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Li Q, Zhang X, Zhao P, Chen Y, Ni D, Wang M. Metal tolerance protein CsMTP4 has dual functions in maintaining zinc homeostasis in tea plant. JOURNAL OF HAZARDOUS MATERIALS 2024; 471:134308. [PMID: 38631255 DOI: 10.1016/j.jhazmat.2024.134308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 04/05/2024] [Accepted: 04/13/2024] [Indexed: 04/19/2024]
Abstract
Plants have evolved a series of zinc (Zn) homeostasis mechanisms to cope with the fluctuating Zn in the environment. How Zn is taken up, translocated and tolerate by tea plant remains unknown. In this study, on the basis of RNA-Sequencing, we isolated a plasma membrane-localized Metal Tolerance Protein (MTP) family member CsMTP4 from Zn-deficient tea plant roots and investigated its role in regulation of Zn homeostasis in tea plant. Heterologous expression of CsMTP4 specifically enhanced the tolerance of transgenic yeast to Zn excess. Moreover, overexpression of CsMTP4 in tea plant hairy roots stimulated Zn uptake under Zn deficiency. In addition, CsMTP4 promoted the growth of transgenic Arabidopsis plants by translocating Zn from roots to shoots under Zn deficiency and conferred the tolerance to Zn excess by enhancing the efflux of Zn from root cells. Transcriptome analysis of the CsMTP4 transgenic Arabidopsis found that the expression of Zn metabolism-related genes were differentially regulated compared with wild-type plants when exposed to Zn deficiency and excess conditions. This study provides a mechanistic understanding of Zn uptake and translocation in plants and a new strategy to improve phytoremediation efficiency.
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Affiliation(s)
- Qinghui Li
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, PR China; Joint International Research Laboratory of Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Xuyang Zhang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, PR China; Joint International Research Laboratory of Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Peiling Zhao
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, PR China; Joint International Research Laboratory of Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Yuqiong Chen
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, PR China; Joint International Research Laboratory of Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Dejiang Ni
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, PR China; Joint International Research Laboratory of Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Mingle Wang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, PR China; Joint International Research Laboratory of Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, PR China.
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2
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Siqueira JA, Zsögön A, Fernie AR, Nunes-Nesi A, Araújo WL. Does day length matter for nutrient responsiveness? TRENDS IN PLANT SCIENCE 2023; 28:1113-1123. [PMID: 37268488 DOI: 10.1016/j.tplants.2023.04.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 04/11/2023] [Accepted: 04/24/2023] [Indexed: 06/04/2023]
Abstract
For over 2500 years, considerable agronomic interest has been paid to soil fertility. Both crop domestication and the Green Revolution shifted photoperiodism and the circadian clock in cultivated species, although this contributed to an increase in the demand for chemical fertilisers. Thus, the uptake of nutrients depends on light signalling, whereas diel growth and circadian rhythms are affected by nutrient levels. Here, we argue that day length and circadian rhythms may be central regulators of the uptake and usage of nutrients, also modulating responses to toxic elements (e.g., aluminium and cadmium). Thus, we suggest that knowledge in this area might assist in developing next-generation crops with improved uptake and use efficiency of nutrients.
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Affiliation(s)
- João Antonio Siqueira
- National Institute of Science and Technology on Plant Physiology under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, MG, Brazil.
| | - Agustin Zsögön
- National Institute of Science and Technology on Plant Physiology under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, MG, Brazil
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Adriano Nunes-Nesi
- National Institute of Science and Technology on Plant Physiology under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, MG, Brazil
| | - Wagner L Araújo
- National Institute of Science and Technology on Plant Physiology under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, MG, Brazil.
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3
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Abulfaraj AA. Relationships between some transcription factors and concordantly expressed drought stress-related genes in bread wheat. Saudi J Biol Sci 2023; 30:103652. [PMID: 37206446 PMCID: PMC10189290 DOI: 10.1016/j.sjbs.2023.103652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/18/2023] [Accepted: 04/09/2023] [Indexed: 05/21/2023] Open
Abstract
The challenge of climate change makes it mandatory to improve tolerance to drought stress in bread wheat (Triticum aestivum) via biotechnological approaches. Drought stress experiment was conducted followed by RNA-Seq analysis for leaves of two wheat cultivars namely Giza 168 and Gemmiza 10 with contrasting genotypes. Expression patterns of the regulated stress-related genes and concordantly expressed TFs were detected, then, validated via qPCR for two loss-of-function mutants in Arabidopsis background harboring mutated genes analogue to those in wheat. Drought-stress related genes were searched for concordantly expressed TFs and a total of eight TFs were shown to coexpress with 14 stress-related genes. Among these genes, one TF belongs to the zinc finger protein CONSTANS family and proved via qPCR to drive expression of a gene encoding a speculative TF namely zinc transporter 3-like and two other stress related genes encoding tryptophan synthase alpha chain and asparagine synthetase. Known functions of the two TFs under drought stress complement those of the two concordantly expressed stress-related genes, thus, it is likely that they are related. This study highlights the possibility to utilize metabolic engineering approaches to decipher and incorporate existing regulatory frameworks under drought stress in future breeding programs of bread wheat.
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Tan QW, Lim PK, Chen Z, Pasha A, Provart N, Arend M, Nikoloski Z, Mutwil M. Cross-stress gene expression atlas of Marchantia polymorpha reveals the hierarchy and regulatory principles of abiotic stress responses. Nat Commun 2023; 14:986. [PMID: 36813788 PMCID: PMC9946954 DOI: 10.1038/s41467-023-36517-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 02/03/2023] [Indexed: 02/24/2023] Open
Abstract
Abiotic stresses negatively impact ecosystems and the yield of crops, and climate change will increase their frequency and intensity. Despite progress in understanding how plants respond to individual stresses, our knowledge of plant acclimatization to combined stresses typically occurring in nature is still lacking. Here, we used a plant with minimal regulatory network redundancy, Marchantia polymorpha, to study how seven abiotic stresses, alone and in 19 pairwise combinations, affect the phenotype, gene expression, and activity of cellular pathways. While the transcriptomic responses show a conserved differential gene expression between Arabidopsis and Marchantia, we also observe a strong functional and transcriptional divergence between the two species. The reconstructed high-confidence gene regulatory network demonstrates that the response to specific stresses dominates those of others by relying on a large ensemble of transcription factors. We also show that a regression model could accurately predict the gene expression under combined stresses, indicating that Marchantia performs arithmetic multiplication to respond to multiple stresses. Lastly, two online resources ( https://conekt.plant.tools and http://bar.utoronto.ca/efp_marchantia/cgi-bin/efpWeb.cgi ) are provided to facilitate the study of gene expression in Marchantia exposed to abiotic stresses.
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Affiliation(s)
- Qiao Wen Tan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Peng Ken Lim
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Zhong Chen
- Amoeba Education Hub, 1 West Coast Road, 128020, Singapore, Singapore
| | - Asher Pasha
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Nicholas Provart
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Marius Arend
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany.,Systems Biology and Mathematical Modeling, Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Zoran Nikoloski
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany.,Systems Biology and Mathematical Modeling, Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Marek Mutwil
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
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5
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Xing X, Liu H, Ye J, Yao Y, Li K, Li Y, Du D. QTL analysis and candidate gene prediction for seed density per silique by QTL-seq and RNA-seq in spring Brassica napus L. PLoS One 2023; 18:e0281875. [PMID: 36877715 PMCID: PMC9987769 DOI: 10.1371/journal.pone.0281875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 02/01/2023] [Indexed: 03/07/2023] Open
Abstract
Seed density per silique (SD) is an important agricultural trait and plays an important role in the yield performance of Brassica napus L. (B. napus). In this study, a genetic linkage map was constructed using a double haploid (DH) population with 213 lines derived from a cross between a low SD line No. 935 and a high SD line No. 3641, and a total of 1,098,259 SNP (single-nucleotide polymorphisms) markers and 2,102 bins were mapped to 19 linkage groups. Twenty-eight QTLs for SD were detected on chromosomes A02, A04, A05, A09, C02, C03, C06, and C09 of B. napus, of which eight QTLs were on chromosome A09 and explained 5.89%-13.24% of the phenotypic variation. Furthermore, a consistent QTL for SD on chromosome A09, cqSD-A9a, was identified in four environments by QTL meta-analysis, explaining 10.68% of the phenotypic variation. In addition, four pairs of epistatic interactions were detected in the DH population via QTL epistasis analysis, indicating that SD is controlled not only by additive effects but also by epistatic effects that play an important role in spring B. napus., but with little environmental effect. Moreover, 18 closely linked SSR markers for cqSD-A9a were developed, as a result, it was mapped to a 1.86Mb (7.80-9.66 Mb) region on chromosome A09. A total of 13 differentially expressed genes (DEGs) were screened in the candidate interval by RNA-seq analysis, which were differentially expressed in buds, leaves and siliques both between and siliques both between two parents and two pools of extremely high-SD and low-SD lines in the DH population. Three of 13 DEGs were possible candidate genes that might control SD: BnaA09g14070D, which encodes a callose synthase that plays an important role in development and stress responses; BnaA09g14800D, a plant synaptic protein that encodes a membrane component; and BnaA09g18250D, which is responsible for DNA binding, transcriptional regulation, and sequence-specific DNA binding and is involved in the response to growth hormone stimulation. Overall, these results lay a foundation for fine mapping and gene cloning for SD in B. napus.
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Affiliation(s)
- Xiaorong Xing
- Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, Qinghai, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Key, Chengdu, China
- Laboratory of Spring Rapeseed Genetic Improvement of Qinghai Province, National Key, Xining, China
- Laboratory Breeding Base for Innovation and Utilization of Plateau Crop Germplasm, Xining, China
| | - Haidong Liu
- Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, Qinghai, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Key, Chengdu, China
- Laboratory of Spring Rapeseed Genetic Improvement of Qinghai Province, National Key, Xining, China
- Laboratory Breeding Base for Innovation and Utilization of Plateau Crop Germplasm, Xining, China
- * E-mail: (HL); (DD)
| | - Jingxiu Ye
- Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, Qinghai, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Key, Chengdu, China
- Laboratory of Spring Rapeseed Genetic Improvement of Qinghai Province, National Key, Xining, China
- Laboratory Breeding Base for Innovation and Utilization of Plateau Crop Germplasm, Xining, China
| | - Yanmei Yao
- Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, Qinghai, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Key, Chengdu, China
- Laboratory of Spring Rapeseed Genetic Improvement of Qinghai Province, National Key, Xining, China
- Laboratory Breeding Base for Innovation and Utilization of Plateau Crop Germplasm, Xining, China
| | - Kaixiang Li
- Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, Qinghai, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Key, Chengdu, China
- Laboratory of Spring Rapeseed Genetic Improvement of Qinghai Province, National Key, Xining, China
- Laboratory Breeding Base for Innovation and Utilization of Plateau Crop Germplasm, Xining, China
| | - Yanling Li
- Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, Qinghai, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Key, Chengdu, China
- Laboratory of Spring Rapeseed Genetic Improvement of Qinghai Province, National Key, Xining, China
- Laboratory Breeding Base for Innovation and Utilization of Plateau Crop Germplasm, Xining, China
| | - Dezhi Du
- Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, Qinghai, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Key, Chengdu, China
- Laboratory of Spring Rapeseed Genetic Improvement of Qinghai Province, National Key, Xining, China
- Laboratory Breeding Base for Innovation and Utilization of Plateau Crop Germplasm, Xining, China
- * E-mail: (HL); (DD)
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Assunção AGL. The F-bZIP-regulated Zn deficiency response in land plants. PLANTA 2022; 256:108. [PMID: 36348172 PMCID: PMC9643250 DOI: 10.1007/s00425-022-04019-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 10/22/2022] [Indexed: 06/16/2023]
Abstract
This review describes zinc sensing and transcriptional regulation of the zinc deficiency response in Arabidopsis, and discusses how their evolutionary conservation in land plants facilitates translational approaches for improving the Zn nutritional value of crop species. Zinc is an essential micronutrient for all living organisms due to its presence in a large number of proteins, as a structural or catalytic cofactor. In plants, zinc homeostasis mechanisms comprise uptake from soil, transport and distribution throughout the plant to provide adequate cellular zinc availability. Here, I discuss the transcriptional regulation of the response to zinc deficiency and the zinc sensing mechanisms in Arabidopsis, and their evolutionary conservation in land plants. The Arabidopsis F-group basic region leucine-zipper (F-bZIP) transcription factors bZIP19 and bZIP23 function simultaneously as sensors of intracellular zinc status, by direct binding of zinc ions, and as the central regulators of the zinc deficiency response, with their target genes including zinc transporters from the ZRT/IRT-like Protein (ZIP) family and nicotianamine synthase enzymes that produce the zinc ligand nicotianamine. I note that this relatively simple mechanism of zinc sensing and regulation, together with the evolutionary conservation of F-bZIP transcription factors across land plants, offer important research opportunities. One of them is to use the F-bZIP-regulated zinc deficiency response as a tractable module for evolutionary and comparative functional studies. Another research opportunity is translational research in crop plants, modulating F-bZIP activity as a molecular switch to enhance zinc accumulation. This should become a useful plant-based solution to alleviate effects of zinc deficiency in soils, which impact crop production and crop zinc content, with consequences for human nutrition globally.
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Affiliation(s)
- Ana G L Assunção
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871, Frederiksberg, Denmark.
- CIBIO-InBIO, Research Centre in Biodiversity and Genetic Resources, University of Porto, 4485-661, Vairão, Portugal.
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Liao F, Lilay GH, Castro PH, Azevedo H, Assunção AGL. Regulation of the Zinc Deficiency Response in the Legume Model Medicago truncatula. FRONTIERS IN PLANT SCIENCE 2022; 13:916168. [PMID: 35845702 PMCID: PMC9279927 DOI: 10.3389/fpls.2022.916168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 05/30/2022] [Indexed: 06/15/2023]
Abstract
The zinc deficiency response in Arabidopsis thaliana is regulated by F-group basic region leucine-zipper (F-bZIP) transcription factors, and there is evidence of evolutionary conservation of this regulatory network in land plants. Fundamental knowledge on the zinc homeostasis regulation in crop species will contribute to improving their zinc nutritional value. Legumes are protein-rich crops, used worldwide as part of traditional diets and as animal forage, being therefore a good target for micronutrient biofortification. Here, we identified F-bZIP transcription factors in representative legume species and functionally characterized the two F-bZIPs from Medicago truncatula. Results indicate that MtFbZIP1 is the functional homolog of A. thaliana bZIP19 and bZIP23, while MtFbZIP2 does not play a role in the zinc deficiency response. Additionally, analysis of M. truncatula genes from the Zrt/Irt-like protein (ZIP) family of zinc transporters or encoding nicotianamine synthase enzymes that produce the zinc ligand nicotianamine, support the conservation of the F-bZIP-regulated zinc deficiency response in M. truncatula. Phylogenetic analysis of F-bZIP homologs enriched in legume species reinforces the branching into two groups, with MtFbZIP1 and MtFbZIP2 mapping in Groups 1 and 2, respectively. This phylogeny combined with the functional characterization of MtFbZIPs supports the suggested conservation of the zinc deficiency response associated with Group 1 F-bZIPs, and the more variable evolutionary paths associated with Group 2. Overall, we provide novel insight on the mechanisms of response to zinc deficiency in M. truncatula, which contributes to developing strategies for improving zinc content in legume crops.
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Affiliation(s)
- Feixue Liao
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Grmay Hailu Lilay
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Pedro Humberto Castro
- CIBIO-InBIO Research Centre in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal
- BIOPOLIS Biodiversity and Land Planning, Vairão, Portugal
| | - Herlander Azevedo
- CIBIO-InBIO Research Centre in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal
- BIOPOLIS Biodiversity and Land Planning, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Ana G. L. Assunção
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
- CIBIO-InBIO Research Centre in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal
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8
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Zou J, Han J, Wang Y, Jiang Y, Han B, Wu K, Wang B, Wu Y, Fan X. Cytological and physiological tolerance of transgenic tobacco to Cd stress is enhanced by the ectopic expression of SmZIP8. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 319:111252. [PMID: 35487660 DOI: 10.1016/j.plantsci.2022.111252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/18/2022] [Accepted: 03/10/2022] [Indexed: 06/14/2023]
Abstract
Zrt and Irt-like proteins (ZIPs) are responsible for transporting various divalent metal cations. However, information about the characteristics of the cellular and physiological tolerance of plant ZIPs to Cd stress is still limited. The expression levels of SmZIP8 in Salix matsudana Koidz were upregulated by Cd stress. The complete length of SmZIP8 from S. matsudana was cloned, and transgenic tobacco was obtained by Agrobacterium-mediated transformation. Then, the tolerance to Cd stress of wild-type (WT) and transgenic tobacco seedlings was analyzed and compared by studying the cytotoxicity of the root tip cells, photosynthetic parameters, histochemical staining of O2- and H2O2, the activities of antioxidant enzymes, and malondialdehyde content under Cd stress. In comparison with WT tobacco, the ectopic expression of SmZIP8 in tobacco promoted the cytological tolerance of the transgenic tobacco to Cd stress by reducing cell damage, raising the mitotic indexes, and reducing the rate of chromosome aberration of the root cells. Meanwhile, the results of increased photosynthetic capacity, decreased oxidative damage, and activated antioxidant enzymes showed that the physiological tolerance of transgenic tobacco to Cd was enhanced. The principal component analysis for the above physiological parameters explained 96.08% of the total variance (PC1, 77.77%; PC2, 18.31%), indicating a significant difference in Cd tolerance abilities between the tobacco expressing SmZIP8 and WT tobacco. Therefore, SmZIP8 may be considered as an important genetic resource for the phytoremediation of Cd or other heavy metal pollution via the use of transgenic plants obtained through genetic transformation.
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Affiliation(s)
- Jinhua Zou
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, China.
| | - Jiahui Han
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, China
| | - Yuerui Wang
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, China
| | - Yi Jiang
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, China
| | - Bowen Han
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, China
| | - Kongfen Wu
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, China
| | - Binghan Wang
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, China
| | - Yuyang Wu
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, China
| | - Xiaotan Fan
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, China
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Amini S, Arsova B, Hanikenne M. The molecular basis of zinc homeostasis in cereals. PLANT, CELL & ENVIRONMENT 2022; 45:1339-1361. [PMID: 35037265 DOI: 10.1111/pce.14257] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 11/12/2021] [Accepted: 12/16/2021] [Indexed: 06/14/2023]
Abstract
Plants require zinc (Zn) as an essential cofactor for diverse molecular, cellular and physiological functions. Zn is crucial for crop yield, but is one of the most limiting micronutrients in soils. Grasses like rice, wheat, maize and barley are crucial sources of food and nutrients for humans. Zn deficiency in these species therefore not only reduces annual yield but also directly results in Zn malnutrition of more than two billion people in the world. There has been good progress in understanding Zn homeostasis and Zn deficiency mechanisms in plants. However, our current knowledge of monocots, including grasses, remains insufficient. In this review, we provide a summary of our knowledge of molecular Zn homeostasis mechanisms in monocots, with a focus on important cereal crops. We additionally highlight divergences in Zn homeostasis of monocots and the dicot model Arabidopsis thaliana, as well as important gaps in our knowledge that need to be addressed in future research on Zn homeostasis in cereal monocots.
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Affiliation(s)
- Sahand Amini
- InBioS-PhytoSystems, Translational Plant Biology, University of Liège, Liège, Belgium
| | - Borjana Arsova
- Root Dynamics Group, IBG-2 - Plant Sciences, Institut für Bio- und Geowissenschaften (IBG), Forschungszentrum, Jülich, Germany
| | - Marc Hanikenne
- InBioS-PhytoSystems, Translational Plant Biology, University of Liège, Liège, Belgium
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10
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Abstract
Nutrients are scarce and valuable resources, so plants developed sophisticated mechanisms to optimize nutrient use efficiency. A crucial part of this is monitoring external and internal nutrient levels to adjust processes such as uptake, redistribution, and cellular compartmentation. Measurement of nutrient levels is carried out by primary sensors that typically involve either transceptors or transcription factors. Primary sensors are only now starting to be identified in plants for some nutrients. In particular, for nitrate, there is detailed insight concerning how the external nitrate status is sensed by members of the nitrate transporter 1 (NRT1) family. Potential sensors for other macronutrients such as potassium and sodium have also been identified recently, whereas for micronutrients such as zinc and iron, transcription factor type sensors have been reported. This review provides an overview that interprets and evaluates our current understanding of how plants sense macro and micronutrients in the rhizosphere and root symplast.
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11
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Thiébaut N, Hanikenne M. Zinc deficiency responses: bridging the gap between Arabidopsis and dicotyledonous crops. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:1699-1716. [PMID: 34791143 DOI: 10.1093/jxb/erab491] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 11/05/2021] [Indexed: 06/13/2023]
Abstract
Zinc (Zn) deficiency is a widespread phenomenon in agricultural soils worldwide and has a major impact on crop yield and quality, and hence on human nutrition and health. Although dicotyledonous crops represent >30% of human plant-based nutrition, relatively few efforts have been dedicated to the investigation of Zn deficiency response mechanisms in dicotyledonous, in contrast to monocotyledonous crops, such as rice or barley. Here, we describe the Zn requirement and impact of Zn deficiency in several economically important dicotyledonous crops, Phaseolus vulgaris, Glycine max, Brassica oleracea, and Solanum lycopersicum. We briefly review our current knowledge of the Zn deficiency response in Arabidopsis and outline how this knowledge is translated in dicotyledonous crops. We highlight commonalities and differences between dicotyledonous species (and with monocotyledonous species) regarding the function and regulation of Zn transporters and chelators, as well as the Zn-sensing mechanisms and the role of hormones in the Zn deficiency response. Moreover, we show how the Zn homeostatic network intimately interacts with other nutrients, such as iron or phosphate. Finally, we outline how variation in Zn deficiency tolerance and Zn use efficiency among cultivars of dicotyledonous species can be leveraged for the design of Zn biofortification strategies.
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Affiliation(s)
- Noémie Thiébaut
- InBioS - PhytoSystems, Translational Plant Biology, University of Liège, 4000 Liège, Belgium
| | - Marc Hanikenne
- InBioS - PhytoSystems, Translational Plant Biology, University of Liège, 4000 Liège, Belgium
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12
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Yang Z, Yang F, Liu JL, Wu HT, Yang H, Shi Y, Liu J, Zhang YF, Luo YR, Chen KM. Heavy metal transporters: Functional mechanisms, regulation, and application in phytoremediation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 809:151099. [PMID: 34688763 DOI: 10.1016/j.scitotenv.2021.151099] [Citation(s) in RCA: 60] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 10/15/2021] [Accepted: 10/16/2021] [Indexed: 05/22/2023]
Abstract
Heavy metal pollution in soil is a global problem with serious impacts on human health and ecological security. Phytoextraction in phytoremediation, in which plants uptake and transport heavy metals (HMs) to the tissues of aerial parts, is the most environmentally friendly method to reduce the total amount of HMs in soil and has wide application prospects. However, the molecular mechanism of phytoextraction is still under investigation. The uptake, translocation, and retention of HMs in plants are mainly mediated by a variety of transporter proteins. A better understanding of the accumulation strategy of HMs via transporters in plants is a prerequisite for the improvement of phytoextraction. In this review, the biochemical structure and functions of HM transporter families in plants are systematically summarized, with emphasis on their roles in phytoremediation. The accumulation mechanism and regulatory pathways related to hormones, regulators, and reactive oxygen species (ROS) of HMs concerning these transporters are described in detail. Scientific efforts and practices for phytoremediation carried out in recent years suggest that creation of hyperaccumulators by transgenic or gene editing techniques targeted to these transporters and their regulators is the ultimate powerful path for the phytoremediation of HM contaminated soils.
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Affiliation(s)
- Zi Yang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Fan Yang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Jia-Lan Liu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Hai-Tao Wu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Hao Yang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Yi Shi
- Guangdong Kaiyuan Environmental Technology Co., Ltd, Dongguan 523000, China
| | - Jie Liu
- Guangdong Kaiyuan Environmental Technology Co., Ltd, Dongguan 523000, China
| | - Yan-Feng Zhang
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling 712100, Shaanxi, China
| | - Yan-Rong Luo
- Guangdong Kaiyuan Environmental Technology Co., Ltd, Dongguan 523000, China.
| | - Kun-Ming Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China.
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13
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Li M, Hwarari D, Li Y, Ahmad B, Min T, Zhang W, Wang J, Yang L. The bZIP transcription factors in Liriodendron chinense: Genome-wide recognition, characteristics and cold stress response. FRONTIERS IN PLANT SCIENCE 2022; 13:1035627. [PMID: 36420021 PMCID: PMC9676487 DOI: 10.3389/fpls.2022.1035627] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 10/17/2022] [Indexed: 05/08/2023]
Abstract
The basic leucine zipper (bZIP) is a transcription factor family that plays critical roles in abiotic and biotic stress responses as well as plant development and growth. A comprehensive genome-wide study in Liriodendron chinense was conducted to identify 45 bZIP transcription factors (LchibZIPs), which were divided into 13 subgroups according the phylogenetic analysis. Proteins in the same subgroup shared similar gene structures and conserved domains, and a total of 20 conserved motifs were revealed in LchibZIP proteins. Gene localization analysis revealed that LchibZIP genes were unequally distributed across 16 chromosomes, and that 4 pairs of tandem and 9 segmental gene duplications existed. Concluding that segmental duplication events may be strongly associated with the amplification of the L. chinense bZIP gene family. We also assessed the collinearity of LchibZIPs between the Arabidopsis and Oryza and showed that the LchibZIP is evolutionarily closer to O. sativa as compared to the A. thaliana. The cis-regulatory element analysis showed that LchibZIPs clustered in one subfamily are involved in several functions. In addition, we gathered novel research suggestions for further exploration of the new roles of LchibZIPs from protein-protein interactions and gene ontology annotations of the LchibZIP proteins. Using the RNA-seq data and qRT-PCR we analyzed the gene expression patterns of LchibZIP genes, and showed that LchibZIP genes regulate cold stress, especially LchibZIP4 and LchibZIP7; and LchibZIP2 and LchibZIP28 which were up-regulated and down-regulated by cold stress, respectively. Studies of genetic engineering and gene function in L. chinense can benefit greatly from the thorough investigation and characterization of the L. chinense bZIP gene family.
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Affiliation(s)
- Mingyue Li
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
- Innovation Center of Excellence, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Delight Hwarari
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Yang Li
- Innovation Center of Excellence, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Baseer Ahmad
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Tian Min
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Wenting Zhang
- Innovation Center of Excellence, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Jinyan Wang
- Innovation Center of Excellence, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
- *Correspondence: Jinyan Wang, ; Liming Yang,
| | - Liming Yang
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
- *Correspondence: Jinyan Wang, ; Liming Yang,
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14
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Amini S, Arsova B, Gobert S, Carnol M, Bosman B, Motte P, Watt M, Hanikenne M. Transcriptional regulation of ZIP genes is independent of local zinc status in Brachypodium shoots upon zinc deficiency and resupply. PLANT, CELL & ENVIRONMENT 2021; 44:3376-3397. [PMID: 34263935 DOI: 10.1111/pce.14151] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 07/05/2021] [Accepted: 07/10/2021] [Indexed: 06/13/2023]
Abstract
The biological processes underlying zinc homeostasis are targets for genetic improvement of crops to counter human malnutrition. Detailed phenotyping, ionomic, RNA-Seq analyses and flux measurements with 67 Zn isotope revealed whole-plant molecular events underlying zinc homeostasis upon varying zinc supply and during zinc resupply to starved Brachypodium distachyon (Brachypodium) plants. Although both zinc deficiency and excess hindered Brachypodium growth, accumulation of biomass and micronutrients into roots and shoots differed depending on zinc supply. The zinc resupply dynamics involved 1,893 zinc-responsive genes. Multiple zinc-regulated transporter and iron-regulated transporter (IRT)-like protein (ZIP) transporter genes and dozens of other genes were rapidly and transiently down-regulated in early stages of zinc resupply, suggesting a transient zinc shock, sensed locally in roots. Notably, genes with identical regulation were observed in shoots without zinc accumulation, pointing to root-to-shoot signals mediating whole-plant responses to zinc resupply. Molecular events uncovered in the grass model Brachypodium are useful for the improvement of staple monocots.
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Affiliation(s)
- Sahand Amini
- InBioS - PhytoSystems, Functional Genomics and Plant Molecular Imaging, University of Liège, Liège, Belgium
| | - Borjana Arsova
- Root Dynamics Group, IBG-2 - Plant Sciences, Institut für Bio- und Geowissenschaften (IBG), Forschungszentrum Jülich, Jülich, Germany
| | - Sylvie Gobert
- Laboratory of Oceanology, MARE Center, FOCUS, University of Liège, Liège, Belgium
- Station de Recherches Sous-Marines et Océanographiques (STARESO), Pointe de la Revellata, Calvi, France
| | - Monique Carnol
- InBioS - PhytoSystems, Laboratory of Plant and Microbial Ecology, Department of Biology, Ecology, Evolution, University of Liège, Liège, Belgium
| | - Bernard Bosman
- InBioS - PhytoSystems, Laboratory of Plant and Microbial Ecology, Department of Biology, Ecology, Evolution, University of Liège, Liège, Belgium
| | - Patrick Motte
- InBioS - PhytoSystems, Functional Genomics and Plant Molecular Imaging, University of Liège, Liège, Belgium
| | - Michelle Watt
- Root Dynamics Group, IBG-2 - Plant Sciences, Institut für Bio- und Geowissenschaften (IBG), Forschungszentrum Jülich, Jülich, Germany
| | - Marc Hanikenne
- InBioS - PhytoSystems, Functional Genomics and Plant Molecular Imaging, University of Liège, Liège, Belgium
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15
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Cheah BH, Chen YL, Lo JC, Tang IC, Yeh KC, Lin YF. Divalent nutrient cations: Friend and foe during zinc stress in rice. PLANT, CELL & ENVIRONMENT 2021; 44:3358-3375. [PMID: 34278584 DOI: 10.1111/pce.14154] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 04/27/2021] [Accepted: 07/10/2021] [Indexed: 06/13/2023]
Abstract
Zn deficiency is the most common micronutrient deficit in rice but Zn is also a widespread industrial pollutant. Zn deficiency responses in rice are well documented, but comparative responses to Zn deficiency and excess have not been reported. Therefore, we compared the physiological, transcriptional and biochemical properties of rice subjected to Zn starvation or excess at early and later treatment stages. Both forms of Zn stress inhibited root and shoot growth. Gene ontology analysis of differentially expressed genes highlighted the overrepresentation of Zn transport and antioxidative defense for both Zn stresses, whereas diterpene biosynthesis was solely induced by excess Zn. Divalent cations (Fe, Cu, Ca, Mn and Mg) accumulated in Zn-deficient shoots but Mg and Mn were depleted in the Zn excess shoots, mirroring the gene expression of non-specific Zn transporters and chelators. Ascorbate peroxidase activity was induced after 14 days of Zn starvation, scavenging H2 O2 more effectively to prevent leaf chlorosis via the Fe-dependent Fenton reaction. Conversely, excess Zn triggered the expression of genes encoding Mg/Mn-binding proteins (OsCPS2/4 and OsKSL4/7) required for antimicrobial diterpenoid biosynthesis. Our study reveals the potential role of divalent cations in the shoot, driving the unique responses of rice to each form of Zn stress.
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Affiliation(s)
- Boon Huat Cheah
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
| | - Yu-Ling Chen
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
| | - Jing-Chi Lo
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
- Department of Horticulture and Biotechnology, Chinese Culture University, Taipei, Taiwan
| | - I-Chien Tang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Kuo-Chen Yeh
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Ya-Fen Lin
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
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16
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Jamsheer K M, Kumar M. Transcription Factors as Zinc Sensors in Plants. TRENDS IN PLANT SCIENCE 2021; 26:761-763. [PMID: 33992539 DOI: 10.1016/j.tplants.2021.04.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/27/2021] [Accepted: 04/29/2021] [Indexed: 06/12/2023]
Abstract
Zinc (Zn) is an essential nutrient; however, understanding the sensing of cellular Zn status in plants has remained elusive. Recently, Lilay et al. identified a nuclear Zn-sensing mechanism where the conserved zinc sensor motif of Basic Leucine Zipper 19 (bZIP19) and bZIP23 transcription factors (TFs) bind to Zn2+ and coordinate their activity according to Zn availability.
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Affiliation(s)
- Muhammed Jamsheer K
- Amity Food and Agriculture Foundation, Amity University Uttar Pradesh, Sector 125, Noida 201313, India.
| | - Manoj Kumar
- Amity Food and Agriculture Foundation, Amity University Uttar Pradesh, Sector 125, Noida 201313, India
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17
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Zeng H, Wu H, Yan F, Yi K, Zhu Y. Molecular regulation of zinc deficiency responses in plants. JOURNAL OF PLANT PHYSIOLOGY 2021; 261:153419. [PMID: 33915366 DOI: 10.1016/j.jplph.2021.153419] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/06/2021] [Accepted: 04/09/2021] [Indexed: 05/27/2023]
Abstract
Zinc (Zn) is an essential micronutrient for plants and animals. Because of its low availability in arable soils worldwide, Zn deficiency is becoming a serious agricultural problem resulting in decreases of crop yield and nutritional quality. Plants have evolved multiple responses to adapt to low levels of soil Zn supply, involving biochemical and physiological changes to improve Zn acquisition and utilization, and defend against Zn deficiency stress. In this review, we summarize the physiological and biochemical adaptations of plants to Zn deficiency, the roles of transporters and metal-binding compounds in Zn homeostasis regulation, and the recent progresses in understanding the sophisticated regulatory mechanisms of Zn deficiency responses that have been made by molecular and genetic analyses, as well as diverse 'omics' studies. Zn deficiency responses are tightly controlled by multiple layers of regulation, such as transcriptional regulation that is mediated by transcription factors like F-group bZIP proteins, epigenetic regulation at the level of chromatin, and post-transcriptional regulation mediated by small RNAs and alternative splicing. The insights into the regulatory network underlying Zn deficiency responses and the perspective for further understandings of molecular regulation of Zn deficiency responses have been discussed. The understandings of the regulatory mechanisms will be important for improving Zn deficiency tolerance, Zn use efficiency, and Zn biofortification in plants.
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Affiliation(s)
- Houqing Zeng
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China.
| | - Haicheng Wu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Feng Yan
- Institute of Agronomy and Plant Breeding, Justus Liebig University of Giessen, Giessen, 35392, Germany
| | - Keke Yi
- Key Laboratory of Plant Nutrition and Fertilizers, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yiyong Zhu
- Agricultural Resource and Environment Experiment Teaching Center, College of Resource and Environment Science, Nanjing Agricultural University, Nanjing, 210095, China.
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18
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Lilay GH, Persson DP, Castro PH, Liao F, Alexander RD, Aarts MGM, Assunção AGL. Arabidopsis bZIP19 and bZIP23 act as zinc sensors to control plant zinc status. NATURE PLANTS 2021. [PMID: 33594269 DOI: 10.1101/2020.06.29.177287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Zinc (Zn) is an essential micronutrient for plants and animals owing to its structural and catalytic roles in many proteins1. Zn deficiency affects around 2 billion people, mainly those who live on plant-based diets relying on crops from Zn-deficient soils2,3. Plants maintain adequate Zn levels through tightly regulated Zn homeostasis mechanisms involving Zn uptake, distribution and storage4, but evidence of how they sense Zn status is lacking. Here, we use in vitro and in planta approaches to show that the Arabidopsis thaliana F-group bZIP transcription factors bZIP19 and bZIP23, which are the central regulators of the Zn deficiency response, function as Zn sensors by binding Zn2+ ions to a Zn-sensor motif. Deletions or modifications of this Zn-sensor motif disrupt Zn binding, leading to a constitutive transcriptional Zn deficiency response, which causes a significant increase in plant and seed Zn accumulation. As the Zn-sensor motif is highly conserved in F-group bZIP proteins across land plants, the identification of this plant Zn sensor will promote new strategies to improve the Zn nutritional quality of plant-derived food and feed, and contribute to tackling the global Zn-deficiency health problem.
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Affiliation(s)
- Grmay H Lilay
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Frederiksberg, Denmark
| | - Daniel P Persson
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Frederiksberg, Denmark
| | - Pedro Humberto Castro
- CIBIO-InBIO, Research Centre in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal
| | - Feixue Liao
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Frederiksberg, Denmark
| | - Ross D Alexander
- Laboratory of Genetics, Wageningen University & Research, Wageningen, the Netherlands
- Institute for Life and Earth Sciences, School of Energy, Geosciences, Infrastructure and Society, Heriot-Watt University, Edinburgh, UK
| | - Mark G M Aarts
- Laboratory of Genetics, Wageningen University & Research, Wageningen, the Netherlands
| | - Ana G L Assunção
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Frederiksberg, Denmark.
- CIBIO-InBIO, Research Centre in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal.
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19
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Lilay GH, Persson DP, Castro PH, Liao F, Alexander RD, Aarts MGM, Assunção AGL. Arabidopsis bZIP19 and bZIP23 act as zinc sensors to control plant zinc status. NATURE PLANTS 2021; 7:137-143. [PMID: 33594269 DOI: 10.1038/s41477-021-00856-7] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 01/13/2021] [Indexed: 05/06/2023]
Abstract
Zinc (Zn) is an essential micronutrient for plants and animals owing to its structural and catalytic roles in many proteins1. Zn deficiency affects around 2 billion people, mainly those who live on plant-based diets relying on crops from Zn-deficient soils2,3. Plants maintain adequate Zn levels through tightly regulated Zn homeostasis mechanisms involving Zn uptake, distribution and storage4, but evidence of how they sense Zn status is lacking. Here, we use in vitro and in planta approaches to show that the Arabidopsis thaliana F-group bZIP transcription factors bZIP19 and bZIP23, which are the central regulators of the Zn deficiency response, function as Zn sensors by binding Zn2+ ions to a Zn-sensor motif. Deletions or modifications of this Zn-sensor motif disrupt Zn binding, leading to a constitutive transcriptional Zn deficiency response, which causes a significant increase in plant and seed Zn accumulation. As the Zn-sensor motif is highly conserved in F-group bZIP proteins across land plants, the identification of this plant Zn sensor will promote new strategies to improve the Zn nutritional quality of plant-derived food and feed, and contribute to tackling the global Zn-deficiency health problem.
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Affiliation(s)
- Grmay H Lilay
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Frederiksberg, Denmark
| | - Daniel P Persson
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Frederiksberg, Denmark
| | - Pedro Humberto Castro
- CIBIO-InBIO, Research Centre in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal
| | - Feixue Liao
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Frederiksberg, Denmark
| | - Ross D Alexander
- Laboratory of Genetics, Wageningen University & Research, Wageningen, the Netherlands
- Institute for Life and Earth Sciences, School of Energy, Geosciences, Infrastructure and Society, Heriot-Watt University, Edinburgh, UK
| | - Mark G M Aarts
- Laboratory of Genetics, Wageningen University & Research, Wageningen, the Netherlands
| | - Ana G L Assunção
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Frederiksberg, Denmark.
- CIBIO-InBIO, Research Centre in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal.
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20
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Grosjean N, Blaby-Haas CE. Leveraging computational genomics to understand the molecular basis of metal homeostasis. THE NEW PHYTOLOGIST 2020; 228:1472-1489. [PMID: 32696981 DOI: 10.1111/nph.16820] [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: 04/22/2020] [Accepted: 07/03/2020] [Indexed: 06/11/2023]
Abstract
Genome-based data is helping to reveal the diverse strategies plants and algae use to maintain metal homeostasis. In addition to acquisition, distribution and storage of metals, acclimating to feast or famine can involve a wealth of genes that we are just now starting to understand. The fast-paced acquisition of genome-based data, however, is far outpacing our ability to experimentally characterize protein function. Computational genomic approaches are needed to fill the gap between what is known and unknown. To avoid misconstruing bioinformatically derived data, which is the root cause of the inaccurate functional annotations that plague databases, functional inferences from diverse sources and contextualization of that evidence with a robust understanding of protein family evolution is needed. Phylogenomic- and comparative-genomic-based studies can aid in the interpretation of experimental data or provide a spark for the discovery of a new function. These analyses not only lead to novel insight into a target protein's function but can generate thought-provoking insights across protein families.
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Affiliation(s)
- Nicolas Grosjean
- Biology Department, Brookhaven National Laboratory, Upton, NY, 11973, USA
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21
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Lilay GH, Castro PH, Guedes JG, Almeida DM, Campilho A, Azevedo H, Aarts MGM, Saibo NJM, Assunção AGL. Rice F-bZIP transcription factors regulate the zinc deficiency response. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:3664-3677. [PMID: 32133499 PMCID: PMC7307843 DOI: 10.1093/jxb/eraa115] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 03/02/2020] [Indexed: 05/07/2023]
Abstract
The F-bZIP transcription factors bZIP19 and bZIP23 are the central regulators of the zinc deficiency response in Arabidopsis, and phylogenetic analysis of F-bZIP homologs across land plants indicates that the regulatory mechanism of the zinc deficiency response may be conserved. Here, we identified the rice F-bZIP homologs and investigated their function. OsbZIP48 and OsbZIP50, but not OsbZIP49, complement the zinc deficiency-hypersensitive Arabidopsis bzip19bzip23 double mutant. Ectopic expression of OsbZIP50 in Arabidopsis significantly increases plant zinc accumulation under control zinc supply, suggesting an altered Zn sensing in OsbZIP50. In addition, we performed a phylogenetic analysis of F-bZIP homologs from representative monocot species that supports the branching of plant F-bZIPs into Group 1 and Group 2. Our results suggest that regulation of the zinc deficiency response in rice is conserved, with OsbZIP48 being a functional homolog of AtbZIP19 and AtbZIP23. A better understanding of the mechanisms behind the Zn deficiency response in rice and other important crops will contribute to develop plant-based strategies to address the problems of Zn deficiency in soils, crops, and cereal-based human diets.
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Affiliation(s)
- Grmay H Lilay
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Frederiksberg-C, Denmark
| | - Pedro Humberto Castro
- CIBIO-InBIO, Research Centre in Biodiversity and Genetic Resources, Campus Agrário de Vairão, University of Porto, Vairão, Portugal
| | - Joana G Guedes
- CIBIO-InBIO, Research Centre in Biodiversity and Genetic Resources, Campus Agrário de Vairão, University of Porto, Vairão, Portugal
| | - Diego M Almeida
- Genomics of Plant Stress Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, New University of Lisbon, Oeiras, Portugal
| | - Ana Campilho
- CIBIO-InBIO, Research Centre in Biodiversity and Genetic Resources, Campus Agrário de Vairão, University of Porto, Vairão, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Herlander Azevedo
- CIBIO-InBIO, Research Centre in Biodiversity and Genetic Resources, Campus Agrário de Vairão, University of Porto, Vairão, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Mark G M Aarts
- Laboratory of Genetics, Wageningen University& Research, Wageningen, The Netherlands
| | - Nelson J M Saibo
- Genomics of Plant Stress Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, New University of Lisbon, Oeiras, Portugal
| | - Ana G L Assunção
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Frederiksberg-C, Denmark
- CIBIO-InBIO, Research Centre in Biodiversity and Genetic Resources, Campus Agrário de Vairão, University of Porto, Vairão, Portugal
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22
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Ajeesh Krishna TP, Maharajan T, Victor Roch G, Ignacimuthu S, Antony Ceasar S. Structure, Function, Regulation and Phylogenetic Relationship of ZIP Family Transporters of Plants. FRONTIERS IN PLANT SCIENCE 2020; 11:662. [PMID: 32536933 PMCID: PMC7267038 DOI: 10.3389/fpls.2020.00662] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 04/29/2020] [Indexed: 05/24/2023]
Abstract
Zinc (Zn) is an essential micronutrient for plants and humans. Nearly 50% of the agriculture soils of world are Zn-deficient. The low availability of Zn reduces the yield and quality of the crops. The zinc-regulated, iron-regulated transporter-like proteins (ZIP) family and iron-regulated transporters (IRTs) are involved in cellular uptake of Zn, its intracellular trafficking and detoxification in plants. In addition to Zn, ZIP family transporters also transport other divalent metal cations (such as Cd2+, Fe2+, and Cu2+). ZIP transporters play a crucial role in biofortification of grains with Zn. Only a very limited information is available on structural features and mechanism of Zn transport of plant ZIP family transporters. In this article, we present a detailed account on structure, function, regulations and phylogenetic relationships of plant ZIP transporters. We give an insight to structure of plant ZIPs through homology modeling and multiple sequence alignment with Bordetella bronchiseptica ZIP (BbZIP) protein whose crystal structure has been solved recently. We also provide details on ZIP transporter genes identified and characterized in rice and other plants till date. Functional characterization of plant ZIP transporters will help for the better crop yield and human health in future.
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Affiliation(s)
- T. P. Ajeesh Krishna
- Division of Plant Biotechnology, Entomology Research Institute, Loyola College, University of Madras, Chennai, India
| | - T. Maharajan
- Division of Plant Biotechnology, Entomology Research Institute, Loyola College, University of Madras, Chennai, India
| | - G. Victor Roch
- Division of Plant Biotechnology, Entomology Research Institute, Loyola College, University of Madras, Chennai, India
| | | | - Stanislaus Antony Ceasar
- Division of Plant Biotechnology, Entomology Research Institute, Loyola College, University of Madras, Chennai, India
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23
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Jones DM, Vandepoele K. Identification and evolution of gene regulatory networks: insights from comparative studies in plants. CURRENT OPINION IN PLANT BIOLOGY 2020; 54:42-48. [PMID: 32062128 DOI: 10.1016/j.pbi.2019.12.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 12/10/2019] [Accepted: 12/18/2019] [Indexed: 05/04/2023]
Abstract
The availability of genome sequences, genome-wide assays of transcription factor binding, and accessible chromatin maps have unveiled gene regulatory landscapes in plants. This understanding has ushered in comparative gene regulatory network studies that assess network rewiring between species, across time, and between biological tissues. Comparisons of cis-regulatory elements across the plant kingdom have uncovered examples of conserved sequences, but also of divergence, indicating that selective pressures can vary in different plant families. Transcription factor duplication, followed by spatiotemporal expression divergence of the duplicates, also appears to be a key mechanism of network evolution. Here, we review recent literature describing the regulation of gene expression in plants, and how comparative studies provide insights into how these regulatory interactions change and lead to gene regulatory network rewiring.
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Affiliation(s)
- D Marc Jones
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium; Bioinformatics Institute Ghent, Ghent University, 9052 Ghent, Belgium
| | - Klaas Vandepoele
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium; Bioinformatics Institute Ghent, Ghent University, 9052 Ghent, Belgium.
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24
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Ceasar SA, Lekeux G, Motte P, Xiao Z, Galleni M, Hanikenne M. di-Cysteine Residues of the Arabidopsis thaliana HMA4 C-Terminus Are Only Partially Required for Cadmium Transport. FRONTIERS IN PLANT SCIENCE 2020; 11:560. [PMID: 32528485 PMCID: PMC7264368 DOI: 10.3389/fpls.2020.00560] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 04/15/2020] [Indexed: 05/12/2023]
Abstract
Cadmium (Cd) is highly toxic to the environment and humans. Plants are capable of absorbing Cd from the soil and of transporting part of this Cd to their shoot tissues. In Arabidopsis, the plasma membrane Heavy Metal ATPase 4 (HMA4) transporter mediates Cd xylem loading for export to shoots, in addition to zinc (Zn). A recent study showed that di-Cys motifs present in the HMA4 C-terminal extension (AtHMA4c) are essential for high-affinity Zn binding and transport in planta. In this study, we have characterized the role of the AtHMA4c di-Cys motifs in Cd transport in planta and in Cd-binding in vitro. In contrast to the case for Zn, the di-Cys motifs seem to be partly dispensable for Cd transport as evidenced by limited variation in Cd accumulation in shoot tissues of hma2hma4 double mutant plants expressing native or di-Cys mutated variants of AtHMA4. Expression analysis of metal homeostasis marker genes, such as AtIRT1, excluded that maintained Cd accumulation in shoot tissues was the result of increased Cd uptake by roots. In vitro Cd-binding assays further revealed that mutating di-Cys motifs in AtHMA4c had a more limited impact on Cd-binding than it has on Zn-binding. The contributions of the AtHMA4 C-terminal domain to metal transport and binding therefore differ for Zn and Cd. Our data suggest that it is possible to identify HMA4 variants that discriminate Zn and Cd for transport.
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Affiliation(s)
- Stanislaus Antony Ceasar
- InBioS – PhytoSystems, Functional Genomics and Plant Molecular Imaging, University of Liège, Liège, Belgium
- InBioS – Center for Protein Engineering, Biological Macromolecules, University of Liège, Liège, Belgium
| | - Gilles Lekeux
- InBioS – PhytoSystems, Functional Genomics and Plant Molecular Imaging, University of Liège, Liège, Belgium
- InBioS – Center for Protein Engineering, Biological Macromolecules, University of Liège, Liège, Belgium
| | - Patrick Motte
- InBioS – PhytoSystems, Functional Genomics and Plant Molecular Imaging, University of Liège, Liège, Belgium
| | - Zhiguang Xiao
- Melbourne Dementia Research Centre, Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, Australia
| | - Moreno Galleni
- InBioS – Center for Protein Engineering, Biological Macromolecules, University of Liège, Liège, Belgium
| | - Marc Hanikenne
- InBioS – PhytoSystems, Functional Genomics and Plant Molecular Imaging, University of Liège, Liège, Belgium
- *Correspondence: Marc Hanikenne,
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25
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Zeng H, Zhang X, Ding M, Zhang X, Zhu Y. Transcriptome profiles of soybean leaves and roots in response to zinc deficiency. PHYSIOLOGIA PLANTARUM 2019; 167:330-351. [PMID: 30536844 DOI: 10.1111/ppl.12894] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 11/25/2018] [Accepted: 12/03/2018] [Indexed: 05/27/2023]
Abstract
Zinc (Zn) deficiency is a widespread agricultural problem in arable soils of the whole world. However, the molecular mechanisms underlying Zn-deficiency response are largely unknown. Here, we analyzed the transcriptomic profilings of soybean leaves and roots in response to Zn deficiency through Illumina's high-throughput RNA sequencing in order to understand the molecular basis of Zn-deficiency response in the plants. A total of 614 and 1011 gene loci were found to be differentially expressed in leaves and roots, respectively, and 88 loci were commonly found in both leaves and roots. Twelve differentially expressed genes (DEGs) were randomly selected for validation by quantitative reverse transcription polymerase chain reaction, and their fold changes were similar to those of RNA-seq. Gene ontology enrichment analysis showed that ion transport, nicotianamine (NA) biosynthetic process and queuosine biosynthetic process were enriched in the upregulated genes, while oxidation-reduction process and defense response were enriched in the downregulated genes. Among the DEGs, 20 DEGs are potentially involved in Zn homeostasis, including seven ZRT, IRT-related protein (ZIP) transporter genes, three NA synthase genes, and seven metallothionein genes; 40 DEGs are possibly involved in diverse hormonal signals such as auxin, cytokinin, ethylene and gibberellin; nine DEGs are putatively involved in calcium signaling; 85 DEGs are putative transcription factor genes. Nine DEGs were found to contain zinc-deficiency-response element in their promoter regions. These results could provide comprehensive insights into the soybean response to Zn deficiency and will be helpful for further elucidation of the molecular mechanisms of Zn-deficiency response and Zn-deficiency tolerance in plants.
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Affiliation(s)
- Houqing Zeng
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Xin Zhang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Ming Ding
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiajun Zhang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Yiyong Zhu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
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26
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Van Bel M, Diels T, Vancaester E, Kreft L, Botzki A, Van de Peer Y, Coppens F, Vandepoele K. PLAZA 4.0: an integrative resource for functional, evolutionary and comparative plant genomics. Nucleic Acids Res 2019; 46:D1190-D1196. [PMID: 29069403 PMCID: PMC5753339 DOI: 10.1093/nar/gkx1002] [Citation(s) in RCA: 292] [Impact Index Per Article: 58.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 10/12/2017] [Indexed: 11/14/2022] Open
Abstract
PLAZA (https://bioinformatics.psb.ugent.be/plaza) is a plant-oriented online resource for comparative, evolutionary and functional genomics. The PLAZA platform consists of multiple independent instances focusing on different plant clades, while also providing access to a consistent set of reference species. Each PLAZA instance contains structural and functional gene annotations, gene family data and phylogenetic trees and detailed gene colinearity information. A user-friendly web interface makes the necessary tools and visualizations accessible, specific for each data type. Here we present PLAZA 4.0, the latest iteration of the PLAZA framework. This version consists of two new instances (Dicots 4.0 and Monocots 4.0) providing a large increase in newly available species, and offers access to updated and newly implemented tools and visualizations, helping users with the ever-increasing demands for complex and in-depth analyzes. The total number of species across both instances nearly doubles from 37 species in PLAZA 3.0 to 71 species in PLAZA 4.0, with a much broader coverage of crop species (e.g. wheat, palm oil) and species of evolutionary interest (e.g. spruce, Marchantia). The new PLAZA instances can also be accessed by a programming interface through a RESTful web service, thus allowing bioinformaticians to optimally leverage the power of the PLAZA platform.
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Affiliation(s)
- Michiel Van Bel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Tim Diels
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Emmelien Vancaester
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | | | | | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
- Genomics Research Institute, University of Pretoria, Private bag X20, Pretoria 0028, South Africa
- Bioinformatics Institute Ghent, Ghent University, 9052 Ghent, Belgium
| | - Frederik Coppens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, 9052 Ghent, Belgium
- To whom correspondence should be addressed. Tel: +32 9 331 3822; Fax: +32 9 331 3809;
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27
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He Y, Zhang M, Zhou W, Ai L, You J, Liu H, You J, Wang H, Wassie M, Wang M, Li H. Transcriptome analysis reveals novel insights into the continuous cropping induced response in Codonopsis tangshen, a medicinal herb. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 141:279-290. [PMID: 31202192 DOI: 10.1016/j.plaphy.2019.06.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 05/15/2019] [Accepted: 06/02/2019] [Indexed: 05/05/2023]
Abstract
Codonopsis tangshen Oliv. (C. tangshen Oliv.), a famous medicinal herb in China, is seriously affected by continuous cropping (C-cro). The physiological and biochemical results indicated that C-cro significantly affected the malonaldehyde (MDA) and chlorophyll content, as well as activities of catalase (CAT) and superoxide dismutase (SOD) when compared with the non-continuous cropping (NC-cro) group. Transcriptome profiling found 762 differentially expressed genes, including 430 up-regulated and 332 down-regulated genes by C-cro. In addition, pathway enrichment analysis revealed that genes related to 'Tyrosine degradation I', 'Glycogen synthesis' and 'Phenylalanine and tyrosine catabolism' were up-regulated, and genes associated with 'Signal transduction', 'Immune system', etc. were down-regulated by C-cro. The expression of target genes was further validated by Q-PCR. In this study, we demonstrated the effects of C-cro on C. tangshen at the transcriptome level, and found possible C-cro responsive candidate genes. These findings could be further beneficial for improving the continuous cropping tolerance.
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Affiliation(s)
- Yinsheng He
- College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan City, Hubei, 430070, PR China; Institute of Chinese Herbal Medicine, Hubei Academy of Agricultural Sciences, Enshi City, Hubei, 445000, PR China
| | - Meide Zhang
- Institute of Chinese Herbal Medicine, Hubei Academy of Agricultural Sciences, Enshi City, Hubei, 445000, PR China
| | - Wuxian Zhou
- Institute of Chinese Herbal Medicine, Hubei Academy of Agricultural Sciences, Enshi City, Hubei, 445000, PR China
| | - Lunqiang Ai
- Institute of Chinese Herbal Medicine, Hubei Academy of Agricultural Sciences, Enshi City, Hubei, 445000, PR China
| | - Jinwen You
- Institute of Chinese Herbal Medicine, Hubei Academy of Agricultural Sciences, Enshi City, Hubei, 445000, PR China
| | - Haihua Liu
- Institute of Chinese Herbal Medicine, Hubei Academy of Agricultural Sciences, Enshi City, Hubei, 445000, PR China
| | - Jingmao You
- Institute of Chinese Herbal Medicine, Hubei Academy of Agricultural Sciences, Enshi City, Hubei, 445000, PR China
| | - Hua Wang
- Institute of Chinese Herbal Medicine, Hubei Academy of Agricultural Sciences, Enshi City, Hubei, 445000, PR China
| | - Misganaw Wassie
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan City, Hubei, 430074, PR China
| | - Mo Wang
- College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan City, Hubei, 430070, PR China.
| | - Huiying Li
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan City, Hubei, 430074, PR China.
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28
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Suratanee A, Chokrathok C, Chutimanukul P, Khrueasan N, Buaboocha T, Chadchawan S, Plaimas K. Two-State Co-Expression Network Analysis to Identify Genes Related to Salt Tolerance in Thai rice. Genes (Basel) 2018; 9:E594. [PMID: 30501128 PMCID: PMC6316690 DOI: 10.3390/genes9120594] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 11/08/2018] [Accepted: 11/19/2018] [Indexed: 12/18/2022] Open
Abstract
Khao Dawk Mali 105 (KDML105) rice is one of the most important crops of Thailand. It is a challenging task to identify the genes responding to salinity in KDML105 rice. The analysis of the gene co-expression network has been widely performed to prioritize significant genes, in order to select the key genes in a specific condition. In this work, we analyzed the two-state co-expression networks of KDML105 rice under salt-stress and normal grown conditions. The clustering coefficient was applied to both networks and exhibited significantly different structures between the salt-stress state network and the original (normal-grown) network. With higher clustering coefficients, the genes that responded to the salt stress formed a dense cluster. To prioritize and select the genes responding to the salinity, we investigated genes with small partners under normal conditions that were highly expressed and were co-working with many more partners under salt-stress conditions. The results showed that the genes responding to the abiotic stimulus and relating to the generation of the precursor metabolites and energy were the great candidates, as salt tolerant marker genes. In conclusion, in the case of the complexity of the environmental conditions, gaining more information in order to deal with the co-expression network provides better candidates for further analysis.
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Affiliation(s)
- Apichat Suratanee
- Department of Mathematics, Faculty of Applied Science, King Mongkut's University of Technology North Bangkok 10800, Thailand.
| | - Chidchanok Chokrathok
- Advanced Virtual and Intelligent Computing (AVIC) Center, Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.
| | - Panita Chutimanukul
- Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.
| | | | - Teerapong Buaboocha
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.
| | - Supachitra Chadchawan
- Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.
| | - Kitiporn Plaimas
- Advanced Virtual and Intelligent Computing (AVIC) Center, Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.
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29
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Dröge-Laser W, Snoek BL, Snel B, Weiste C. The Arabidopsis bZIP transcription factor family-an update. CURRENT OPINION IN PLANT BIOLOGY 2018; 45:36-49. [PMID: 29860175 DOI: 10.1016/j.pbi.2018.05.001] [Citation(s) in RCA: 230] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Revised: 03/30/2018] [Accepted: 05/02/2018] [Indexed: 05/18/2023]
Abstract
The basic (region) leucine zippers (bZIPs) are evolutionarily conserved transcription factors in eukaryotic organisms. Here, we have updated the classification of the Arabidopsis thaliana bZIP-family, comprising 78 members, which have been assorted into 13 groups. Arabidopsis bZIPs are involved in a plethora of functions related to plant development, environmental signalling and stress response. Based on the classification, we have highlighted functional and regulatory aspects of selected well-studied bZIPs, which may serve as prototypic examples for the particular groups.
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Affiliation(s)
- Wolfgang Dröge-Laser
- Department of Pharmaceutical Biology, Julius-von-Sachs-Institute, Biocenter, Julius-Maximilians-Universität Würzburg, Würzburg 97082, Germany.
| | - Basten L Snoek
- Theoretical Biology and Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, Utrecht 3584 CH, The Netherlands
| | - Berend Snel
- Theoretical Biology and Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, Utrecht 3584 CH, The Netherlands
| | - Christoph Weiste
- Department of Pharmaceutical Biology, Julius-von-Sachs-Institute, Biocenter, Julius-Maximilians-Universität Würzburg, Würzburg 97082, Germany.
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30
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Zhu YP, Wang M, Xiang Y, Qiu L, Hu S, Zhang Z, Mattjus P, Zhu X, Zhang Y. Nach Is a Novel Subgroup at an Early Evolutionary Stage of the CNC-bZIP Subfamily Transcription Factors from the Marine Bacteria to Humans. Int J Mol Sci 2018; 19:ijms19102927. [PMID: 30261635 PMCID: PMC6213907 DOI: 10.3390/ijms19102927] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 09/19/2018] [Accepted: 09/22/2018] [Indexed: 02/07/2023] Open
Abstract
Normal growth and development, as well as adaptive responses to various intracellular and environmental stresses, are tightly controlled by transcriptional networks. The evolutionarily conserved genomic sequences across species highlights the architecture of such certain regulatory elements. Among them, one of the most conserved transcription factors is the basic-region leucine zipper (bZIP) family. Herein, we have performed phylogenetic analysis of these bZIP proteins and found, to our surprise, that there exist a few homologous proteins of the family members Jun, Fos, ATF2, BATF, C/EBP and CNC (cap’n’collar) in either viruses or bacteria, albeit expansion and diversification of this bZIP superfamily have occurred in vertebrates from metazoan. Interestingly, a specific group of bZIP proteins is identified, designated Nach (Nrf and CNC homology), because of their strong conservation with all the known CNC and NF-E2 p45 subunit-related factors Nrf1 and Nrf2. Further experimental evidence has also been provided, revealing that Nach1 and Nach2 from the marine bacteria exert distinctive functions, when compared with human Nrf1 and Nrf2, in the transcriptional regulation of antioxidant response element (ARE)-battery genes. Collectively, further insights into these Nach/CNC-bZIP subfamily transcription factors provide a novel better understanding of distinct biological functions of these factors expressed in distinct species from the marine bacteria to humans.
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Affiliation(s)
- Yu-Ping Zhu
- The Laboratory of Cell Biochemistry and Topogenetic Regulation, College of Bioengineering and Faculty of Sciences, Chongqing University, No. 174 Shazheng Street, Shapingba District, Chongqing 400044, China.
| | - Meng Wang
- The Laboratory of Cell Biochemistry and Topogenetic Regulation, College of Bioengineering and Faculty of Sciences, Chongqing University, No. 174 Shazheng Street, Shapingba District, Chongqing 400044, China.
| | - Yuancai Xiang
- The Laboratory of Cell Biochemistry and Topogenetic Regulation, College of Bioengineering and Faculty of Sciences, Chongqing University, No. 174 Shazheng Street, Shapingba District, Chongqing 400044, China.
| | - Lu Qiu
- The Laboratory of Cell Biochemistry and Topogenetic Regulation, College of Bioengineering and Faculty of Sciences, Chongqing University, No. 174 Shazheng Street, Shapingba District, Chongqing 400044, China.
| | - Shaofan Hu
- The Laboratory of Cell Biochemistry and Topogenetic Regulation, College of Bioengineering and Faculty of Sciences, Chongqing University, No. 174 Shazheng Street, Shapingba District, Chongqing 400044, China.
| | - Zhengwen Zhang
- Institute of Neuroscience and Psychology, School of Life Sciences, University of Glasgow, 42 Western Common Road, Glasgow G22 5PQ, Scotland, UK.
| | - Peter Mattjus
- Department of Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Artillerigatan 6A, III, BioCity, FI-20520 Turku, Finland.
| | - Xiaomei Zhu
- Shanghai Center for Quantitative Life Science and Department of Physics, Shanghai University, 99 Shangda Road, Shanghai 200444, China.
| | - Yiguo Zhang
- The Laboratory of Cell Biochemistry and Topogenetic Regulation, College of Bioengineering and Faculty of Sciences, Chongqing University, No. 174 Shazheng Street, Shapingba District, Chongqing 400044, China.
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31
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Castro PH, Santos MÂ, Freitas S, Cana-Quijada P, Lourenço T, Rodrigues MAA, Fonseca F, Ruiz-Albert J, Azevedo JE, Tavares RM, Castillo AG, Bejarano ER, Azevedo H. Arabidopsis thaliana SPF1 and SPF2 are nuclear-located ULP2-like SUMO proteases that act downstream of SIZ1 in plant development. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:4633-4649. [PMID: 30053161 PMCID: PMC6117582 DOI: 10.1093/jxb/ery265] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Post-translational modifiers such as the small ubiquitin-like modifier (SUMO) peptide act as fast and reversible protein regulators. Functional characterization of the sumoylation machinery has determined the key regulatory role that SUMO plays in plant development. Unlike components of the SUMO conjugation pathway, SUMO proteases (ULPs) are encoded by a relatively large gene family and are potential sources of specificity within the pathway. This study reports a thorough comparative genomics and phylogenetic characterization of plant ULPs, revealing the presence of one ULP1-like and three ULP2-like SUMO protease subgroups within plant genomes. As representatives of an under-studied subgroup, Arabidopsis SPF1 and SPF2 were subjected to functional characterization. Loss-of-function mutants implicated both proteins with vegetative growth, flowering time, and seed size and yield. Mutants constitutively accumulated SUMO conjugates, and yeast complementation assays associated these proteins with the function of ScUlp2 but not ScUlp1. Fluorescence imaging placed both proteins in the plant cell nucleoplasm. Transcriptomics analysis indicated strong regulatory involvement in secondary metabolism, cell wall remodelling, and nitrate assimilation. Furthermore, developmental defects of the spf1-1 spf2-2 (spf1/2) double-mutant opposed those of the major E3 ligase siz1 mutant and, most significantly, developmental and transcriptomic characterization of the siz1 spf1/2 triple-mutant placed SIZ1 as epistatic to SPF1 and SPF2.
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Affiliation(s)
- Pedro Humberto Castro
- Biosystems & Integrative Sciences Institute (BioISI), Plant Functional Biology Center (CBFP), University of Minho, Campus de Gualtar, Braga, Portugal
- Area de Genética, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Campus Teatinos, Málaga, Spain
- CIBIO, InBIO—Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
| | - Miguel Ângelo Santos
- Biosystems & Integrative Sciences Institute (BioISI), Plant Functional Biology Center (CBFP), University of Minho, Campus de Gualtar, Braga, Portugal
| | - Sara Freitas
- Biosystems & Integrative Sciences Institute (BioISI), Plant Functional Biology Center (CBFP), University of Minho, Campus de Gualtar, Braga, Portugal
- CIBIO, InBIO—Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
| | - Pepe Cana-Quijada
- Area de Genética, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Campus Teatinos, Málaga, Spain
| | - Tiago Lourenço
- Biosystems & Integrative Sciences Institute (BioISI), Plant Functional Biology Center (CBFP), University of Minho, Campus de Gualtar, Braga, Portugal
| | - Mafalda A A Rodrigues
- PRPlants Lab, GPlantS Unit, Instituto de Tecnologia Química e Biológica—Universidade Nova de Lisboa, Estação Agronómica Nacional, Oeiras, Portugal
| | - Fátima Fonseca
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
| | - Javier Ruiz-Albert
- Area de Genética, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Campus Teatinos, Málaga, Spain
| | - Jorge E Azevedo
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
- Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto, Porto, Portugal
| | - Rui Manuel Tavares
- Biosystems & Integrative Sciences Institute (BioISI), Plant Functional Biology Center (CBFP), University of Minho, Campus de Gualtar, Braga, Portugal
| | - Araceli G Castillo
- Area de Genética, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Campus Teatinos, Málaga, Spain
| | - Eduardo R Bejarano
- Area de Genética, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Campus Teatinos, Málaga, Spain
| | - Herlander Azevedo
- CIBIO, InBIO—Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
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32
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Martin RC, Vining K, Dombrowski JE. Genome-wide (ChIP-seq) identification of target genes regulated by BdbZIP10 during paraquat-induced oxidative stress. BMC PLANT BIOLOGY 2018; 18:58. [PMID: 29636001 PMCID: PMC5894230 DOI: 10.1186/s12870-018-1275-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 03/29/2018] [Indexed: 05/12/2023]
Abstract
BACKGROUND bZIP transcription factors play a significant role in many aspects of plant growth and development and also play critical regulatory roles during plant responses to various stresses. Overexpression of the Brachypodium bZIP10 (Bradi1g30140) transcription factor conferred enhanced oxidative stress tolerance and increased viability when plants or cells were exposed to the herbicide paraquat. To gain a better understanding of genes involved in bZIP10 conferred oxidative stress tolerance, chromatin immunoprecipitation followed by high throughput sequencing (ChIP-Seq) was performed on BdbZIP10 overexpressing plants in the presence of oxidative stress. RESULTS We identified a transcription factor binding motif, TGDCGACA, different from most known bZIP TF motifs but with strong homology to the Arabidopsis zinc deficiency response element. Analysis of the immunoprecipitated sequences revealed an enrichment of gene ontology groups with metal ion transmembrane transporter, transferase, catalytic and binding activities. Functional categories including kinases and phosphotransferases, cation/ion transmembrane transporters, transferases (phosphorus-containing and glycosyl groups), and some nucleoside/nucleotide binding activities were also enriched. CONCLUSIONS Brachypodium bZIP10 is involved in zinc homeostasis, as it relates to oxidative stress.
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Affiliation(s)
- Ruth C. Martin
- USDA ARS National Forage Seed and Cereal Research Unit, 3450 SW Campus Way, Corvallis, OR 97330 USA
| | - Kelly Vining
- Department of Horticulture, 4123 Agricultural & Life Sciences, Oregon State University, Corvallis, OR 97330 USA
| | - James E. Dombrowski
- USDA ARS National Forage Seed and Cereal Research Unit, 3450 SW Campus Way, Corvallis, OR 97330 USA
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Lilay GH, Castro PH, Campilho A, Assunção AGL. The Arabidopsis bZIP19 and bZIP23 Activity Requires Zinc Deficiency - Insight on Regulation From Complementation Lines. FRONTIERS IN PLANT SCIENCE 2018; 9:1955. [PMID: 30723487 PMCID: PMC6349776 DOI: 10.3389/fpls.2018.01955] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 12/17/2018] [Indexed: 05/06/2023]
Abstract
All living organisms require zinc as an essential micronutrient. Maintaining appropriate intracellular zinc supply, and avoiding deficiency or toxic excess, requires a tight regulation of zinc homeostasis. In Arabidopsis, bZIP19 and bZIP23 (basic-leucine zipper) transcription factors are the central regulators of the zinc deficiency response. Their targets include members of the ZIP (Zrt/Irt-like Protein) transporter family, involved in cellular zinc uptake, which are up-regulated at zinc deficiency. However, the mechanisms by which these transcription factors are regulated by cellular zinc status are not yet known. Here, to further our insight, we took advantage of the zinc deficiency hypersensitive phenotype of the bzip19 bzip23 double mutant, and used it as background to produce complementation lines of each Arabidopsis F-bZIP transcription factor, including bZIP24. On these lines, we performed complementation and localization studies, analyzed the transcript level of a subset of putative target genes, and performed elemental tissue profiling. We find evidence supporting that the zinc-dependent activity of bZIP19 and bZIP23 is modulated by zinc at protein level, in the nucleus, where cellular zinc sufficiency represses their activity and zinc deficiency is required. In addition, we show that these two transcription factors are functionally redundant to a large extent, and that differential tissue-specific expression patterns might, at least partly, explain distinct regulatory activities. Finally, we show that bZIP24 does not play a central role in the Zn deficiency response. Overall, we provide novel information that advances our understanding of the regulatory activity of bZIP19 and bZIP23.
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Affiliation(s)
- Grmay H. Lilay
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Frederiksberg, Denmark
| | - Pedro Humberto Castro
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Frederiksberg, Denmark
| | - Ana Campilho
- CIBIO/InBIO – Research Centre in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal
- Department of Biology, University of Porto, Porto, Portugal
| | - Ana G. L. Assunção
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Frederiksberg, Denmark
- CIBIO/InBIO – Research Centre in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal
- *Correspondence: Ana G. L. Assunção,
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Zhou Y, Xu D, Jia L, Huang X, Ma G, Wang S, Zhu M, Zhang A, Guan M, Lu K, Xu X, Wang R, Li J, Qu C. Genome-Wide Identification and Structural Analysis of bZIP Transcription Factor Genes in Brassica napus. Genes (Basel) 2017; 8:genes8100288. [PMID: 29064393 PMCID: PMC5664138 DOI: 10.3390/genes8100288] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Revised: 10/16/2017] [Accepted: 10/19/2017] [Indexed: 12/14/2022] Open
Abstract
The basic region/leucine zipper motif (bZIP) transcription factor family is one of the largest families of transcriptional regulators in plants. bZIP genes have been systematically characterized in some plants, but not in rapeseed (Brassica napus). In this study, we identified 247 BnbZIP genes in the rapeseed genome, which we classified into 10 subfamilies based on phylogenetic analysis of their deduced protein sequences. The BnbZIP genes were grouped into functional clades with Arabidopsis genes with similar putative functions, indicating functional conservation. Genome mapping analysis revealed that the BnbZIPs are distributed unevenly across all 19 chromosomes, and that some of these genes arose through whole-genome duplication and dispersed duplication events. All expression profiles of 247 bZIP genes were extracted from RNA-sequencing data obtained from 17 different B. napus ZS11 tissues with 42 various developmental stages. These genes exhibited different expression patterns in various tissues, revealing that these genes are differentially regulated. Our results provide a valuable foundation for functional dissection of the different BnbZIP homologs in B. napus and its parental lines and for molecular breeding studies of bZIP genes in B. napus.
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Affiliation(s)
- Yan Zhou
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China.
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China.
| | - Daixiang Xu
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China.
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China.
| | - Ledong Jia
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China.
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China.
| | - Xiaohu Huang
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China.
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China.
| | - Guoqiang Ma
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China.
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China.
| | - Shuxian Wang
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China.
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China.
| | - Meichen Zhu
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China.
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China.
| | - Aoxiang Zhang
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China.
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China.
| | - Mingwei Guan
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China.
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China.
| | - Kun Lu
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China.
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China.
| | - Xinfu Xu
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China.
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China.
| | - Rui Wang
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China.
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China.
| | - Jiana Li
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China.
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China.
| | - Cunmin Qu
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China.
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China.
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