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Singh S, Praveen A, Bhadrecha P. Genome-wide identification and analysis of SPL gene family in chickpea (Cicer arietinum L.). PROTOPLASMA 2024; 261:799-818. [PMID: 38378886 DOI: 10.1007/s00709-024-01936-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 02/06/2024] [Indexed: 02/22/2024]
Abstract
A transcription factor in plants encodes SQUAMOSA promoter binding protein-like (SPL) serves a broad spectrum of important roles for the plant, like, growth, flowering, and signal transduction. A gene family that encodes SPL proteins is documented in various model plant species, including Arabidopsis thaliana and Oryza sativa. Chickpea (Cicer arietinum), a leguminous crop, has not been thoroughly explored with regard to the SPL protein-encoding gene family. Chickpea SPL family genes were located and characterized computationally using a genomic database. Gene data of chickpea were obtained from the phytozome repository and was examined using bioinformatics methods. For investigating the possible roles of SPLs in chickpea, genome-wide characterization, expression, as well as structural analyses of this SPL gene family were performed. Cicer arietinum genome had 19 SPL genes, whereas, according to phylogenetic analysis, the SPLs in chickpea are segregated among four categories: Group-I has 2 introns, Group-II and IV have 1-2 introns (except CaSPL13 and CaSPL15 having 3 introns), and Group-III has 9 introns (except CaSPL1 and CaSPL11 with 1 and 8 introns, respectively). The SBP domain revealed that SPL proteins featured two zinc-binding sites, i.e., C3H and C2HC and one nuclear localization signal. All CaSPL proteins are found to contain highly conserved motifs, i.e., Motifs 1, 2, and 4, except CaSPL10 in which Motifs 1 and 4 were absent. Following analysis, it was found that Motifs 1 and 2 of the chickpea SBP domain are Zinc finger motifs, and Motif 4 includes a nuclear localization signal. All pairs of CaSPL paralogs developed by purifying selection. The CaSPL promoter investigation discovered cis-elements that are responsive to stress, light, and phytohormones. Examination of their expression patterns highlighted major CaSPLs to be evinced primarily among younger pods and flowers. Indicating their involvement in the plant's growth as well as development, along with their capacity to react as per different situations by handling the regulation of target gene's expression, several CaSPL genes are also expressed under certain stress conditions, namely, cold, salt, and drought. The majority of the CaSPL genes are widely expressed and play crucial roles in terms of the plant's growth, development, and responses to the environmental-stress conditions. Our work provides extensive insight into the gene family CaSPL, which might facilitate further studies related to the evolution and functions of the SPL genes for chickpea and other plant species.
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Affiliation(s)
- Shilpy Singh
- Department of Biotechnology and Microbiology, School of Sciences, Noida International University, Gautam Budh Nagar, 203201, U.P., India.
| | - Afsana Praveen
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 67, India
| | - Pooja Bhadrecha
- University Institute of Biotechnology, Chandigarh University, Mohali, Punjab, India
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De Paola C, Garcia-Carpintero V, Vazquez-Vilar M, Kaminski K, Fernandez-Del-Carmen A, Sierro N, Ivanov NV, Giuliano G, Waterhouse P, Orzaez D. Comparative analysis of the Squamosa Promoter Binding-Like (SPL) gene family in Nicotiana benthamiana and Nicotiana tabacum. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 335:111797. [PMID: 37467788 DOI: 10.1016/j.plantsci.2023.111797] [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: 03/27/2023] [Revised: 07/14/2023] [Accepted: 07/16/2023] [Indexed: 07/21/2023]
Abstract
SQUAMOSA PROMOTER BINDING-LIKE (SPL) proteins constitute a large family of transcription factors known to play key roles in growth and developmental processes, including juvenile-to-adult and vegetative-to-reproductive phase transitions. This makes SPLs interesting targets for precision breeding in plants of the Nicotiana genus used as e.g. recombinant biofactories. We report the identification of 49 SPL genes in Nicotiana tabacum cv. K326 and 43 SPL genes in Nicotiana benthamiana LAB strain, which were classified into eight phylogenetic groups according to the SPL classification in Arabidopsis. Exon-intron gene structure and DNA-binding domains were highly conserved between homeologues and orthologues. Thirty of the NbSPL genes and 33 of the NtSPL genes were found to be possible targets of microRNA 156. The expression of SPL genes in leaves was analysed by RNA-seq at three different stages, revealing that genes not under miR156 control were in general constitutively expressed at high levels, whereas miR156-regulated genes showed lower expression, often developmentally regulated. We selected the N. benthamiana SPL13_1a gene as target for a CRISPR/Cas9 knock-out experiment. We show here that a full knock-out in this single gene leads to a significant delay in flowering time, a trait that could be exploited to increase biomass for recombinant protein production.
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Affiliation(s)
- Carmine De Paola
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Valencia, Spain
| | | | - Marta Vazquez-Vilar
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Valencia, Spain
| | | | | | - Nicolas Sierro
- PMI R&D, Philip Morris Products S.A, Neuchâtel, Switzerland
| | | | | | | | - Diego Orzaez
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Valencia, Spain.
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The NtSPL Gene Family in Nicotiana tabacum: Genome-Wide Investigation and Expression Analysis in Response to Cadmium Stress. Genes (Basel) 2023; 14:genes14010183. [PMID: 36672923 PMCID: PMC9859093 DOI: 10.3390/genes14010183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/04/2023] [Accepted: 01/06/2023] [Indexed: 01/13/2023] Open
Abstract
The SQUAMOSA promoter binding protein-like (SPL)SPL family genes play an important role in regulating plant growth and development, synthesis of secondary metabolites, and resistance to stress. Understanding of the role of the SPL family in tobacco is still limited. In this study, 42 NtSPL genes were identified from the genome of the tobacco variety TN90. According to the results of the conserved motif and phylogenetic tree, the NtSPL genes were divided into eight subgroups, and the genes in the same subgroup showed similar gene structures and conserved domains. The cis-acting element analysis of the NtSPL promoters showed that the NtSPL genes were regulated by plant hormones and stresses. Twenty-eight of the 42 NtSPL genes can be targeted by miR156. Transcriptome data and qPCR results indicated that the expression pattern of miR156-targeted NtSPL genes was usually tissue specific. The expression level of miR156 in tobacco was induced by Cd stress, and the expression pattern of NtSPL4a showed a significant negative correlation with that of miR156. These results suggest that miR156-NtSPL4a may mediate the tobacco response to Cd stress. This study lays a foundation for further research on the function of the NtSPL gene and provides new insights into the involvement of NtSPL genes in the plant response to heavy metal stress.
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Cleophas FN, Zahari NZ, Murugayah P, Rahim SA, Mohd Yatim AN. Phytoremediation: A Novel Approach of Bast Fiber Plants (Hemp, Kenaf, Jute and Flax) for Heavy Metals Decontamination in Soil-Review. TOXICS 2022; 11:5. [PMID: 36668731 PMCID: PMC9864374 DOI: 10.3390/toxics11010005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/01/2022] [Accepted: 12/16/2022] [Indexed: 06/17/2023]
Abstract
Heavy metal pollution in the environment is a major concern for humans as it is non-biodegradable and can have a lot of effects on the environment, humans as well as plants. At present, a solution to this problem is suggested in terms of a new, innovative and eco-friendly technology known as phytoremediation. Bast fiber plants are typically non-edible crops that have a short life cycle. It is one of the significant crops that has attracted interest for many industrial uses because of its constant fiber supply and ease of maintenance. Due to its low maintenance requirements with minimum economic investment, bast fiber plants have been widely used in phytoremediation. Nevertheless, these plants have the ability to extract metals from the soil through their deep roots, combined with their commercial prospects, making them an ideal candidate as a profit-yielding crop for phytoremediation purposes. Therefore, a comprehensive review is needed for a better understanding of the morphology and phytoremediation mechanism of four commonly bast fiber plants, such as hemp (Cannabis sativa), kenaf (Hibiscus cannabinus), jute (Corchorus olitorius) and Flax (Linum usitatissimum). This review article summarizes the existing research on the phytoremediation potential of these plants grown in different toxic pollutants such as Lead (Pb), Cadmium (Cd) and Zinc (Zn). This work also discusses several aids including natural and chemical amendments to improve phytoremediation. The role of these amendments in the bioavailability of contaminants, their uptake, translocation and bioaccumulation, as well as their effect on plant growth and development, has been highlighted in this paper. This paper helps in identifying, comparing and addressing the recent achievements of bast fiber plants for the phytoremediation of heavy metals in contaminated soil.
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Affiliation(s)
- Fera Nony Cleophas
- Environmental Science Programme, Faculty of Science & Natural Resources, Universiti Malaysia Sabah, UMS Road, Kota Kinabalu 88400, Sabah, Malaysia
- Small Islands Research Center, Universiti Malaysia Sabah, UMS Road, Kota Kinabalu 88400, Sabah, Malaysia
| | - Nur Zaida Zahari
- Environmental Science Programme, Faculty of Science & Natural Resources, Universiti Malaysia Sabah, UMS Road, Kota Kinabalu 88400, Sabah, Malaysia
- Small Islands Research Center, Universiti Malaysia Sabah, UMS Road, Kota Kinabalu 88400, Sabah, Malaysia
| | - Pavitra Murugayah
- Environmental Science Programme, Faculty of Science & Natural Resources, Universiti Malaysia Sabah, UMS Road, Kota Kinabalu 88400, Sabah, Malaysia
| | - Sahibin Abd Rahim
- Environmental Science Programme, Faculty of Science & Natural Resources, Universiti Malaysia Sabah, UMS Road, Kota Kinabalu 88400, Sabah, Malaysia
| | - Ahmad Norazhar Mohd Yatim
- Environmental Science Programme, Faculty of Science & Natural Resources, Universiti Malaysia Sabah, UMS Road, Kota Kinabalu 88400, Sabah, Malaysia
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Prusty S, Sahoo RK, Nayak S, Poosapati S, Swain DM. Proteomic and Genomic Studies of Micronutrient Deficiency and Toxicity in Plants. PLANTS 2022; 11:plants11182424. [PMID: 36145825 PMCID: PMC9501179 DOI: 10.3390/plants11182424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 09/02/2022] [Accepted: 09/04/2022] [Indexed: 11/21/2022]
Abstract
Micronutrients are essential for plants. Their growth, productivity and reproduction are directly influenced by the supply of micronutrients. Currently, there are eight trace elements considered to be essential for higher plants: Fe, Zn, Mn, Cu, Ni, B, Mo, and Cl. Possibly, other essential elements could be discovered because of recent advances in nutrient solution culture techniques and in the commercial availability of highly sensitive analytical instrumentation for elemental analysis. Much remains to be learned about the physiology of micronutrient absorption, translocation and deposition in plants, and about the functions they perform in plant growth and development. With the recent advancements in the proteomic and molecular biology tools, researchers have attempted to explore and address some of these questions. In this review, we summarize the current knowledge of micronutrients in plants and the proteomic/genomic approaches used to study plant nutrient deficiency and toxicity.
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Affiliation(s)
- Suchismita Prusty
- Department of Biotechnology, Centurion University of Technology and Management, Bhubaneswar 752050, Odisha, India
| | - Ranjan Kumar Sahoo
- Department of Biotechnology, Centurion University of Technology and Management, Bhubaneswar 752050, Odisha, India
| | - Subhendu Nayak
- Division of Health Sciences, The Clorox Company, 210W Pettigrew Street, Durham, NC 27701, USA
| | - Sowmya Poosapati
- Division of Biological Sciences, Cell and Developmental Biology Section, University of California, San Diego, CA 92093, USA
- Correspondence: (S.P.); (D.M.S.)
| | - Durga Madhab Swain
- Division of Biological Sciences, Cell and Developmental Biology Section, University of California, San Diego, CA 92093, USA
- Correspondence: (S.P.); (D.M.S.)
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Zhang F, Yang J, Zhang N, Wu J, Si H. Roles of microRNAs in abiotic stress response and characteristics regulation of plant. FRONTIERS IN PLANT SCIENCE 2022; 13:919243. [PMID: 36092392 PMCID: PMC9459240 DOI: 10.3389/fpls.2022.919243] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 08/08/2022] [Indexed: 05/27/2023]
Abstract
MicroRNAs (miRNAs) are a class of non-coding endogenous small RNAs (long 20-24 nucleotides) that negatively regulate eukaryotes gene expression at post-transcriptional level via cleavage or/and translational inhibition of targeting mRNA. Based on the diverse roles of miRNA in regulating eukaryotes gene expression, research on the identification of miRNA target genes has been carried out, and a growing body of research has demonstrated that miRNAs act on target genes and are involved in various biological functions of plants. It has an important influence on plant growth and development, morphogenesis, and stress response. Recent case studies indicate that miRNA-mediated regulation pattern may improve agronomic properties and confer abiotic stress resistance of plants, so as to ensure sustainable agricultural production. In this regard, we focus on the recent updates on miRNAs and their targets involved in responding to abiotic stress including low temperature, high temperature, drought, soil salinity, and heavy metals, as well as plant-growing development. In particular, this review highlights the diverse functions of miRNAs on achieving the desirable agronomic traits in important crops. Herein, the main research strategies of miRNAs involved in abiotic stress resistance and crop traits improvement were summarized. Furthermore, the miRNA-related challenges and future perspectives of plants have been discussed. miRNA-based research lays the foundation for exploring miRNA regulatory mechanism, which aims to provide insights into a potential form of crop improvement and stress resistance breeding.
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Affiliation(s)
- Feiyan Zhang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
- State Key Laboratory of Plant Genomics/Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jiangwei Yang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Ning Zhang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jiahe Wu
- State Key Laboratory of Plant Genomics/Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Huaijun Si
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
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Yang Y, Huang J, Sun Q, Wang J, Huang L, Fu S, Qin S, Xie X, Ge S, Li X, Cheng Z, Wang X, Chen H, Zheng B, He Y. microRNAs: Key Players in Plant Response to Metal Toxicity. Int J Mol Sci 2022; 23:ijms23158642. [PMID: 35955772 PMCID: PMC9369385 DOI: 10.3390/ijms23158642] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 07/28/2022] [Accepted: 07/30/2022] [Indexed: 02/04/2023] Open
Abstract
Environmental metal pollution is a common problem threatening sustainable and safe crop production. Heavy metals (HMs) cause toxicity by targeting key molecules and life processes in plant cells. Plants counteract excess metals in the environment by enhancing defense responses, such as metal chelation, isolation to vacuoles, regulating metal intake through transporters, and strengthening antioxidant mechanisms. In recent years, microRNAs (miRNAs), as a small non-coding RNA, have become the central regulator of a variety of abiotic stresses, including HMs. With the introduction of the latest technologies such as next-generation sequencing (NGS), more and more miRNAs have been widely recognized in several plants due to their diverse roles. Metal-regulated miRNAs and their target genes are part of a complex regulatory network. Known miRNAs coordinate plant responses to metal stress through antioxidant functions, root growth, hormone signals, transcription factors (TF), and metal transporters. This article reviews the research progress of miRNAs in the stress response of plants to the accumulation of HMs, such as Cu, Cd, Hg, Cr, and Al, and the toxicity of heavy metal ions.
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Affiliation(s)
- Ying Yang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; (Y.Y.); (Q.S.); (J.W.); (L.H.); (S.F.); (S.Q.); (X.X.); (S.G.); (X.L.); (Z.C.); (X.W.)
| | - Jiu Huang
- School of Environment Science and Spatial Informaftics, China University of Mining and Technology, Xuzhou 221116, China;
| | - Qiumin Sun
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; (Y.Y.); (Q.S.); (J.W.); (L.H.); (S.F.); (S.Q.); (X.X.); (S.G.); (X.L.); (Z.C.); (X.W.)
| | - Jingqi Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; (Y.Y.); (Q.S.); (J.W.); (L.H.); (S.F.); (S.Q.); (X.X.); (S.G.); (X.L.); (Z.C.); (X.W.)
| | - Lichao Huang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; (Y.Y.); (Q.S.); (J.W.); (L.H.); (S.F.); (S.Q.); (X.X.); (S.G.); (X.L.); (Z.C.); (X.W.)
| | - Siyi Fu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; (Y.Y.); (Q.S.); (J.W.); (L.H.); (S.F.); (S.Q.); (X.X.); (S.G.); (X.L.); (Z.C.); (X.W.)
| | - Sini Qin
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; (Y.Y.); (Q.S.); (J.W.); (L.H.); (S.F.); (S.Q.); (X.X.); (S.G.); (X.L.); (Z.C.); (X.W.)
| | - Xiaoting Xie
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; (Y.Y.); (Q.S.); (J.W.); (L.H.); (S.F.); (S.Q.); (X.X.); (S.G.); (X.L.); (Z.C.); (X.W.)
| | - Sisi Ge
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; (Y.Y.); (Q.S.); (J.W.); (L.H.); (S.F.); (S.Q.); (X.X.); (S.G.); (X.L.); (Z.C.); (X.W.)
| | - Xiang Li
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; (Y.Y.); (Q.S.); (J.W.); (L.H.); (S.F.); (S.Q.); (X.X.); (S.G.); (X.L.); (Z.C.); (X.W.)
| | - Zhuo Cheng
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; (Y.Y.); (Q.S.); (J.W.); (L.H.); (S.F.); (S.Q.); (X.X.); (S.G.); (X.L.); (Z.C.); (X.W.)
| | - Xiaofei Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; (Y.Y.); (Q.S.); (J.W.); (L.H.); (S.F.); (S.Q.); (X.X.); (S.G.); (X.L.); (Z.C.); (X.W.)
| | - Houming Chen
- Max Planck Institute for Biology, Max Planck Ring 5, 72076 Tübingen, Germany;
| | - Bingsong Zheng
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; (Y.Y.); (Q.S.); (J.W.); (L.H.); (S.F.); (S.Q.); (X.X.); (S.G.); (X.L.); (Z.C.); (X.W.)
- Correspondence: (B.Z.); (Y.H.); Tel./Fax: +86-0571-8663-3652 (Y.H.)
| | - Yi He
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; (Y.Y.); (Q.S.); (J.W.); (L.H.); (S.F.); (S.Q.); (X.X.); (S.G.); (X.L.); (Z.C.); (X.W.)
- Correspondence: (B.Z.); (Y.H.); Tel./Fax: +86-0571-8663-3652 (Y.H.)
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Begum Y. Regulatory role of microRNAs (miRNAs) in the recent development of abiotic stress tolerance of plants. Gene 2022; 821:146283. [PMID: 35143944 DOI: 10.1016/j.gene.2022.146283] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 01/12/2022] [Accepted: 02/03/2022] [Indexed: 12/21/2022]
Abstract
MicroRNAs (miRNAs) are a distinct groups of single-stranded non-coding, tiny regulatory RNAs approximately 20-24 nucleotides in length. miRNAs negatively influence gene expression at the post-transcriptional level and have evolved considerably in the development of abiotic stress tolerance in a number of model plants and economically important crop species. The present review aims to deliver the information on miRNA-mediated regulation of the expression of major genes or Transcription Factors (TFs), as well as genetic and regulatory pathways. Also, the information on adaptive mechanisms involved in plant abiotic stress responses, prediction, and validation of targets, computational tools, and databases available for plant miRNAs, specifically focus on their exploration for engineering abiotic stress tolerance in plants. The regulatory function of miRNAs in plant growth, development, and abiotic stresses consider in this review, which uses high-throughput sequencing (HTS) technologies to generate large-scale libraries of small RNAs (sRNAs) for conventional screening of known and novel abiotic stress-responsive miRNAs adds complexity to regulatory networks in plants. The discoveries of miRNA-mediated tolerance to multiple abiotic stresses, including salinity, drought, cold, heat stress, nutritional deficiency, UV-radiation, oxidative stress, hypoxia, and heavy metal toxicity, are highlighted and discussed in this review.
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Affiliation(s)
- Yasmin Begum
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, APC Road, Kolkata 700009, West Bengal, India; Center of Excellence in Systems Biology and Biomedical Engineering (TEQIP Phase-III), University of Calcutta, JD-2, Sector III, Salt Lake, Kolkata 700106, West Bengal, India.
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van Dijk JR, Kranchev M, Blust R, Cuypers A, Vissenberg K. Arabidopsis root growth and development under metal exposure presented in an adverse outcome pathway framework. PLANT, CELL & ENVIRONMENT 2022; 45:737-750. [PMID: 34240430 PMCID: PMC9290988 DOI: 10.1111/pce.14147] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 05/06/2021] [Accepted: 07/02/2021] [Indexed: 06/13/2023]
Abstract
Due to human activities, soils become more and more polluted with metals, which imposes risks for human health and wildlife welfare. As most of the metals end up in the food chain through accumulation in plants, we need to establish science-based environmental criteria and risk management policies. To meet these necessities, a thorough understanding is required of how these metals accumulate in and affect plants. Many studies have been conducted towards this aim, but strikingly, only a few entries can be found in ecotoxicological databases, especially on Arabidopsis thaliana, which serves as a model species for plant (cell) physiology and genetic studies. As experimental conditions seem to vary considerably throughout literature, extrapolation or comparison of data is rather difficult or should be approached with caution. Furthermore, metal-polluted soils often contain more than one metal, yet limited studies investigated the impact of metal mixtures on plants. This review aims to compile all data concerning root system architecture under Cu, Cd and Zn stress, in single or multi-metal exposure in A. thaliana, and link it to metal-induced responses at different biological levels. Global incorporation into an adverse outcome pathway framework is presented.
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Affiliation(s)
- Jesper R. van Dijk
- Integrated Molecular Plant Physiology Research, Department of BiologyUniversity of AntwerpAntwerpBelgium
- Adrem Data Lab, Department of Mathematics and Computer Science and Biomedical Informatics Research Network Antwerp (Biomina)University of AntwerpAntwerpBelgium
| | - Mario Kranchev
- Integrated Molecular Plant Physiology Research, Department of BiologyUniversity of AntwerpAntwerpBelgium
| | - Ronny Blust
- Systemic Physiological and Ecotoxicological Research, Department of BiologyUniversity of AntwerpAntwerpBelgium
| | - Ann Cuypers
- Environmental Biology, Centre for Environmental SciencesHasselt UniversityHasseltBelgium
| | - Kris Vissenberg
- Integrated Molecular Plant Physiology Research, Department of BiologyUniversity of AntwerpAntwerpBelgium
- Plant Biochemistry & Biotechnology Lab, Department of AgricultureHellenic Mediterranean UniversityHeraklionGreece
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Liu D, Zheng K, Wang Y, Zhang Y, Lao R, Qin Z, Li T, Zhao Z. Harnessing an arbuscular mycorrhizal fungus to improve the adaptability of a facultative metallophytic poplar (Populus yunnanensis) to cadmium stress: Physiological and molecular responses. JOURNAL OF HAZARDOUS MATERIALS 2022; 424:127430. [PMID: 34678563 DOI: 10.1016/j.jhazmat.2021.127430] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 09/24/2021] [Accepted: 10/02/2021] [Indexed: 06/13/2023]
Abstract
Populus yunnanensis Dode, a facultative metallophytic poplar, exhibits afforestation potential in barren mine tailing areas. However, the interactions and functional roles of arbuscular mycorrhizal fungus (AMF) in P. yunnanensis adaptability to heavy metal stress remain unclear. Physiological and molecular responses of P. yunnanensis plantlets to AMF (Funneliformis mosseae) under cadmium (Cd) stress (50 mg kg-1) were investigated. Results showed attenuation of Cd phytotoxicity effects on cell organelles upon AMF inoculation, which also reduced the Cd concentration in the poplar leaves, stems, and roots. Under Cd stress, AMF-blocking of metal transporter (e.g., Ca2+ channel) activity occurred, decreasing root cell Cd influx by reducing H+ efflux. Bioaugmentation of rhizosphere sediments by AMF to stabilize metals with a decreasing DTPA-extractable Cd also occurred. The AMF inoculation promoted Cd conversion into inactive, less phytotoxic forms, and helped to maintain ion homeostasis and relieve nutritional ion (e.g., Ca, Mg) disorders caused by excessive Cd. Leaf enzyme and non-enzyme antioxidant systems were triggered. Root and leaf physiological response patterns differed. The AMF regulated the poplar functional genes, and nine metal-responsive gene clusters were identified. We suggest that AMF is a functional component of P. yunnanensis phenotype extension, contributing to strong adaptability to unfavorable mine tailings conditions.
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Affiliation(s)
- Di Liu
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan University, Kunming 650091, PR China; School of Life Sciences, Yunnan University, Kunming 650091, PR China
| | - Kuanyu Zheng
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan University, Kunming 650091, PR China; Key Laboratory of Agricultural Biotechnology of Yunnan Province, Biotechnology and Germplasm Resources Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, PR China
| | - Yue Wang
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan University, Kunming 650091, PR China; School of Life Sciences, Yunnan University, Kunming 650091, PR China
| | - Yan Zhang
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan University, Kunming 650091, PR China; School of Life Sciences, Yunnan University, Kunming 650091, PR China
| | - Ruimin Lao
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan University, Kunming 650091, PR China; School of Life Sciences, Yunnan University, Kunming 650091, PR China
| | - Zhiyang Qin
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan University, Kunming 650091, PR China; School of Life Sciences, Yunnan University, Kunming 650091, PR China
| | - Tao Li
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan University, Kunming 650091, PR China; School of Life Sciences, Yunnan University, Kunming 650091, PR China.
| | - Zhiwei Zhao
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan University, Kunming 650091, PR China; School of Life Sciences, Yunnan University, Kunming 650091, PR China.
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11
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Amaral Dos Reis R, Hendrix S, Mourato MP, Louro Martins L, Vangronsveld J, Cuypers A. Efficient regulation of copper homeostasis underlies accession-specific sensitivities to excess copper and cadmium in roots of Arabidopsis thaliana. JOURNAL OF PLANT PHYSIOLOGY 2021; 261:153434. [PMID: 34020275 DOI: 10.1016/j.jplph.2021.153434] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 04/13/2021] [Accepted: 04/26/2021] [Indexed: 06/12/2023]
Abstract
The commonly used Arabidopsis thaliana natural accessions Columbia (Col-0) and Wassilewskija (Ws) are known to differ in their metal sensitivity, with Col-0 being more sensitive to copper (Cu) and cadmium (Cd) than Ws. As both Cu and Cd are known to affect Cu homeostasis, it was investigated whether this process is part of an accession-specific mechanism underlying their difference in metal sensitivity. As roots are the first contact point during metal exposure, responses were compared between roots of both accessions of hydroponically grown plants exposed to excess Cu or Cd for 24 and 72 h. Root Cu levels increased in both accessions under Cu and Cd exposure. However, under Cu exposure, the downregulation of Cu transporter (COPT) genes in combination with a more pronounced upregulation of metallothionein gene MT2b indicated that Ws plants coped better with the elevated Cu concentrations. The Cd-induced disturbance in Cu homeostasis was more efficiently counteracted in roots of Ws plants than in Col-0 plants. This was indicated by a higher upregulation of the SPL7-mediated pathway, crucial in the regulation of the Cu homeostasis response. In conclusion, maintaining the Cu homeostasis response in roots is key to accession-specific differences in Cu and Cd sensitivity.
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Affiliation(s)
- Rafaela Amaral Dos Reis
- Environmental Biology, Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Sophie Hendrix
- Environmental Biology, Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium; Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
| | | | - Luísa Louro Martins
- LEAF, Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, Portugal
| | - Jaco Vangronsveld
- Environmental Biology, Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Ann Cuypers
- Environmental Biology, Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium.
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12
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Yue E, Tao H, Xu J. Genome-wide analysis of microRNA156 and its targets, the genes encoding SQUAMOSA promoter-binding protein-like (SPL) transcription factors, in the grass family Poaceae. J Zhejiang Univ Sci B 2021; 22:366-382. [PMID: 33973419 DOI: 10.1631/jzus.b2000519] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
MicroRNAs (miRNAs) are endogenous small non-coding RNAs that play an important role in post-transcriptional gene regulation in plants and animals by targeting messenger RNAs (mRNAs) for cleavage or repressing translation of specific mRNAs. The first miRNA identified in plants, miRNA156 (miR156), targets the SQUAMOSA promoter-binding protein-like (SPL) transcription factors, which play critical roles in plant phase transition, flower and plant architecture, and fruit development. We identified multiple copies of MIR156 and SPL in the rice, Brachypodium, sorghum, maize, and foxtail millet genomes. Sequence and chromosomal synteny analysis showed that both MIR156s and SPLs are conserved across species in the grass family. Analysis of expression data of the SPLs in eleven juvenile and adult rice tissues revealed that four non-miR156-targeted genes were highly expressed and three miR156-targeted genes were only slightly expressed in all tissues/developmental stages. The remaining SPLs were highly expressed in the juvenile stage, but their expression was lower in the adult stage. It has been proposed that under strong selective pressure, non-miR156-targeted mRNA may be able to re-structure to form a miRNA-responsive element. In our analysis, some non-miR156-targeted SPLs (SPL5/8/10) had gene structure and gene expression patterns similar to those of miR156-targeted genes, suggesting that they could diversify into miR156-targeted genes. DNA methylation profiles of SPLs and MIR156s in different rice tissues showed diverse methylation patterns, and hypomethylation of non-CG sites was observed in rice endosperm. Our findings suggested that MIR156s and SPLs had different origination and evolutionary mechanisms: the SPLs appear to have resulted from vertical evolution, whereas MIR156s appear to have resulted from strong evolutionary selection on mature sequences.
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Affiliation(s)
- Erkui Yue
- Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, China
| | - Hua Tao
- Henan Agricultural Radio and Television School, Zhengzhou 450008, China
| | - Jianhong Xu
- Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, China.
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13
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Pagano L, Rossi R, Paesano L, Marmiroli N, Marmiroli M. miRNA regulation and stress adaptation in plants. ENVIRONMENTAL AND EXPERIMENTAL BOTANY 2021. [PMID: 0 DOI: 10.1016/j.envexpbot.2020.104369] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
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14
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Huang S, Zhou J, Gao L, Tang Y. Plant miR397 and its functions. FUNCTIONAL PLANT BIOLOGY : FPB 2021; 48:361-370. [PMID: 33333000 DOI: 10.1071/fp20342] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 11/23/2020] [Indexed: 06/12/2023]
Abstract
MicroRNAs (miRNAs) are noncoding, small RNAs of 20-24 nucleotides (nt) and function critically at the post-transcriptional level to regulate gene expression through cleaving mRNA targets or interfering with translation of the target mRNAs. They are broadly involved in many biological processes in plants. The miR397 family in plants contains several conserved members either in 21-nt or in 22-nt that mainly target the laccase (LAC) genes functioning in lignin synthesis and are involved in the development of plants under various conditions. Recent findings showed that miR397b in Arabidopsis could also target to Casein Kinase II Subunit Beta 3 (CKB3) and mediate circadian regulation and plant flowering. This review aims to summarise recent updates on miR397 and provides the available basis for understanding the functional mechanisms of miR397 in plant growth and development regulation and in response to external adverse stimulation.
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Affiliation(s)
- Shili Huang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, Guangdong province, China
| | - Jiajie Zhou
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, Guangdong province, China
| | - Lei Gao
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, Guangdong province, China
| | - Yulin Tang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, Guangdong province, China; and Corresponding author.
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15
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Chaâbene Z, Rorat A, Kriaa W, Rekik I, Mejdoub H, Vandenbulcke F, Elleuch A. In-site and Ex-site Date Palm Exposure to Heavy Metals Involved Infra-Individual Biomarkers Upregulation. PLANTS 2021; 10:plants10010137. [PMID: 33445405 PMCID: PMC7826821 DOI: 10.3390/plants10010137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 12/29/2020] [Accepted: 01/06/2021] [Indexed: 11/16/2022]
Abstract
As a tree of considerable importance in arid regions-date palm, Phoenix dactylifera L. survival in contaminated areas of Sfax city has drawn our attention. Leaf samples of the plants grown in the study area showed high levels of cadmium (Cd), copper (Cu), and chromium (Cr). On the basis of this finding, the cellular mechanisms that explain these metal accumulations were investigated in controlled conditions. After four months of exposure to Cd, Cr, or Cu, high bioconcentration and translocation factor (TF>1) have been shown for date palm plantlets exposed to Cd and low TF values were obtained for plantlets treated with Cr and Cu. Moreover, accumulation of oxidants and antioxidant enzyme activities occurred in exposed roots to Cu and Cd. Secondary metabolites, such as polyphenols and flavonoids, were enhanced in plants exposed at low metal concentrations and declined thereafter. Accumulation of flavonoids in cells may be correlated with the expression of the gene encoding Pdmate5, responsible for the transport of secondary metabolites, especially flavonoids. Other transporter genes responded positively to metal incorporation, especially Pdhma2, but also Pdabcc and Pdnramp6. The latter would be a new candidate gene sensitive to metallic stress in plants. Expressions of gene coding metal chelators were also investigated. Pdpcs1 and Pdmt3 exhibited a strong induction in plants exposed to Cr. These modifications of the expression of some biochemical and molecular based-markers in date palm helped to better understand the ability of the plant to tolerate metals. They could be useful in assessing heavy metal contaminations in polluted soils and may improve accumulation capacity of other plants.
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Affiliation(s)
- Zayneb Chaâbene
- Laboratory of Plant Biotechnology, Faculty of Sciences of Sfax, University of Sfax, Sfax 3000, Tunisia; (H.M.); (A.E.)
- Laboratoire de Génie Civil et géo-Environnement–Université de Lille 1, F-59655 Villeneuve d’Ascq, France; (A.R.); (F.V.)
- Correspondence:
| | - Agnieszka Rorat
- Laboratoire de Génie Civil et géo-Environnement–Université de Lille 1, F-59655 Villeneuve d’Ascq, France; (A.R.); (F.V.)
| | - Walid Kriaa
- Environmental Science Center, Qatar University, Doha P.O. Box 2713, Qatar;
| | - Imen Rekik
- High Institute of Applied Biology of Medenine, Medenine 4119, Tunisia;
| | - Hafedh Mejdoub
- Laboratory of Plant Biotechnology, Faculty of Sciences of Sfax, University of Sfax, Sfax 3000, Tunisia; (H.M.); (A.E.)
| | - Franck Vandenbulcke
- Laboratoire de Génie Civil et géo-Environnement–Université de Lille 1, F-59655 Villeneuve d’Ascq, France; (A.R.); (F.V.)
| | - Amine Elleuch
- Laboratory of Plant Biotechnology, Faculty of Sciences of Sfax, University of Sfax, Sfax 3000, Tunisia; (H.M.); (A.E.)
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MicroRNA-Mediated Responses to Cadmium Stress in Arabidopsis thaliana. PLANTS 2021; 10:plants10010130. [PMID: 33435199 PMCID: PMC7827075 DOI: 10.3390/plants10010130] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/06/2021] [Accepted: 01/07/2021] [Indexed: 01/30/2023]
Abstract
In recent decades, the presence of cadmium (Cd) in the environment has increased significantly due to anthropogenic activities. Cd is taken up from the soil by plant roots for its subsequent translocation to shoots. However, Cd is a non-essential heavy metal and is therefore toxic to plants when it over-accumulates. MicroRNA (miRNA)-directed gene expression regulation is central to the response of a plant to Cd stress. Here, we document the miRNA-directed response of wild-type Arabidopsis thaliana (Arabidopsis) plants and the drb1, drb2 and drb4 mutant lines to Cd stress. Phenotypic and physiological analyses revealed the drb1 mutant to display the highest degree of tolerance to the imposed stress while the drb2 mutant was the most sensitive. RT-qPCR-based molecular profiling of miRNA abundance and miRNA target gene expression revealed DRB1 to be the primary double-stranded RNA binding (DRB) protein required for the production of six of the seven Cd-responsive miRNAs analyzed. However, DRB2, and not DRB1, was determined to be required for miR396 production. RT-qPCR further inferred that transcript cleavage was the RNA silencing mechanism directed by each assessed miRNA to control miRNA target gene expression. Taken together, the results presented here reveal the complexity of the miRNA-directed molecular response of Arabidopsis to Cd stress.
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17
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Shi W, Liu W, Ma C, Zhang Y, Ding S, Yu W, Deng S, Zhou J, Li H, Luo ZB. Dissecting MicroRNA-mRNA Regulatory Networks Underlying Sulfur Assimilation and Cadmium Accumulation in Poplar Leaves. PLANT & CELL PHYSIOLOGY 2020; 61:1614-1630. [PMID: 32678905 DOI: 10.1093/pcp/pcaa084] [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: 01/21/2020] [Accepted: 06/15/2020] [Indexed: 05/22/2023]
Abstract
The process of cadmium (Cd) accumulation and detoxification under different sulfur levels remains largely unknown in woody plants. To investigate the physiological and transcriptomic regulation mechanisms of poplars in response to different sulfate (S) supply levels and Cd exposure, we exposed Populus deltoides saplings to one of the low, moderate and high S levels together with either 0 or 50 µM Cd. Cd accumulation was decreased in low S-treated poplar leaves, and it tended to be increased in high S-supplied leaves under the Cd exposure condition. Sulfur nutrition was deficient in low S-supplied poplars, and it was improved in high S-treated leaves. Cd exposure resulted in lower sulfur level in the leaves supplied with moderate S, it exacerbated a Cd-induced sulfur decrease in low S-treated leaves and it caused a higher sulfur concentration in high S-supplied leaves. In line with the physiological changes, a number of mRNAs and microRNAs (miRNAs) involved in Cd accumulation and sulfur assimilation were identified and the miRNA-mRNA networks were dissected. In the networks, miR395 and miR399 members were identified as hub miRNAs and their targets were ATP sulfurylase 3 (ATPS3) and phosphate 2 (PHO2), respectively. These results suggest that Cd accumulation and sulfur assimilation are constrained by low and enhanced by high S supply, and Cd toxicity is aggravated by low and relieved by high S in poplar leaves, and that miRNA-mRNA regulatory networks play pivotal roles in sulfur-mediated Cd accumulation and detoxification in Cd-exposed poplars.
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Affiliation(s)
- Wenguang Shi
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Wenzhe Liu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Chaofeng Ma
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
- College of Forestry, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yuhong Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
- Annoroad Gene Technology Co., Ltd, 6 Kechuang Road, Beijing 100176, China
| | - Shen Ding
- College of Forestry, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Wenjian Yu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Shurong Deng
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Jing Zhou
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Hong Li
- Postgraduate School, Chinese Academy of Forestry, Beijing 100091, China
| | - Zhi-Bin Luo
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
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Sun Z, Shu L, Zhang W, Wang Z. Cca-miR398 increases copper sulfate stress sensitivity via the regulation of CSD mRNA transcription levels in transgenic Arabidopsis thaliana. PeerJ 2020; 8:e9105. [PMID: 32518719 PMCID: PMC7258901 DOI: 10.7717/peerj.9105] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 04/10/2020] [Indexed: 01/07/2023] Open
Abstract
MicroRNAs play crucial roles during the process of plant development under stress conditions. Copper is an essential micronutrient for most organisms and serves as an important redox-active cofactor for various functional proteins. In the present study, we investigated the effects of copper sulfate stress on hickory (Carya cathayensis) root development. We identified that hickory cca-miR398 was related to copper sulfate stress response, targeting Copper/Zinc superoxide dismutases (cytosolic (CSD1) and chloroplastic (CSD2)) and a 5b subunit of mitochondrial cytochrome C oxidase (COX5b.1) that are linked directly to stress regulatory networks. The sequence of hickory cca-miR398 is highly similar to that of Arabidopsis miR398b and miR398c, regardless of one nucleotide variation. Therefore, target genes of cca-miR398 were investigated by using 5′-Rapid-amplification of cDNA ends. An overexpression of cca-miR398 in Arabidopsis caused a reduction not only in root length and cotyledon greening, but also in the CSD1, CSD2, and CSD3 transcription levels. These reductions had greater significance in transgenic Arabidopsis than in wild-type Arabidopsis under copper sulfate stress. The level of physiological indicators also changed in transgenic Arabidopsis. In addition, the expressions of copper-responsive microRNAs, such as miR397 and miR408, were affected by the copper sulfate stress. These results showed that CSD possesses the ability to enhance copper sulfate stress response in both transgenic Arabidopsis and hickory roots by increasing the production of superoxide dismutase. Our results also demonstrated that cca-miR398 weakens hickory tolerance to copper sulfate by regulating CSD targets.
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Affiliation(s)
- Zhichao Sun
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Lilu Shu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Wei Zhang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Zhengjia Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang, China
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Wei H, Zhou J, Xu C, Movahedi A, Sun W, Li D, Zhuge Q. Identification and Characterization of an OSH1 Thiol Reductase from Populus Trichocarpa. Cells 2019; 9:E76. [PMID: 31892265 PMCID: PMC7017176 DOI: 10.3390/cells9010076] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 12/24/2019] [Accepted: 12/25/2019] [Indexed: 01/11/2023] Open
Abstract
Interferon gamma-induced lysosomal thiol reductase (GILT) is abundantly expressed in antigen-presenting cells and participates in the treatment and presentation of antigens by major histocompatibility complex II. Also, GILT catalyzes the reduction of disulfide bonds, which plays an important role in cellular immunity. (1) Background: At present, the studies of GILT have mainly focused on animals. In plants, GILT homologous gene (Arabidopsis thalianaOSH1: AtOSH1) was discovered in the forward screen of mutants with compromised responses to sulphur nutrition. However, the complete properties and functions of poplar OSH1 are unclear. In addition, CdCl2 stress is swiftly engulfing the limited land resources on which humans depend, restricting agricultural production. (2) Methods: A prokaryotic expression system was used to produce recombinant PtOSH1 protein, and Western blotting was performed to identify its activity. In addition, a simplified version of the floral-dip method was used to transform A. thaliana. (3) Results: Here, we describe the identification and characterization of OSH1 from Populus trichocarpa. The deduced PtOSH1 sequence contained CQHGX2ECX2NX4C and CXXC motifs. The transcript level of PtOSH1 was increased by cadmium (Cd) treatment. In addition, recombinant PtOSH1 reduced disulfide bonds. A stress assay showed that PtOSH1-overexpressing (OE) A. thaliana lines had greater resistance to Cd than wild-type (WT) plants. Also, the activities of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) in PtOSH1-OE plants were significantly higher than those in WT A. thaliana. These results indicate that PtOSH1 likely plays an important role in the response to Cd by regulating the reactive oxygen species (ROS)-scavenging system. (4) Conclusions: PtOSH1 catalyzes the reduction of disulfide bonds and behaves as a sulfhydryl reductase under acidic conditions. The overexpression of PtOSH1 in A. thaliana promoted root development, fresh weight, and dry weight; upregulated the expression levels of ROS scavenging-related genes; and improved the activity of antioxidant enzymes, enhancing plant tolerance to cadmium (Cd) stress. This study aimed to provide guidance that will facilitate future studies of the function of PtOSH1 in the response of plants to Cd stress.
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Affiliation(s)
- Hui Wei
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China; (H.W.); (C.X.); (A.M.); (W.S.); (D.L.)
| | - Jie Zhou
- Jiangsu Academy of Forestry, Nanjing 211153, China;
| | - Chen Xu
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China; (H.W.); (C.X.); (A.M.); (W.S.); (D.L.)
- Jiangsu Provincial Key Construction Laboratory of Special Biomass Resource Utilization, Nanjing Key Laboratory of Quality and Safety of Agricultural Products, Nanjing Xiaozhuang University, Nanjing 211171, China
| | - Ali Movahedi
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China; (H.W.); (C.X.); (A.M.); (W.S.); (D.L.)
| | - Weibo Sun
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China; (H.W.); (C.X.); (A.M.); (W.S.); (D.L.)
| | - Dawei Li
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China; (H.W.); (C.X.); (A.M.); (W.S.); (D.L.)
| | - Qiang Zhuge
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China; (H.W.); (C.X.); (A.M.); (W.S.); (D.L.)
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20
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Fu XZ, Zhang XY, Qiu JY, Zhou X, Yuan M, He YZ, Chun CP, Cao L, Ling LL, Peng LZ. Whole-transcriptome RNA sequencing reveals the global molecular responses and ceRNA regulatory network of mRNAs, lncRNAs, miRNAs and circRNAs in response to copper toxicity in Ziyang Xiangcheng (Citrus junos Sieb. Ex Tanaka). BMC PLANT BIOLOGY 2019; 19:509. [PMID: 31752684 PMCID: PMC6873749 DOI: 10.1186/s12870-019-2087-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 10/20/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND Copper (Cu) toxicity has become a potential threat for citrus production, but little is known about related mechanisms. This study aims to uncover the global landscape of mRNAs, long non-coding RNAs (lncRNAs), circular RNAs (circRNAs) and microRNAs (miRNAs) in response to Cu toxicity so as to construct a regulatory network of competing endogenous RNAs (ceRNAs) and to provide valuable knowledge pertinent to Cu response in citrus. RESULTS Tolerance of four commonly used rootstocks to Cu toxicity was evaluated, and 'Ziyang Xiangcheng' (Citrus junos) was found to be the most tolerant genotype. Then the roots and leaves sampled from 'Ziyang Xiangcheng' with or without Cu treatment were used for whole-transcriptome sequencing. In total, 5734 and 222 mRNAs, 164 and 5 lncRNAs, 45 and 17 circRNAs, and 147 and 130 miRNAs were identified to be differentially expressed (DE) in Cu-treated roots and leaves, respectively, in comparison with the control. Gene ontology enrichment analysis showed that most of the DEmRNAs and targets of DElncRNAs and DEmiRNAs were annotated to the categories of 'oxidation-reduction', 'phosphorylation', 'membrane', and 'ion binding'. The ceRNA network was then constructed with the predicted pairs of DEmRNAs-DEmiRNAs and DElncRNAs-DEmiRNAs, which further revealed regulatory roles of these DERNAs in Cu toxicity. CONCLUSIONS A large number of mRNAs, lncRNAs, circRNAs, and miRNAs in 'Ziyang Xiangcheng' were altered in response to Cu toxicity, which may play crucial roles in mitigation of Cu toxicity through the ceRNA regulatory network in this Cu-tolerant rootstock.
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Affiliation(s)
- Xing-Zheng Fu
- Citrus Research Institute, Southwest University, Chongqing, 400712, China.
- Citrus Research Institute, Chinese Academy of Agricultural Sciences, Chongqing, 400712, China.
| | - Xiao-Yong Zhang
- Citrus Research Institute, Southwest University, Chongqing, 400712, China
- Citrus Research Institute, Chinese Academy of Agricultural Sciences, Chongqing, 400712, China
| | - Jie-Ya Qiu
- Citrus Research Institute, Southwest University, Chongqing, 400712, China
- Citrus Research Institute, Chinese Academy of Agricultural Sciences, Chongqing, 400712, China
| | - Xue Zhou
- Citrus Research Institute, Southwest University, Chongqing, 400712, China
- Citrus Research Institute, Chinese Academy of Agricultural Sciences, Chongqing, 400712, China
| | - Meng Yuan
- Citrus Research Institute, Southwest University, Chongqing, 400712, China
- Citrus Research Institute, Chinese Academy of Agricultural Sciences, Chongqing, 400712, China
| | - Yi-Zhong He
- Citrus Research Institute, Southwest University, Chongqing, 400712, China
- Citrus Research Institute, Chinese Academy of Agricultural Sciences, Chongqing, 400712, China
| | - Chang-Pin Chun
- Citrus Research Institute, Southwest University, Chongqing, 400712, China
- Citrus Research Institute, Chinese Academy of Agricultural Sciences, Chongqing, 400712, China
| | - Li Cao
- Citrus Research Institute, Southwest University, Chongqing, 400712, China
- Citrus Research Institute, Chinese Academy of Agricultural Sciences, Chongqing, 400712, China
| | - Li-Li Ling
- Citrus Research Institute, Southwest University, Chongqing, 400712, China
- Citrus Research Institute, Chinese Academy of Agricultural Sciences, Chongqing, 400712, China
| | - Liang-Zhi Peng
- Citrus Research Institute, Southwest University, Chongqing, 400712, China.
- Citrus Research Institute, Chinese Academy of Agricultural Sciences, Chongqing, 400712, China.
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21
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Chen Q, Lu X, Guo X, Pan Y, Yu B, Tang Z, Guo Q. Differential responses to Cd stress induced by exogenous application of Cu, Zn or Ca in the medicinal plant Catharanthus roseus. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 157:266-275. [PMID: 29626640 DOI: 10.1016/j.ecoenv.2018.03.055] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 03/12/2018] [Accepted: 03/23/2018] [Indexed: 05/08/2023]
Abstract
Cd(II) is one of the most widespread and toxic heavy metals and seriously threatens plant growth, furthermore negatively affecting human health. For survival from this metal stress, plants always fight with Cd(II) toxicity by themselves or using other external factors. The effects of second metals copper (Cu(II)), zinc (Zn(II)) and calcium (Ca(II)) on the Cd(II)-affected root morphology, Cd(II) translocation and metabolic responses in Catharanthus roseus were investigated under hydroponic conditions. We found that the Cd-stressed plants displayed the browning and rot root symptom, excess H2O2 content, lipid peroxidation and Cd(II) accumulation in plants. However, the supplement with second metals largely alleviated Cd-induced toxicity, including browning and rot roots, oxidative stress and internal Cd(II) accumulation. The amended effects at metabolic and transcriptional levels involved in different second metals share either common or divergent strategies. They commonly repressed Cd uptake and promoted Cd(II) translocation from roots to shoots with divergent mechanisms. High Zn(II) could activate MTs expression in roots, while Cu(II) or Ca(II) did not under Cd(II) stress condition. The presence of Ca(II) under Cd stress condition largely initiated occurrence of lateral roots. We then grouped a metabolic diagram integrating terpenoid indole alkaloid (TIA) accumulation and TIA pathway gene expression to elucidate the metabolic response of C. roseus to Cd(II) alone or combined with second metals. The treatment with 100 Cd(II) alone largely promoted accumulation of vinblastine, vindoline, catharanthine and loganin, whereas depressed or little changed the expression levels of genes detected here, compared to 0 Cd(II) control. In the presence of Cd(II), the supplement with second metals displayed specific effect on different alkaloid. Among them, the metal Ca(II) is especially beneficial for serpentine accumulation, Zn(II) mainly promoted tabersonine production. However, the addition of Cu(II) commonly depressed accumulation of most alkaloids detected here. Generally, we presented different mechanisms by which the second metals used to alleviate Cd (II) toxicity. This plant has potential application in phytoremediation of Cd(II), due to relatively substantial accumulation of biomass, as well as secondary metabolites TIAs used as pharmaceutical materials when facing Cd stress.
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Affiliation(s)
- Qi Chen
- Center for Ecological Research, Northeast Forestry University, Harbin 150040, PR China
| | - Xueyan Lu
- Center for Ecological Research, Northeast Forestry University, Harbin 150040, PR China
| | - Xiaorui Guo
- Key Laboratory of Plant Ecology, Northeast Forestry University, Harbin 150040, PR China
| | - Yajie Pan
- Key Laboratory of Plant Ecology, Northeast Forestry University, Harbin 150040, PR China
| | - Bofan Yu
- Key Laboratory of Plant Ecology, Northeast Forestry University, Harbin 150040, PR China
| | - Zhonghua Tang
- Key Laboratory of Plant Ecology, Northeast Forestry University, Harbin 150040, PR China.
| | - Qingxi Guo
- Center for Ecological Research, Northeast Forestry University, Harbin 150040, PR China.
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22
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Ding Y, Gong S, Wang Y, Wang F, Bao H, Sun J, Cai C, Yi K, Chen Z, Zhu C. MicroRNA166 Modulates Cadmium Tolerance and Accumulation in Rice. PLANT PHYSIOLOGY 2018; 177:1691-1703. [PMID: 29925586 PMCID: PMC6084659 DOI: 10.1104/pp.18.00485] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 06/04/2018] [Indexed: 05/04/2023]
Abstract
MicroRNAs (miRNAs) are 20- to 24-nucleotide small noncoding RNAs that regulate gene expression in eukaryotic organisms. Several plant miRNAs, such as miR166, have vital roles in plant growth, development and responses to environmental stresses. One such environmental stress encountered by crop plants is exposure to cadmium (Cd), an element highly toxic to most organisms, including humans and plants. In this study, we analyzed the role of miR166 in Cd accumulation and tolerance in rice (Oryza sativa). The expression levels of miR166 in both root and leaf tissues were significantly higher in the reproductive stage than in the seedling stage in rice. The expression of miR166 in the roots of rice seedlings was reduced after Cd treatment. Overexpression of miR166 in rice improved Cd tolerance, a result associated with the reduction of Cd-induced oxidative stress in transgenic rice plants. Furthermore, overexpression of miR166 reduced both Cd translocation from roots to shoots and Cd accumulation in the grains. miR166 targets genes encoding the class-III homeodomain-Leu zipper (HD-Zip) family proteins in plants. In rice, HOMEODOMAIN CONTAINING PROTEIN4 (OsHB4) gene (Os03g43930), which encodes an HD-Zip protein, was up-regulated by Cd treatment but down-regulated by overexpression of miR166 in transgenic rice plants. Overexpression of OsHB4 increased Cd sensitivity and Cd accumulation in the leaves and grains of transgenic rice plants. By contrast, silencing OsHB4 by RNA interference enhanced Cd tolerance in transgenic rice plants. These results indicate a critical role for miR166 in Cd accumulation and tolerance through regulation of its target gene, OsHB4, in rice.
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Affiliation(s)
- Yanfei Ding
- Key Laboratory of Marine, Food Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, People's Republic of China
| | - Shaohua Gong
- Key Laboratory of Marine, Food Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, People's Republic of China
| | - Yi Wang
- Key Laboratory of Marine, Food Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, People's Republic of China
| | - Feijuan Wang
- Key Laboratory of Marine, Food Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, People's Republic of China
| | - Hexigeduleng Bao
- Key Laboratory of Marine, Food Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, People's Republic of China
| | - Junwei Sun
- Key Laboratory of Marine, Food Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, People's Republic of China
| | - Chong Cai
- Key Laboratory of Marine, Food Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, People's Republic of China
| | - Keke Yi
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Science, Beijing 100081, China
| | - Zhixiang Chen
- Key Laboratory of Marine, Food Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, People's Republic of China
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907-2054
| | - Cheng Zhu
- Key Laboratory of Marine, Food Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, People's Republic of China
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23
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Amaral Dos Reis R, Keunen E, Mourato MP, Martins LL, Vangronsveld J, Cuypers A. Accession-specific life strategies affect responses in leaves of Arabidopsis thaliana plants exposed to excess Cu and Cd. JOURNAL OF PLANT PHYSIOLOGY 2018; 223:37-46. [PMID: 29471274 DOI: 10.1016/j.jplph.2018.01.008] [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] [Received: 10/23/2017] [Revised: 01/20/2018] [Accepted: 01/25/2018] [Indexed: 06/08/2023]
Abstract
The natural accession Columbia (Col-0) is considered as the reference genome of the model plant Arabidopsis thaliana. Nonetheless, Col-0 plants are more sensitive to excess copper (Cu) and cadmium (Cd) than other widely used accessions such as Wassilewskija (Ws) plants. In the current study, this accession-specific metal sensitivity is further explored by comparing the responses in leaves of Col-0 and Ws plants exposed to excess Cu and Cd. Our results suggest that different life strategies favored by both accessions under physiological conditions affect their response to metal exposure. While Col-0 plants mainly invest in metal detoxification, Ws plants center on nutrient homeostasis. In particular, the higher expression of genes related to Cu homeostasis genes in non-exposed conditions indicates that Ws plants possess a constitutively efficient metal homeostasis. On the other hand, oxidative stress-related MAPK signaling appears to be boosted in leaves of Col-0 plants exposed to excess Cu. Furthermore, the upregulation of the glutathione (GSH) biosynthesis GSH2 gene and the increased GSH concentration after Cd exposure suggest the activation of detoxification mechanisms, such as phytochelatin production, to counteract the more severe Cd-induced oxidative stress in leaves of Col-0 plants. Exposure to Cd also led to a more pronounced ethylene signaling response in leaves of Col-0 as compared to Ws plants, which could be related to Cd-induced GSH metabolism. In conclusion, accession-specific life strategies clearly affect the way in which leaves of A. thaliana plants cope with excess Cu and Cd.
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Affiliation(s)
- Rafaela Amaral Dos Reis
- Environmental Biology, Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium.
| | - Els Keunen
- Environmental Biology, Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium.
| | - Miguel Pedro Mourato
- LEAF, Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, Portugal.
| | - Luísa Louro Martins
- LEAF, Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, Portugal.
| | - Jaco Vangronsveld
- Environmental Biology, Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium.
| | - Ann Cuypers
- Environmental Biology, Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium.
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Zhou Q, Zhang S, Chen F, Liu B, Wu L, Li F, Zhang J, Bao M, Liu G. Genome-wide identification and characterization of the SBP-box gene family in Petunia. BMC Genomics 2018; 19:193. [PMID: 29703141 PMCID: PMC6389188 DOI: 10.1186/s12864-018-4537-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 02/08/2018] [Indexed: 11/29/2022] Open
Abstract
Background SQUAMOSA PROMOTER BINDING PROTEIN (SBP)-box genes encode a family of plant-specific transcription factors (TFs) that play important roles in many growth and development processes including phase transition, leaf initiation, shoot and inflorescence branching, fruit development and ripening etc. The SBP-box gene family has been identified and characterized in many species, but has not been well studied in Petunia, an important ornamental genus. Results We identified 21 putative SPL genes of Petunia axillaris and P. inflata from the reference genome of P. axillaris N and P. inflata S6, respectively, which were supported by the transcriptome data. For further confirmation, all the 21 genes were also cloned from P. hybrida line W115 (Mitchel diploid). Phylogenetic analysis based on the highly conserved SBP domains arranged PhSPLs in eight groups, analogous to those from Arabidopsis and tomato. Furthermore, the Petunia SPL genes had similar exon-intron structure and the deduced proteins contained very similar conserved motifs within the same subgroup. Out of 21 PhSPL genes, fourteen were predicted to be potential targets of PhmiR156/157, and the putative miR156/157 response elements (MREs) were located in the coding region of group IV, V, VII and VIII genes, but in the 3’-UTR regions of group VI genes. SPL genes were also identified from another two wild Petunia species, P. integrifolia and P. exserta, based on their transcriptome databases to investigate the origin of PhSPLs. Phylogenetic analysis and multiple alignments of the coding sequences of PhSPLs and their orthologs from wild species indicated that PhSPLs were originated mainly from P. axillaris. qRT-PCR analysis demonstrated differential spatiotemperal expression patterns of PhSPL genes in petunia and many were expressed predominantly in the axillary buds and/or inflorescences. In addition, overexpression of PhSPL9a and PhSPL9b in Arabidopsis suggested that these genes play a conserved role in promoting the vegetative-to-reproductive phase transition. Conclusion Petunia genome contains at least 21 SPL genes, and most of the genes are expressed in different tissues. The PhSPL genes may play conserved and diverse roles in plant growth and development, including flowering regulation, leaf initiation, axillary bud and inflorescence development. This work provides a comprehensive understanding of the SBP-box gene family in Petunia and lays a significant foundation for future studies on the function and evolution of SPL genes in petunia. Electronic supplementary material The online version of this article (10.1186/s12864-018-4537-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Qin Zhou
- Key Laboratory of Horticultural Plant Biology, Ministry of Education; Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Shizishan Street No. 1, Wuhan, 430070, China
| | - Sisi Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education; Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Shizishan Street No. 1, Wuhan, 430070, China.,Wuhan Institute of Landscape Architecture, Peace Avenue No. 1240, Wuhan, 430081, China
| | - Feng Chen
- Key Laboratory of Horticultural Plant Biology, Ministry of Education; Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Shizishan Street No. 1, Wuhan, 430070, China
| | - Baojun Liu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education; Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Shizishan Street No. 1, Wuhan, 430070, China
| | - Lan Wu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education; Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Shizishan Street No. 1, Wuhan, 430070, China
| | - Fei Li
- Key Laboratory of Horticultural Plant Biology, Ministry of Education; Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Shizishan Street No. 1, Wuhan, 430070, China
| | - Jiaqi Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education; Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Shizishan Street No. 1, Wuhan, 430070, China
| | - Manzhu Bao
- Key Laboratory of Horticultural Plant Biology, Ministry of Education; Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Shizishan Street No. 1, Wuhan, 430070, China
| | - Guofeng Liu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education; Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Shizishan Street No. 1, Wuhan, 430070, China.
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25
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Proteomic and genomic responses of plants to nutritional stress. Biometals 2018; 31:161-187. [PMID: 29453655 DOI: 10.1007/s10534-018-0083-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Accepted: 02/10/2018] [Indexed: 12/17/2022]
Abstract
Minerals or trace elements in small amount are essential nutrients for every plant, but when the internal concentration exceeds the threshold, these essential elements do create phytotoxicity. Plant responses to elemental stresses are very common due to different anthropogenic activities; however it is a complex phenomenon with individual characteristics for various species. To cope up with the situation, a plant produces a group of strategies both in proteomic and genomic level to overcome it. Controlling the metal stress is known to activate a multigene response resulting in the changes in various proteins, which directly affects almost all biological processes in a living cell. Therefore, proteomic and genomic approaches can be useful for elucidating the molecular responses under metal stress. For this, it is tried to provide the latest knowledge and techniques used in proteomic and genomic study during nutritional stress and is represented here in review form.
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26
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Carneiro JMT, Chacón-Madrid K, Galazzi RM, Campos BK, Arruda SCC, Azevedo RA, Arruda MAZ. Evaluation of silicon influence on the mitigation of cadmium-stress in the development of Arabidopsis thaliana through total metal content, proteomic and enzymatic approaches. J Trace Elem Med Biol 2017; 44:50-58. [PMID: 28965600 DOI: 10.1016/j.jtemb.2017.05.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 05/18/2017] [Accepted: 05/30/2017] [Indexed: 12/20/2022]
Abstract
The mitigation of Cd-stress through Si addition to Arabidopsis thaliana cultivation is evaluated in terms of total metal content, proteomic and enzymatic approaches. Four different treatment are evaluated: TC (control, without Si or Cd addition), T1 (with Si addition), T2 (with Cd addition), and T3 (with Si and Cd addition). Through the total determination of Cd and Si in Arabidopsis leaves, the Cd concentration decreased by half when T2 is compared with T3 treatment. In terms of proteomic approach, some differential protein species are achieved by comparative proteomics through 2-D DIGE of all treatments evaluated. Fifty six differential abundant proteins spots (abundance factor ≥1.5) are detected, and 32 of them accurately characterized and identified through nESI-LC-MS/MS. These proteins are differentially produced due to Cd and/or Si treatments, which mainly include proteins associated with disease/defense, energy and metabolism. The most difference in the abundance of proteins is found due to the presence or absence of Si in plants treated with Cd. Regarding the enzymatic approaches, a major increase is found on APX, CAT and GR activities (5.0, 3.5, and 1.5-fold, respectively). The same is observed for the MDA concentration because an increase of 3-fold is found when TC are compared to those treated with T2. However, when T3 plants are evaluated, the enzymes activities are similar to TC plants. Differences ranging from 6.5 to 21% are detected considering the activity of SOD in the treatments (T1-T3 x TC). The decreased activities of CAT, APX and GR and lower MDA concentration indicate a lower reactive oxygen species production in plants treated with Cd and Si. Based on a proteomics point of view it is possible to conclude that Si-Cd interactions occur at protein level and allow plants to respond effectively to the Cd toxicity, revealing the active involvement of Si on mechanisms involved in Si-induced Cd tolerance in Arabidopsis plants. Additionally, from an enzymatic point of view, it is possible to conclude that Si positively interferes diminishing the negative effects of Cd in Arabidopsis by decreasing the reactive oxygen species generation and increasing the antioxidative enzyme activity.
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Affiliation(s)
- Josiane M T Carneiro
- Spectrometry, Sample Preparation and Mechanization Group-GEPAM, Institute of Chemistry, University of Campinas-Unicamp, P.O. Box 6154, 13083-970, Campinas, SP, Brazil; National Institute of Science and Technology for Bioanalytics, Institute of Chemistry, University of Campinas-Unicamp, P.O. Box 6154, 13083-970, Campinas, SP, Brazil
| | - Katherine Chacón-Madrid
- Spectrometry, Sample Preparation and Mechanization Group-GEPAM, Institute of Chemistry, University of Campinas-Unicamp, P.O. Box 6154, 13083-970, Campinas, SP, Brazil; National Institute of Science and Technology for Bioanalytics, Institute of Chemistry, University of Campinas-Unicamp, P.O. Box 6154, 13083-970, Campinas, SP, Brazil
| | - Rodrigo M Galazzi
- Spectrometry, Sample Preparation and Mechanization Group-GEPAM, Institute of Chemistry, University of Campinas-Unicamp, P.O. Box 6154, 13083-970, Campinas, SP, Brazil; National Institute of Science and Technology for Bioanalytics, Institute of Chemistry, University of Campinas-Unicamp, P.O. Box 6154, 13083-970, Campinas, SP, Brazil
| | - Bruna K Campos
- Spectrometry, Sample Preparation and Mechanization Group-GEPAM, Institute of Chemistry, University of Campinas-Unicamp, P.O. Box 6154, 13083-970, Campinas, SP, Brazil; National Institute of Science and Technology for Bioanalytics, Institute of Chemistry, University of Campinas-Unicamp, P.O. Box 6154, 13083-970, Campinas, SP, Brazil
| | - Sandra C C Arruda
- Department of Genetics, Laboratory of Biochemistry and Genetics of Plants, Escola Superior de Agricultura Luiz de Queiroz, ESALQ-University of São Paulo, 13400-970, Piracicaba, SP, Brazil
| | - Ricardo A Azevedo
- Department of Genetics, Laboratory of Biochemistry and Genetics of Plants, Escola Superior de Agricultura Luiz de Queiroz, ESALQ-University of São Paulo, 13400-970, Piracicaba, SP, Brazil
| | - Marco A Z Arruda
- Spectrometry, Sample Preparation and Mechanization Group-GEPAM, Institute of Chemistry, University of Campinas-Unicamp, P.O. Box 6154, 13083-970, Campinas, SP, Brazil; National Institute of Science and Technology for Bioanalytics, Institute of Chemistry, University of Campinas-Unicamp, P.O. Box 6154, 13083-970, Campinas, SP, Brazil.
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27
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Loix C, Huybrechts M, Vangronsveld J, Gielen M, Keunen E, Cuypers A. Reciprocal Interactions between Cadmium-Induced Cell Wall Responses and Oxidative Stress in Plants. FRONTIERS IN PLANT SCIENCE 2017; 8:1867. [PMID: 29163592 PMCID: PMC5671638 DOI: 10.3389/fpls.2017.01867] [Citation(s) in RCA: 148] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 10/12/2017] [Indexed: 05/18/2023]
Abstract
Cadmium (Cd) pollution renders many soils across the world unsuited or unsafe for food- or feed-orientated agriculture. The main mechanism of Cd phytotoxicity is the induction of oxidative stress, amongst others through the depletion of glutathione. Oxidative stress can damage lipids, proteins, and nucleic acids, leading to growth inhibition or even cell death. The plant cell has a variety of tools to defend itself against Cd stress. First and foremost, cell walls might prevent Cd from entering and damaging the protoplast. Both the primary and secondary cell wall have an array of defensive mechanisms that can be adapted to cope with Cd. Pectin, which contains most of the negative charges within the primary cell wall, can sequester Cd very effectively. In the secondary cell wall, lignification can serve to immobilize Cd and create a tougher barrier for entry. Changes in cell wall composition are, however, dependent on nutrients and conversely might affect their uptake. Additionally, the role of ascorbate (AsA) as most important apoplastic antioxidant is of considerable interest, due to the fact that oxidative stress is a major mechanism underlying Cd toxicity, and that AsA biosynthesis shares several links with cell wall construction. In this review, modifications of the plant cell wall in response to Cd exposure are discussed. Focus lies on pectin in the primary cell wall, lignification in the secondary cell wall and the importance of AsA in the apoplast. Regarding lignification, we attempt to answer the question whether increased lignification is merely a consequence of Cd toxicity, or rather an elicited defense response. We propose a model for lignification as defense response, with a central role for hydrogen peroxide as substrate and signaling molecule.
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Affiliation(s)
| | | | | | | | | | - Ann Cuypers
- Environmental Biology, Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
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28
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Sofo A, Bochicchio R, Amato M, Rendina N, Vitti A, Nuzzaci M, Altamura MM, Falasca G, Rovere FD, Scopa A. Plant architecture, auxin homeostasis and phenol content in Arabidopsis thaliana grown in cadmium- and zinc-enriched media. JOURNAL OF PLANT PHYSIOLOGY 2017; 216:174-180. [PMID: 28704702 DOI: 10.1016/j.jplph.2017.06.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 06/12/2017] [Accepted: 06/13/2017] [Indexed: 05/27/2023]
Abstract
A screening strategy using micropropagation glass tubes with a gradient of distances between germinating seeds and a metal-contaminated medium was used for studying alterations in root architecture and morphology of Arabidopsis thaliana treated with cadmium (Cd) and zinc (Zn) at the concentration of 10-20μM and 100-200μM, respectively. Metal concentrations in plant shoots and roots were measured by quadrupole inductively coupled plasma mass spectrometry. After 21days from germination, all plants in the tubes were scanned at high resolution and the root systems analyzed. The localization of indole-3-acetic acid (IAA) in the primary root and lateral root apices was monitored using DR5:GUS, LAX3:GUS and AUX1:GUS Arabidopsis transgenic lines. Total phenol content in leaves was measured spectrophotometrically. Shoot and root dry weight and leaf area did not change in Zn-exposed plants and significantly decreased in Cd-exposed plants, compared to control plants. Cadmium induced a reduction of root length, of mean number of roots and of total root surface. Both Cd- and Zn-exposed plants showed a reduced specific root length. This morphological behavior, together with an observed increase in root diameter in metal-exposed plants could be interpreted as compensatory growth, and the observed thicker roots could act as a barrier to protect root from the metals. In comparison with the apical localization of the IAA signal in the control plants, Zn generally reinforced the intensity of IAA signal, without affecting its localization. In Cd-exposed plants, IAA localization remained apical but weaker compared to control plants. Total phenols decreased in plants exposed to Zn and Cd. Therefore, we propose that the remodelling of the root architecture and the production of some secondary metabolites, such as IAA and phenols could be two responses of plants subjected to metal stress. This knowledge can open the way to future phytoremediation strategies of contaminated sites.
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Affiliation(s)
- Adriano Sofo
- School of Agricultural, Forestry, Food and Environmental Sciences, University of Basilicata, Viale dell'Ateneo Lucano 10, I-85100, Potenza, Italy.
| | - Rocco Bochicchio
- School of Agricultural, Forestry, Food and Environmental Sciences, University of Basilicata, Viale dell'Ateneo Lucano 10, I-85100, Potenza, Italy.
| | - Mariana Amato
- School of Agricultural, Forestry, Food and Environmental Sciences, University of Basilicata, Viale dell'Ateneo Lucano 10, I-85100, Potenza, Italy.
| | - Nunzia Rendina
- School of Agricultural, Forestry, Food and Environmental Sciences, University of Basilicata, Viale dell'Ateneo Lucano 10, I-85100, Potenza, Italy.
| | - Antonella Vitti
- School of Agricultural, Forestry, Food and Environmental Sciences, University of Basilicata, Viale dell'Ateneo Lucano 10, I-85100, Potenza, Italy.
| | - Maria Nuzzaci
- School of Agricultural, Forestry, Food and Environmental Sciences, University of Basilicata, Viale dell'Ateneo Lucano 10, I-85100, Potenza, Italy.
| | - Maria Maddalena Altamura
- Department of Environmental Biology, "Sapienza" University of Rome, Piazzale A. Moro 5, I-00185 Rome, Italy.
| | - Giuseppina Falasca
- Department of Environmental Biology, "Sapienza" University of Rome, Piazzale A. Moro 5, I-00185 Rome, Italy.
| | - Federica Della Rovere
- Department of Environmental Biology, "Sapienza" University of Rome, Piazzale A. Moro 5, I-00185 Rome, Italy.
| | - Antonio Scopa
- School of Agricultural, Forestry, Food and Environmental Sciences, University of Basilicata, Viale dell'Ateneo Lucano 10, I-85100, Potenza, Italy.
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Sanz-Fernández M, Rodríguez-Serrano M, Sevilla-Perea A, Pena L, Mingorance MD, Sandalio LM, Romero-Puertas MC. Screening Arabidopsis mutants in genes useful for phytoremediation. JOURNAL OF HAZARDOUS MATERIALS 2017; 335:143-151. [PMID: 28441590 DOI: 10.1016/j.jhazmat.2017.04.021] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 03/21/2017] [Accepted: 04/05/2017] [Indexed: 06/07/2023]
Abstract
Emissions of heavy metals have risen over the past 200 years and significantly exceed those from natural sources. Phytoremediation strategies may be able to recover soil productivity in self-sustaining ecosystems; however, our knowledge of the molecular mechanisms involved in plant heavy-metal perception and signalling is scarce. The aim of this study was to assemble a "molecular tool box" of genes useful for phytoremediation. To identify mutants with different heavy-metal-tolerance, we first selected a medium from mixtures containing three metals based on their presence in two Spanish mining areas and then screened about 7000 lines of Arabidopsis T-DNA mutants and found 74 lines more resistant and 56 more susceptible than the wild type (WT). Classification of the genes showed that they were mainly linked to transport, protein modification and signalling, with RNA metabolism being the most representative category in the resistant phenotypes and protein metabolism in the sensitive ones. We have characterized one resistant mutant, Athpp9 and one sensitive, Atala4. These mutants showed differences in growth and metal translocation. Additionally, we found that these mutants keep their phenotype in amended former soils, suggesting that these genes may be useful for phytoremediation and the recovery of contaminated soils.
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Affiliation(s)
- María Sanz-Fernández
- Department of Biochemistry, Cell and Molecular Biology of Plants, EEZ, CSIC, Granada, Spain
| | | | | | - Liliana Pena
- Department of Biological Chemistry, University of Buenos Aires and IQUIFIB, CONICET, Argentina
| | | | - Luisa M Sandalio
- Department of Biochemistry, Cell and Molecular Biology of Plants, EEZ, CSIC, Granada, Spain
| | - María C Romero-Puertas
- Department of Biochemistry, Cell and Molecular Biology of Plants, EEZ, CSIC, Granada, Spain.
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Gielen H, Vangronsveld J, Cuypers A. Cd-induced Cu deficiency responses in Arabidopsis thaliana: are phytochelatins involved? PLANT, CELL & ENVIRONMENT 2017; 40:390-400. [PMID: 27943310 DOI: 10.1111/pce.12876] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 11/18/2016] [Accepted: 11/20/2016] [Indexed: 06/06/2023]
Abstract
Cadmium (Cd) exposure can disturb the homeostasis of essential elements. In Arabidopsis thaliana, Cd induces a squamosa promoter binding protein-like 7 (SPL7)-dependent Cu deficiency response. We investigated how Cd induces a Cu deficiency response. The Cu deficiency response consists of the active SPL7 transcription factor binding to GTAC motifs in promoters of among others several Cu transporters, a Cu chaperone, and cupro-miRNAs to regulate Cu homeostasis. We demonstrated that the addition of supplemental Cu to Cd-exposed A. thaliana plants diminished the Cu deficiency response in roots, while it even disappeared in leaves. Exposure of plants to Cd in combination with extra Cu reduced Cd levels in both roots and leaves resulting in an improved cellular oxidative state. Furthermore, we demonstrated a role for phytochelatins (PCs) in the Cd-induced Cu deficiency response, because it was reduced in roots of cad1-3 mutant plants exposed to Cd. In conclusion, a working mechanism is provided in which it is suggested that Cd increases PC levels that can complex both Cd and Cu. This results in cellular Cu deficiency and subsequently the activation of SPL7 and hence the induction of the Cu deficiency response.
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Affiliation(s)
- Heidi Gielen
- Environmental Biology, Centre for Environmental Sciences, Hasselt University, B-3590, Diepenbeek, Belgium
| | - Jaco Vangronsveld
- Environmental Biology, Centre for Environmental Sciences, Hasselt University, B-3590, Diepenbeek, Belgium
| | - Ann Cuypers
- Environmental Biology, Centre for Environmental Sciences, Hasselt University, B-3590, Diepenbeek, Belgium
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