.1104/pp.109.146076] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2009] [Accepted: 10/10/2009] [Indexed: 05/19/2023]
Abstract
Storage protein activator (SPA) is a key regulator of the transcription of wheat (Triticum aestivum) grain storage protein genes and belongs to the Opaque2 transcription factor subfamily. We analyzed the sequence polymorphism of the three homoeologous Spa genes in hexaploid wheat. The level of polymorphism in these genes was high particularly in the promoter. The deduced protein sequences of each homoeolog and haplotype show greater than 93% identity. Two major haplotypes were studied for each Spa gene. The three Spa homoeologs have similar patterns of expression during grain development, with a peak in expression around 300 degree days after anthesis. On average, Spa-B is 10 and seven times more strongly expressed than Spa-A and Spa-D, respectively. The haplotypes are associated with significant quantitative differences in Spa expression, especially for Spa-A and Spa-D. Significant differences were found in the quantity of total grain nitrogen allocated to the gliadin protein fractions for the Spa-A haplotypes, whereas the synthesis of glutenins is not modified. Genetic association analysis between Spa and dough viscoelasticity revealed that Spa polymorphisms are associated with dough tenacity, extensibility, and strength. Except for Spa-A, these associations can be explained by differences in grain hardness. No association was found between Spa markers and the average single grain dry mass or grain protein concentration. These results demonstrate that in planta Spa is involved in the regulation of grain storage protein synthesis. The associations between Spa and dough viscoelasticity and grain hardness strongly suggest that Spa has complex pleiotropic functions during grain development.
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Affiliation(s)
- Catherine Ravel
- INRA, UMR1095, Genetics, Diversity, and Ecophysiology of Cereals, F-63100 Clermont-Ferrand, France.
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18
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Hu XW, Liu SX, Guo JC, Li JT, Duan RJ, Fu SP. Embryo and anther regulation of the mabinlin II sweet protein gene in Capparis masaikai Lévl. Funct Integr Genomics 2009; 9:351-61. [PMID: 19266222 DOI: 10.1007/s10142-009-0117-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2008] [Revised: 02/05/2009] [Accepted: 02/13/2009] [Indexed: 11/26/2022]
Abstract
Mabinlin II is one of the major sweet proteins stored in the seeds of Capparis masaikai Lévl. Its promoter region (779 bp) located 5' upstream of the mabinlin II gene has been isolated and named as MBL-779 (GenBank accession number, EU014073). This promoter contains two typical TATA box regions and a series of motifs related to seed-specific promoters, such as ACGT motifs, RY motif, napin motif, and G box. The MBL-779 promoter drove GUS gene to transiently express in the embryos of bean, maize, and rice seeds or to constantly express in the embryos and anthers of the transgenic Arabidopsis. The MBL-779 promoter regulated gene expression from approximately the 12th day and peaked on approximately the 16th day after flowering in Arabidopsis. The -300-bp promoter region is a minimal sequence required to functionally regulate gene expression. The CAATs at -325 to -322 bp and -419 to -416 bp and the region at -485 to -770 bp play a role in the quantitative regulation of gene expression. The RY motif, CATGAC, at -117 to -112 bp and the ACGT within the G box (CACGTG) at -126 to -123 bp positively regulate gene expression.
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19
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Khan N, Katsube-Tanaka T, Iida S, Yamaguchi T, Nakano J, Tsujimoto H. Diversity of rice glutelin polypeptides in wild species assessed by the higher-temperature sodium dodecyl sulfate-polyacrylamide gel electrophoresis and subunit-specific antibodies. Electrophoresis 2008; 29:1308-16. [DOI: 10.1002/elps.200700732] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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20
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Freitas RL, Carvalho CM, Fietto LG, Loureiro ME, Almeida AM, Fontes EPB. Distinct repressing modules on the distal region of the SBP2 promoter contribute to its vascular tissue-specific expression in different vegetative organs. PLANT MOLECULAR BIOLOGY 2007; 65:603-14. [PMID: 17710554 DOI: 10.1007/s11103-007-9225-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2007] [Accepted: 08/08/2007] [Indexed: 05/16/2023]
Abstract
The Glycine max sucrose binding protein (GmSBP2) promoter directs vascular tissue-specific expression of reporter genes in transgenic tobacco. Here we showed that an SBP2-GFP fusion protein under the control of the GmSBP2 promoter accumulates in the vascular tissues of vegetative organs, which is consistent with the proposed involvement of SBP in sucrose transport-dependent physiological processes. Through gain-of-function experiments we confirmed that the tissue-specific determinants of the SBP2 promoter reside in the distal cis-regulatory domain A, CRD-A (position -2000 to -700) that is organized into a modular configuration to suppress promoter activity in tissues other than vascular tissues. The four analyzed CRD-A sub-modules, designates Frag II (-1785/-1508), Frag III (-1507/-1237), Frag IV (-1236/-971) and Frag V (-970/-700), act independently to alter the constitutive pattern of -92pSBP2-mediated GUS expression in different organs. Frag V fused to -92pSBP2-GUS restored the tissue-specific pattern of the full-length promoter in the shoot apex, but not in other organs. Likewise, Frag IV confined GUS expression to the vascular bundle of leaves, whereas Frag II mediated vascular specific expression in roots. Strong stem expression-repressing elements were located at positions -1485 to -1212, as Frag III limited GUS expression to the inner phloem. We have also mapped a procambium silencer to the consensus sequence CAGTTnCaAccACATTcCT which is located in both distal and proximal upstream modules. Fusion of either repressing element-containing module to the constitutive -92pSBP2 promoter suppresses GUS expression in the elongation zone of roots. Together our results demonstrate the unusual aspect of distal sequences negatively controlling tissue-specificity of a plant promoter.
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Affiliation(s)
- Rejane L Freitas
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36571-000 Vicosa, MG, Brazil
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21
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Yamamoto MP, Onodera Y, Touno SM, Takaiwa F. Synergism between RPBF Dof and RISBZ1 bZIP activators in the regulation of rice seed expression genes. PLANT PHYSIOLOGY 2006; 141:1694-707. [PMID: 16798940 PMCID: PMC1533958 DOI: 10.1104/pp.106.082826] [Citation(s) in RCA: 140] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The Dof (DNA binding with one finger) transcriptional activator rice (Oryza sativa) prolamin box binding factor (RPBF), which is involved in gene regulation of rice seed storage proteins, has been isolated from rice cDNA expressed sequence tag clones containing the conserved Dof. RPBF is found as a single gene per haploid genome. Comparison of RPBF genomic and cDNA sequences revealed that the genomic copy is interrupted by one long intron of 1,892 bp in the 5' noncoding region. We demonstrated by transient expression in rice callus protoplasts that the isolated RPBF trans-activated several storage protein genes via an AAAG target sequence located within their promoters, and with methylation interference experiments the additional AAAG-like sequences in promoters of genes expressed in maturing seeds were recognized by the RPBF protein. Binding was sequence specific, since mutation of the AAAG motif or its derivatives decreased both binding and trans-activation by RPBF. Synergism between RPBF and RISBZ1 recognizing the GCN4 motif [TGA(G/C)TCA] was observed in the expression of many storage protein genes. Overexpression of both transcription factors gave rise to much higher levels of expression than the sum of individual activities elicited by either RPBF or RISBZ1 alone. Furthermore, mutation of recognition sites suppressed reciprocal trans-activation ability, indicating that there are mutual interactions between RISBZ1 and RPBF. The RPBF gene is predominantly expressed in maturing endosperm and coordinately expressed with seed storage protein genes, and is involved in the quantitative regulation of genes expressed in the endosperm in cooperation with RISBZ1.
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Affiliation(s)
- Masayuki P Yamamoto
- Transgenic Crop Research and Development Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
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22
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Liang CW, Zhao FQ, Meng CX, Tan CP, Qin S. Molecular Cloning, Characterization and Evolutionary Analysis of Phytoene Desaturase (PDS) Gene from Haematococcus pluvialis. World J Microbiol Biotechnol 2006. [DOI: 10.1007/s11274-005-5775-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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23
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Katsube-Tanaka T, Duldulao JBA, Kimura Y, Iida S, Yamaguchi T, Nakano J, Utsumi S. The two subfamilies of rice glutelin differ in both primary and higher-order structures. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2004; 1699:95-102. [PMID: 15158716 DOI: 10.1016/j.bbapap.2004.02.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2003] [Revised: 12/16/2003] [Accepted: 02/02/2004] [Indexed: 10/26/2022]
Abstract
Rice glutelin, which accounts for 70-80% of the total proteins of the seeds, consists of two nutritionally different subfamilies (A and B types). Although the similarity in primary sequences between the two subfamilies is as high as 60%, we established conditions to discriminate the two subfamilies when low amounts of antigen are analyzed by immunoblot methods. The glutelin alpha polypeptides can be resolved into six bands labeled alpha1 to alpha6 by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). Gel filtration analysis showed that glutelin exists as a polymerized and a smaller molecular weight form. Immunoblot analysis of SDS-PAGE resolved polypeptides showed that alpha2, alpha3, and alpha4 are an A type and that these A types as well as alpha1, a B type, are polymerized. The polymerization tendency clearly differed between the two subfamilies except for alpha1, which may be derived from GluB-4 as suggested by analysis using Escherichia coli expression systems of glutelin cDNA regions corresponding to alpha polypeptides. GluB-4 and all the A type subunits have an extra Cys residue in the hypervariable regions, corresponding to the C-terminal region of alpha polypeptide. Accordingly, the extra Cys residue is hypothesized to be responsible for the polymerization of glutelin.
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Qu LQ, Takaiwa F. Evaluation of tissue specificity and expression strength of rice seed component gene promoters in transgenic rice. PLANT BIOTECHNOLOGY JOURNAL 2004; 2:113-25. [PMID: 17147604 DOI: 10.1111/j.1467-7652.2004.00055.x] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Using stable transgenic rice plants, the promoters of 15 genes expressed in rice seed were analysed for their spatial and temporal expression pattern and their potential to promote the expression of recombinant proteins in seeds. The 15 genes included 10 seed storage protein genes and five genes for enzymes involved in carbohydrate and nitrogen metabolism. The promoters for the glutelins and the 13 kDa and 16 kDa prolamins directed endosperm-specific expression, especially in the outer portion (peripheral region) of the endosperm, whilst the embryo globulin and 18 kDa oleosin promoters directed expression in the embryo and aleurone layer. Fusion of the GUS gene to the 26 kDa globulin promoter resulted in expression in the inner starchy endosperm tissue. It should be noted that the 10 kDa prolamin gene was the only one tested that required both the 5' and 3' flanking regions for intrinsic endosperm-specific expression. The promoters from the pyruvate orthophosphate dikinase (PPDK) and ADP-glucose pyrophosphorylase (AGPase) small subunit genes were active not only in the seed, but also in the phloem of vegetative tissues. Within the seed, the expression from these two promoters differed in that the PPDK gene was only expressed in the endosperm, whereas the AGPase small subunit gene was expressed throughout the seed. The GUS reporter gene fused to the alanine aminotransferase (AlaAT) promoter was expressed in the inner portion of the starchy endosperm, whilst the starch branching enzyme (SBE1) and the glutamate synthase (GOGAT) genes were mainly expressed in the scutellum (between the endosperm and embryo). When promoter activities were examined during seed maturation, the glutelin GluB-4, 26 kDa globulin and 10 kDa and 16 kDa prolamin promoters exhibited much higher activities than the others. The seed promoters analysed here exhibited a wide variety of activities and expression patterns, thus providing many choices suitable for various applications in plant biotechnology.
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Affiliation(s)
- Le Qing Qu
- Department of Plant Biotechnology, National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba, Ibaraki 305-8602, Japan
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25
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Kobayashi T, Nakayama Y, Itai RN, Nakanishi H, Yoshihara T, Mori S, Nishizawa NK. Identification of novel cis-acting elements, IDE1 and IDE2, of the barley IDS2 gene promoter conferring iron-deficiency-inducible, root-specific expression in heterogeneous tobacco plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2003; 36:780-93. [PMID: 14675444 DOI: 10.1046/j.1365-313x.2003.01920.x] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The molecular mechanisms of plant responses to iron (Fe) deficiency remain largely unknown. To identify the cis-acting elements responsible for Fe-deficiency-inducible expression in higher plants, the barley IDS2 (iron deficiency specific clone no. 2) gene promoter was analyzed using a transgenic tobacco system. Deletion analysis revealed that the sequence between -272 and -91 from the translational start site (-272/-91) was both sufficient and necessary for specific expression in tobacco roots. Further deletion and linker-scanning analysis of this region clearly identified two cis-acting elements: iron-deficiency-responsive element 1 (IDE1) at -153/-136 (ATCAAGCATGCTTCTTGC) and IDE2 at -262/-236 (TTGAACGGCAAGTTTCACGCTGTCACT). The co-existence of IDE1 and IDE2 was essential for specific expression when the -46/+8 region (relative to the transcriptional start site) of the CaMV 35S promoter was used as a minimal promoter. Expression occurred mainly in the root pericycle, endodermis, and cortex. When the -90/+8 region of the CaMV 35S promoter was fused, the -272/-227 region, which consists of IDE2 and an additional 19 bp, could drive Fe-deficiency-inducible expression without IDE1 throughout almost the entire root. The principal modules of IDE1 and IDE2 were homologous. Sequences homologous to IDE1 were also found in many other Fe-deficiency-inducible promoters, including: nicotianamine aminotransferase (HvNAAT)-A, HvNAAT-B, nicotianamine synthase (HvNAS1), HvIDS3, OsNAS1, OsNAS2, OsIRT1, AtIRT1, and AtFRO2, suggesting the conservation of cis-acting elements in various genes and species. The identification of novel cis-acting elements, IDE1 and IDE2, will provide powerful tools to clarify the molecular mechanisms regulating Fe homeostasis in higher plants.
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Affiliation(s)
- Takanori Kobayashi
- Laboratory of Plant Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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26
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Onodera Y, Suzuki A, Wu CY, Washida H, Takaiwa F. A rice functional transcriptional activator, RISBZ1, responsible for endosperm-specific expression of storage protein genes through GCN4 motif. J Biol Chem 2001; 276:14139-52. [PMID: 11133985 DOI: 10.1074/jbc.m007405200] [Citation(s) in RCA: 130] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The GCN4 motif, a cis-element that is highly conserved in the promoters of cereal seed storage protein genes, plays a central role in controlling endosperm-specific expression. This motif is the recognition site for a basic leucine zipper transcriptional factor that belongs to the group of maize Opaque-2 (O2)-like proteins. Five different basic leucine zipper cDNA clones, designated RISBZ1-5, have been isolated from a rice seed cDNA library. The predicted gene products can be divided into two groups based on their amino acid sequences. Although all the RISBZ proteins are able to interact with the GCN4 motif, only RISBZ1 is capable of activating (more than 100-fold expression) the expression of a reporter gene under a minimal promoter fused to a pentamer of the GCN4 motif. Loss-of-function and gain-of-function experiments using the yeast GAL4 DNA binding domain revealed that the proline-rich N-terminal domain (27 amino acids in length) is responsible for transactivation. The RISBZ1 protein is capable of forming homodimers as well as heterodimers with other RISBZ subunit proteins. RISBZ1 gene expression is restricted to the seed, where it precedes the expression of storage protein genes. When the RISBZ1 promoter was transcriptionally fused to the beta-glucuronidase reporter gene and the chimeric gene was introduced into rice, the beta-glucuronidase gene is specifically expressed in aleurone and subaleurone layer of the developing endosperm. These findings suggest that the specific expression of transcriptional activator RISBZ1 gene may determine the endosperm specificity of the storage protein genes.
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MESH Headings
- Amino Acid Motifs
- Amino Acid Sequence
- Base Sequence
- Basic-Leucine Zipper Transcription Factors
- Binding Sites
- Binding, Competitive
- Blotting, Northern
- Cloning, Molecular
- DNA Methylation
- DNA, Complementary/metabolism
- DNA-Binding Proteins
- Dimerization
- Exons
- Fungal Proteins/metabolism
- Gene Deletion
- Gene Library
- Genes, Reporter
- Genome, Plant
- Glucuronidase/genetics
- Glutathione Transferase/metabolism
- Leucine Zippers
- Models, Genetic
- Molecular Sequence Data
- Mutagenesis, Site-Directed
- Oryza/chemistry
- Oryza/genetics
- Oryza/physiology
- Phylogeny
- Plant Physiological Phenomena
- Plant Proteins/chemistry
- Plant Proteins/genetics
- Plants, Genetically Modified
- Plasmids/metabolism
- Promoter Regions, Genetic
- Protein Biosynthesis
- Protein Kinases/metabolism
- Protein Structure, Tertiary
- Recombinant Fusion Proteins/metabolism
- Saccharomyces cerevisiae Proteins
- Sequence Homology, Amino Acid
- Tissue Distribution
- Trans-Activators/biosynthesis
- Trans-Activators/chemistry
- Trans-Activators/genetics
- Transcription, Genetic
- Transcriptional Activation
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Affiliation(s)
- Y Onodera
- Department of Biotechnology, National Institute of Agrobiological Resources, Kannondai 2-1-2, Tsukuba, Ibaraki 305-8602, Japan
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Wu C, Washida H, Onodera Y, Harada K, Takaiwa F. Quantitative nature of the Prolamin-box, ACGT and AACA motifs in a rice glutelin gene promoter: minimal cis-element requirements for endosperm-specific gene expression. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2000; 23:415-21. [PMID: 10929134 DOI: 10.1046/j.1365-313x.2000.00797.x] [Citation(s) in RCA: 118] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The -197 bp promoter of the rice seed storage protein gene, GluB-1, is capable of conferring endosperm-specific gene expression. This proximal 5' flanking region contains four motifs, GCN4, AACA, ACGT and Prolamin-box, which are conserved in many seed storage protein genes. We previously showed that multiple copies of GCN4 conferred endosperm expression pattern when fused to the -46 core promoter of CaMV 35S. In this paper we demonstrate, using a similar approach, that tandem repeated copies of any of the other three motifs are unable to direct expression in seeds as well as other tissues of transgenic rice plants. Mutational analysis of individual motifs in the -197 bp promoter resulted in remarkable reductions in promoter activity. These results indicate that the GCN4 motif acts as an essential element determining endosperm-specific expression and that the AACA, ACGT and Prolamin-box are involved in quantitative regulation of the GluB-1 gene. A set of gain-of-function experiments using transgenic rice showed that either the Prolamin-box or AACA, although often coupled with GCN4 in many genes, is insufficient to form a functional promoter unit with GCN4, whereas a combination of GCN4, AACA and ACGT motifs was found sufficient to confer a detectable level of endosperm expression. Taken together, our results provide direct insight into the importance of combinatorial interplay between cis-elements in regulating the expression of seed storage protein genes.
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Affiliation(s)
- C Wu
- Department of Biotechnology, National Institute of Agrobiological Resources, Kannondai 2-1-2, Tsukuba, Ibaraki 305-8602, Japan
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Marzábal P, Busk PK, Ludevid MD, Torrent M. The bifactorial endosperm box of gamma-zein gene: characterisation and function of the Pb3 and GZM cis-acting elements. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 1998; 16:41-52. [PMID: 9807826 DOI: 10.1046/j.1365-313x.1998.00272.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The proximal region of the gamma-zein promoter (gamma Z) has a functional bifactorial prolamin box element containing two cis-acting elements, a prolamin-box motif (Pb3) and a GCN4-like motif (GZM). By particle bombardment of maize endosperms with 5' deletions and internal deletions of gamma Z fused to the GUS gene, we have shown that a 135 bp region containing the bifactorial element is involved in the transcriptional activation of the gamma Z promoter. However, the 135 bp region was unable to activate the gamma Z promoter in the absence of a 84 bp downstream sequence. Using in vivo footprinting and gel mobility shift assays with 15 DAP endosperm nuclear extracts, we have demonstrated the presence of trans-acting factors that interact with Pb3 and GZM target sites. Base-substitution mutations within Pb3 and GZM decreased transcription activity of the gamma Z promoter suggesting a co-ordinated function between the two cis-acting elements. Two additional cis-motifs upstream of the bifactorial prolamin element have been identified: a motif with high homology to the AACA elements of rice glutelin genes and an AZM motif containing an ACGT core which binds nuclear proteins other than the Opaque 2 (O2).
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Affiliation(s)
- P Marzábal
- Departament de Genètica Molecular, Centre de Investigació i Desenvolupament, (C.S.I.C.), Barcelona, Spain
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Wu CY, Suzuki A, Washida H, Takaiwa F. The GCN4 motif in a rice glutelin gene is essential for endosperm-specific gene expression and is activated by Opaque-2 in transgenic rice plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 1998; 14:673-83. [PMID: 9681032 DOI: 10.1046/j.1365-313x.1998.00167.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The GCN4 motif is conserved in a number of seed storage protein genes, and promoter fragments containing this motif have been shown to be involved in controlling seed-specific expression of the genes studied. All genes encoding the rice seed storage protein glutelin contain the GCN4 motif at similar sites in their 5' flanking regions. Using a stable homologous transgenic system, we have analysed the promoter of the rice glutelin gene GluB-1 and demonstrated that the GCN4 motif functions as an essential cis-element for endosperm-specific gene expression. Moreover, a 21 bp GluB-1 promoter fragment spanning the GCN4 motif, as a multimer, directed GUS gene expression in endosperm of transgenic rice plants, when fused directly to the core promoter (-46) of CaMV 35S. In transiently transfected rice protoplasts, over a hundred-fold transactivation was observed from the 21 bp sequence by the bZIP type transcriptional activator Opaque-2 (O2) co-expressed under a CaMV 35S promoter. The transactivation was also evident in transgenic plants containing both O2 and the 21 bp sequence/GUS fusion. The O2-mediated activation requires binding of O2 to an intact GCN4 motif. Our results suggest that a bZIP protein functionally similar to O2 may exist in rice and participate in controlling the endosperm-specific expression of GluB-1 through the GCN4 motif.
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Affiliation(s)
- C Y Wu
- Department of Biotechnology, National Institute of Agrobiological Resources, Ibaraki, Japan
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Suzuki A, Suzuki T, Tanabe F, Toki S, Washida H, Wu CY, Takaiwa F. Cloning and expression of five myb-related genes from rice seed. Gene 1997; 198:393-8. [PMID: 9370307 DOI: 10.1016/s0378-1119(97)00344-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Three elements in the promoter of rice glutelin genes are important for their endosperm specific expression. One of these, an AACA motif, has been shown to be a negative regulator in non-seed tissues and has a similarity to the barley gibberellin responsive element recognized by MYB-like DNA binding proteins. A cDNA library constructed from immature rice seed was screened using two types of myb gene probes to isolate cDNA clones representing genes encoding MYB-like DNA binding proteins that may recognize the AACA motif in rice glutelin gene promoter. We obtained four cDNA clones encoding MYB-related proteins, Oryza sativa MYB (OSMYB) 1-4, using the maize C1 probe. Another myb-like clone, Osmyb5, was obtained by screening a rice seed cDNA library with probes designed to recognize the AACA-like binding domain in GAMYB and PHMYB3. RT-PCR was used to analyze Osmyb expression during rice seed development and their presence in other rice tissues, as it was not possible to detect these mRNAs by conventional Northern analysis. RT-PCR analysis showed that Osmyb2, Osmyb3 and Osmyb5 genes were expressed in all tissues examined. In seed, the mRNA levels of Osmyb1 and Osmyb4 genes reached a maximum at 14 days after flowering (DAF), suggesting that these genes may play a role in seed maturation. As Osmyb5 exhibits a high similarity to the regions in both GAMYB and PHMYB3, which can bind to the AACA motif, there is a possibility that the OSMYB5 protein may bind to the AACA motif of glutelin genes.
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Affiliation(s)
- A Suzuki
- Department of Biotechnology, National Institute of Agrobiological Resources, Tsukuba, Ibaraki, Japan
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Nakase M, Yamada T, Kira T, Yamaguchi J, Aoki N, Nakamura R, Matsuda T, Adachi T. The same nuclear proteins bind to the 5'-flanking regions of genes for the rice seed storage protein: 16 kDa albumin, 13 kDa prolamin and type II glutelin. PLANT MOLECULAR BIOLOGY 1996; 32:621-630. [PMID: 8980514 DOI: 10.1007/bf00020203] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Expression of rice seed storage-protein genes is dramatically regulated over a short period of seed maturation. To characterize the expression mechanism of the rice seed storage protein genes, their expression of major storage protein genes (16 kDa albumin, 13 kDa prolamin and type II glutelin) were compared by RNA blot analysis. Their coordinate expression suggests that the transcriptional regulatory machinery is shared among the glutelin, prolamin and albumin-genes. We isolated two novel genomic genes for prolamins (PG5a and PG5b) and obtained the promoter region of the glutelin gene by PCR. The 5'-flanking regions of these three rice seed storage protein genes were found to contain some similar conserved sequences. Nuclear extract partially purified from maturing rice seeds was used for the gel shift assay of the 5' region of the RA gene. We identified two DNA sequences of RA gene which were recognized by independent DNA-binding proteins. The complexes of these DNA sequences and DNA-binding proteins were inhibited by the fragments containing the 5' regions of the prolamin and glutelin genes, suggesting that these three genes share transcription factors.
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Affiliation(s)
- M Nakase
- Department of Applied Biological Sciences, School of Agricultural Sciences, Nagoya University, Japan
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