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Jiang P, Zhong X, Zhang X, You S, Liu J, Yu G. Effect of Mn on Cd 2+ uptake by protoplasts of the Cd/Mn hyperaccumulator Celosia argentea Linn. differs by treatment method. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 214:108925. [PMID: 39002306 DOI: 10.1016/j.plaphy.2024.108925] [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: 02/20/2024] [Revised: 06/15/2024] [Accepted: 07/08/2024] [Indexed: 07/15/2024]
Abstract
The effect mechanism of Mn on Cd uptake by Celosia argentea was investigated via a series of hydroponics experiments. The results showed that different manganese treatments had different effects on Cd uptake by C. argentea. Mn pretreatment increased Cd uptake by root protoplasts at Cd concentrations (4 and 6 μM). Protoplasts reached peak Cd uptake rate at 6 μM Cd and 25 °C, with 67.71 ± 0.13 μM h-1 mL-1 in the control, and 77.99 ± 0.49 μM h-1 mL-1 in the 50 μM Mn pretreatment group. However, simultaneous treatment with Cd and Mn reduced the Cd2+ uptake by root protoplasts. This discrepancy may be attributed to the fact that cadmium and manganese share some transporters in root cells. The transcriptome analysis in roots revealed that ten genes (including ABCC, ABCA, ABCG, ABCB, ABC1, BZIP19, and ZIP5) were significantly upregulated in response to Mn stress (p < 0.05). These genes regulate the expression of transporters belonging to the ABC, and ZIP families, which may be involved in Cd uptake by root cells of C. argentea. Mn pretreatment upregulates the expression of Mn/Cd transporters, enhancing Cd uptake by root protoplasts. For the simultaneous treatment of Cd and Mn, inhibition of Cd uptake was due to the competition of the same transporters. These findings provide helpful insights for understanding the mechanism of Mn and Cd uptake in hyperaccumulators and give implications to improve the phytoremediation of Cd-contaminated soil by C. argentea.
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Affiliation(s)
- Pingping Jiang
- College of Earth Sciences, Guilin University of Technology, Guilin, 541004, China; Guangxi Key Laboratory of Exploration for Hidden Metallic Ore Deposits, Guilin, 541004, China
| | - Xia Zhong
- Guangxi Key Laboratory of Environmental Pollution Control Theory and Technology, Guilin University of Technology, Guilin, 541004, China
| | - Xuehong Zhang
- Guangxi Key Laboratory of Environmental Pollution Control Theory and Technology, Guilin University of Technology, Guilin, 541004, China
| | - Shaohong You
- Guangxi Key Laboratory of Environmental Pollution Control Theory and Technology, Guilin University of Technology, Guilin, 541004, China; Guangxi Science and Technology Normal University, Laibin, 546199, China.
| | - Jie Liu
- Guangxi Key Laboratory of Environmental Pollution Control Theory and Technology, Guilin University of Technology, Guilin, 541004, China
| | - Guo Yu
- Guangxi Key Laboratory of Environmental Pollution Control Theory and Technology, Guilin University of Technology, Guilin, 541004, China
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Singh D, Tripathi A, Mitra R, Bhati J, Rani V, Taunk J, Singh D, Yadav RK, Siddiqui MH, Pal M. Genome-wide identification of MATE and ALMT genes and their expression profiling in mungbean (Vigna radiata L.) under aluminium stress. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 280:116558. [PMID: 38850702 DOI: 10.1016/j.ecoenv.2024.116558] [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: 03/21/2024] [Revised: 06/03/2024] [Accepted: 06/04/2024] [Indexed: 06/10/2024]
Abstract
The Multidrug and toxic compound extrusion (MATE) and aluminium activated malate transporter (ALMT) gene families are involved in response to aluminium (Al) stress. In this study, we identified 48 MATE and 14 ALMT gene families in Vigna radiata genome and classified into 5 (MATE) and 3 (ALMT) clades by phylogenetic analysis. All the VrMATE and VrALMT genes were distributed across mungbean chromosomes. Tandem duplication was the main driving force for evolution and expansion of MATE gene family. Collinearity of mungbean with soybean indicated that MATE gene family is closely linked to Glycine max. Eight MATE transporters in clade 2 were found to be associated with previously characterized Al tolerance related MATEs in various plant species. Citrate exuding motif (CEM) was present in seven VrMATEs of clade 2. Promoter analysis revealed abundant plant hormone and stress responsive cis-elements. Results from quantitative real time-polymerase chain reaction (qRT-PCR) revealed that VrMATE19, VrMATE30 and VrALMT13 genes were markedly up-regulated at different time points under Al stress. Overall, this study offers a new direction for further molecular characterization of the MATE and ALMT genes in mungbean for Al tolerance.
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Affiliation(s)
- Dharmendra Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India.
| | - Ankita Tripathi
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Raktim Mitra
- Division of Plant Physiology, ICAR, Indian Agricultural Research Institute, New Delhi 110012, India
| | - Jyotika Bhati
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110012, India
| | - Varsha Rani
- Department of Agriculture, Meerut Institute of Technology, Meerut 250103, India
| | - Jyoti Taunk
- Division of Plant Physiology, ICAR, Indian Agricultural Research Institute, New Delhi 110012, India
| | - Deepti Singh
- Department of Botany, Meerut College, Meerut 250103, India
| | - Rajendra Kumar Yadav
- Department of Genetics and Plant Breeding, Chandra Shekhar Azad University of Agriculture and Technology, Kanpur 208002, India
| | - Manzer H Siddiqui
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Madan Pal
- Division of Plant Physiology, ICAR, Indian Agricultural Research Institute, New Delhi 110012, India
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Liu P, An L, Ma L, Zou L, Du S, Shen Y. MTP family analysis and association study reveal the role of ZmMTP11 in lead (Pb) accumulation. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 212:108740. [PMID: 38797007 DOI: 10.1016/j.plaphy.2024.108740] [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: 02/04/2024] [Revised: 05/15/2024] [Accepted: 05/16/2024] [Indexed: 05/29/2024]
Abstract
The metal tolerance protein (MTP) gene family plays an essential role in the transport of heavy metals, however the function of the MTP family in transporting lead (Pb) was still unclear in plants. In this study, we identified and characterized 12 ZmMTPs in the whole genome of maize. These ZmMTP genes were divided into three subfamilies in evolution, namely Zn-CDF, Zn/Fe-CDF, Mn-CDF subfamilies, which showed diverse expression patterns in different tissues of maize. Using gene-based association analyses, we identified a Pb accumulation-related MTP member in maize, ZmMTP11, which was located in plasma membrane and had the potential of transporting Pb ion. Under the Pb treatment, ZmMTP11 showed a generally decreased expression relative to the normal conditions. Heterologous expressions of ZmMTP11 in yeast, Arabidopsis, and rice demonstrated that ZmMTP11 enhanced Pb accumulation in the cells without affecting yeast and plant growth under Pb stress. Remarkably, the increased Pb concentration in the plant roots did not cause changes in Pb content in the shoots. Our study provides new insights into the genetic improvement of heavy metal tolerance in plants and contributes to bioremediation of Pb-contaminant soils.
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Affiliation(s)
- Peng Liu
- College of Life Science & Biotechnology, Mianyang Normal University, Mianyang, 621000, China; State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Lijun An
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Langlang Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Lijuan Zou
- College of Life Science & Biotechnology, Mianyang Normal University, Mianyang, 621000, China; Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, China
| | - Shizhang Du
- College of Life Science & Biotechnology, Mianyang Normal University, Mianyang, 621000, China
| | - Yaou Shen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
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Xiao C, Du S, Zhou S, Cheng H, Rao S, Wang Y, Cheng S, Lei M, Li L. Identification and functional characterization of ABC transporters for selenium accumulation and tolerance in soybean. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 211:108676. [PMID: 38714125 DOI: 10.1016/j.plaphy.2024.108676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 03/16/2024] [Accepted: 04/28/2024] [Indexed: 05/09/2024]
Abstract
ATP-binding cassette (ABC) transporters were crucial for various physiological processes like nutrition, development, and environmental interactions. Selenium (Se) is an essential micronutrient for humans, and its role in plants depends on applied dosage. ABC transporters are considered to participate in Se translocation in plants, but detailed studies in soybean are still lacking. We identified 196 ABC genes in soybean transcriptome under Se exposure using next-generation sequencing and single-molecule real-time sequencing technology. These proteins fell into eight subfamilies: 8 GmABCA, 51 GmABCB, 39 GmABCC, 5 GmABCD, 1 GmABCE, 10 GmABCF, 74 GmABCG, and 8 GmABCI, with amino acid length 121-3022 aa, molecular weight 13.50-341.04 kDa, and isoelectric point 4.06-9.82. We predicted a total of 15 motifs, some of which were specific to certain subfamilies (especially GmABCB, GmABCC, and GmABCG). We also found predicted alternative splicing in GmABCs: 60 events in selenium nanoparticles (SeNPs)-treated, 37 in sodium selenite (Na2SeO3)-treated samples. The GmABC genes showed differential expression in leaves and roots under different application of Se species and Se levels, most of which are belonged to GmABCB, GmABCC, and GmABCG subfamilies with functions in auxin transport, barrier formation, and detoxification. Protein-protein interaction and weighted gene co-expression network analysis suggested functional gene networks with hub ABC genes, contributing to our understanding of their biological functions. Our results illuminate the contributions of GmABC genes to Se accumulation and tolerance in soybean and provide insight for a better understanding of their roles in soybean as well as in other plants.
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Affiliation(s)
- Chunmei Xiao
- National R&D for Se-rich Agricultural Products Processing Technology, Wuhan Polytechnic University, Wuhan, 430023, China; School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan, 430023, China
| | - Sainan Du
- National R&D for Se-rich Agricultural Products Processing Technology, Wuhan Polytechnic University, Wuhan, 430023, China; School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan, 430023, China
| | - Shengli Zhou
- National R&D for Se-rich Agricultural Products Processing Technology, Wuhan Polytechnic University, Wuhan, 430023, China; School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan, 430023, China
| | - Hua Cheng
- National R&D for Se-rich Agricultural Products Processing Technology, Wuhan Polytechnic University, Wuhan, 430023, China; School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan, 430023, China
| | - Shen Rao
- National R&D for Se-rich Agricultural Products Processing Technology, Wuhan Polytechnic University, Wuhan, 430023, China; School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan, 430023, China
| | - Yuan Wang
- National R&D for Se-rich Agricultural Products Processing Technology, Wuhan Polytechnic University, Wuhan, 430023, China; School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan, 430023, China
| | - Shuiyuan Cheng
- National R&D for Se-rich Agricultural Products Processing Technology, Wuhan Polytechnic University, Wuhan, 430023, China; School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan, 430023, China
| | - Ming Lei
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023, China.
| | - Li Li
- National R&D for Se-rich Agricultural Products Processing Technology, Wuhan Polytechnic University, Wuhan, 430023, China; School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan, 430023, China.
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Singh D, Tripathi A, Bhati J, Taunk J, Singh D, Siddiqui MH, Singh MP. Genome wide identification and expression profiling of ATP binding cassette (ABC) transporters gene family in lentil (Lens culinaris Medikus) under aluminium stress condition. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 211:108710. [PMID: 38735154 DOI: 10.1016/j.plaphy.2024.108710] [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: 02/16/2024] [Revised: 04/22/2024] [Accepted: 05/06/2024] [Indexed: 05/14/2024]
Abstract
Adenosine triphosphate-binding cassette transporters (ABC transporters) are involved in regulating plant growth, development and tolerance to environmental stresses. In this study, a total of 138 ABC transporter genes were identified in the lentil genome that were classified into eight subfamilies. Four lentil ABC transporters from subfamily B and I were clustered together with the previously characterized ABC transporter proteins related to aluminium (Al) detoxification. Lentil ABC transporter genes were distributed across the chromosomes. Tandem duplication was the main driving force for expansion of the ABC gene family. Collinearity of lentil with soybean indicated that ABC gene family is closely linked to Glycine max. ABC genes in the same subfamily showed similar gene structure and conserved motifs. The ABC promoter regions harboured a large number of plant hormones and multiple stress responsive cis-regulatory elements. The qRT-PCR showed that ABC genes had varied expression in roots of lentil at different time points under Al stress. This is the first report on genome wide identification and expression analyses of genes encoding ABC transporter genes in lentil which has provided in-depth insight for future research on evolution and elucidation of molecular mechanisms for aluminium tolerance.
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Affiliation(s)
- Dharmendra Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
| | - Ankita Tripathi
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Jyotika Bhati
- ICAR-India Agricultural Statistics Research Institute, New Delhi, 110012, India
| | - Jyoti Taunk
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Deepti Singh
- Department of Botany, Meerut College, Meerut, 250001, India
| | - Manzer H Siddiqui
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Madan Pal Singh
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
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Khan NM, Ali A, Wan Y, Zhou G. Genome-wide identification of heavy-metal ATPases genes in Areca catechu: investigating their functionality under heavy metal exposure. BMC PLANT BIOLOGY 2024; 24:484. [PMID: 38822228 PMCID: PMC11141028 DOI: 10.1186/s12870-024-05201-6] [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: 04/16/2024] [Accepted: 05/26/2024] [Indexed: 06/02/2024]
Abstract
Heavy-metal ATPases (HMAs) play a vital role in plants, helping to transport heavy metal ions across cell membranes.However, insufficient data exists concerning HMAs genes within the Arecaceae family.In this study, 12 AcHMA genes were identified within the genome of Areca catechu, grouped into two main clusters based on their phylogenetic relationships.Genomic distribution analysis reveals that the AcHMA genes were unevenly distributed across six chromosomes. We further analyzed their physicochemical properties, collinearity, and gene structure.Furthermore, RNA-seq data analysis exhibited varied expressions in different tissues of A. catechu and found that AcHMA1, AcHMA2, and AcHMA7 were highly expressed in roots, leaves, pericarp, and male/female flowers. A total of six AcHMA candidate genes were selected based on gene expression patterns, and their expression in the roots and leaves was determined using RT-qPCR under heavy metal stress. Results showed that the expression levels of AcHMA1 and AcHMA3 genes were significantly up-regulated under Cd2 + and Zn2 + stress. Similarly, in response to Cu2+, the AcHMA5 and AcHMA8 revealed the highest expression in roots and leaves, respectively. In conclusion, this study will offer a foundation for exploring the role of the HMAs gene family in dealing with heavy metal stress conditions in A. catechu.
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Affiliation(s)
- Noor Muhammad Khan
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, School of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Akhtar Ali
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, School of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Yinglang Wan
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, Hainan, China
| | - Guangzhen Zhou
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, Hainan, China.
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7
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Kou X, Zhao Z, Xu X, Li C, Wu J, Zhang S. Identification and expression analysis of ATP-binding cassette (ABC) transporters revealed its role in regulating stress response in pear (Pyrus bretchneideri). BMC Genomics 2024; 25:169. [PMID: 38347517 PMCID: PMC10863237 DOI: 10.1186/s12864-024-10063-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 01/29/2024] [Indexed: 02/15/2024] Open
Abstract
BACKGROUND ATP-binding cassette (ABC) transporter proteins constitute a plant gene superfamily crucial for growth, development, and responses to environmental stresses. Despite their identification in various plants like maize, rice, and Arabidopsis, little is known about the information on ABC transporters in pear. To investigate the functions of ABC transporters in pear development and abiotic stress response, we conducted an extensive analysis of ABC gene family in the pear genome. RESULTS In this study, 177 ABC transporter genes were successfully identified in the pear genome, classified into seven subfamilies: 8 ABCAs, 40 ABCBs, 24 ABCCs, 8 ABCDs, 9 ABCEs, 8 ABCFs, and 80 ABCGs. Ten motifs were common among all ABC transporter proteins, while distinct motif structures were observed for each subfamily. Distribution analysis revealed 85 PbrABC transporter genes across 17 chromosomes, driven primarily by WGD and dispersed duplication. Cis-regulatory element analysis of PbrABC promoters indicated associations with phytohormones and stress responses. Tissue-specific expression profiles demonstrated varied expression levels across tissues, suggesting diverse functions in development. Furthermore, several PbrABC genes responded to abiotic stresses, with 82 genes sensitive to salt stress, including 40 upregulated and 23 downregulated genes. Additionally, 91 genes were responsive to drought stress, with 22 upregulated and 36 downregulated genes. These findings highlight the pivotal role of PbrABC genes in abiotic stress responses. CONCLUSION This study provides evolutionary insights into PbrABC transporter genes, establishing a foundation for future research on their functions in pear. The identified motifs, distribution patterns, and stress-responsive expressions contribute to understanding the regulatory mechanisms of ABC transporters in pear. The observed tissue-specific expression profiles suggest diverse roles in developmental processes. Notably, the significant responses to salt and drought stress emphasize the importance of PbrABC genes in mediating adaptive responses. Overall, our study advances the understanding of PbrABC transporter genes in pear, opening avenues for further investigations in plant molecular biology and stress physiology.
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Affiliation(s)
- Xiaobing Kou
- School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, People's Republic of China.
| | - Zhen Zhao
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xinqi Xu
- School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, People's Republic of China
| | - Chang Li
- School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, People's Republic of China
| | - Juyou Wu
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shaoling Zhang
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
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Li J, Zhang Z, Shi G. Genome-Wide Identification and Expression Profiling of Heavy Metal ATPase (HMA) Genes in Peanut: Potential Roles in Heavy Metal Transport. Int J Mol Sci 2024; 25:613. [PMID: 38203784 PMCID: PMC10779257 DOI: 10.3390/ijms25010613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 12/29/2023] [Accepted: 12/31/2023] [Indexed: 01/12/2024] Open
Abstract
The heavy metal ATPase (HMA) family belongs to the P-type ATPase superfamily and plays an essential role in the regulation of metal homeostasis in plants. However, the gene family has not been fully investigated in peanut. Here, a genome-wide identification and bioinformatics analysis was performed on AhHMA genes in peanut, and the expression of 12 AhHMA genes in response to Cu, Zn, and Cd was evaluated in two peanut cultivars (Silihong and Fenghua 1) differing in Cd accumulation. A total of 21 AhHMA genes were identified in the peanut genome, including ten paralogous gene pairs derived from whole-genome duplication, and an additional gene resulting from tandem duplication. AhHMA proteins could be divided into six groups (I-VI), belonging to two clades (Zn/Co/Cd/Pb-ATPases and Cu/Ag-ATPases). Most AhHMA proteins within the same clade or group generally have a similar structure. However, significant divergence exists in the exon/intron organization even between duplicated gene pairs. RNA-seq data showed that most AhHMA genes are preferentially expressed in roots, shoots, and reproductive tissues. qRT-PCR results revealed that AhHMA1.1/1.2, AhHMA3.1/3.2, AhHMA7.1/7.4, and AhHMA8.1 might be involved in Zn transport in peanut plants, while AhHMA3.2 and AhHMA7.5 might be involved in Cd transport. Our findings provide clues to further characterize the functions of AhHMA genes in metal uptake and translocation in peanut plants.
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Affiliation(s)
| | | | - Gangrong Shi
- College of Life Sciences, Huaibei Normal University, Huaibei 235000, China; (J.L.); (Z.Z.)
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Zhang D, Yu Z, Zeng B, Liu X. Genome-wide analysis of the ABC gene family in almond and functional predictions during flower development, freezing stress, and salt stress. BMC PLANT BIOLOGY 2024; 24:12. [PMID: 38163883 PMCID: PMC10759767 DOI: 10.1186/s12870-023-04698-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 12/18/2023] [Indexed: 01/03/2024]
Abstract
ABC (ATP-binding cassette) transporter proteins are one of the most extensive protein families known to date and are ubiquitously found in animals, plants, and microorganisms. ABCs have a variety of functions, such as plant tissue development regulation, hormone transport, and biotic and abiotic stress resistance. However, the gene characterization and function of the ABC gene family in almond (Prunus dulcis) have not been thoroughly studied. In this study, we identified 117 PdABC genes using the whole genome of 'Wanfeng' almond obtained by sequencing and explored their protein characterization. The PdABC family members were classified into eight subfamilies. The members of the same subfamily had conserved motifs but poorly conserved numbers of exons and introns and were unevenly distributed among the eight subfamilies and on the eight chromosomes. Expression patterns showed that PdABC family members were significantly differentially expressed during almond development, dormant freezing stress, and salt stress. We found that PdABC59 and PdABC77 had extremely high expression levels in pollen. PdABC63 and PdABC64 had high expression levels during almond petal development and multiple stages of flower development. PdABC98 was highly expressed in annual dormant branches after six temperature-freezing stress treatments. PdABC29, PdABC69, and PdABC98 were highly expressed under different concentrations of salt stress. This study preliminarily investigated the expression characteristics of ABC genes in different tissues of almond during flower development, freezing stress and salt stress, and the results will provide a reference for further in-depth research and breeding of almond in the future.
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Affiliation(s)
- Dongdong Zhang
- College of Horticulture, Xinjiang Agricultural University, Urumqi, 830000, China
| | - Zhenfan Yu
- College of Horticulture, Xinjiang Agricultural University, Urumqi, 830000, China
| | - Bin Zeng
- College of Horticulture, Xinjiang Agricultural University, Urumqi, 830000, China.
| | - Xingyue Liu
- College of Horticulture, Xinjiang Agricultural University, Urumqi, 830000, China
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Song C, Zhang Y, Manzoor MA, Wei P, Yi S, Chu S, Tong Z, Song X, Xu T, Wang F, Peng H, Chen C, Han B. A chromosome-scale genome of Peucedanum praeruptorum provide insights into Apioideae evolution and medicinal ingredient biosynthesis. Int J Biol Macromol 2024; 255:128218. [PMID: 37992933 DOI: 10.1016/j.ijbiomac.2023.128218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 10/20/2023] [Accepted: 11/16/2023] [Indexed: 11/24/2023]
Abstract
Peucedanum praeruptorum Dunn, a traditional Chinese medicine rich in coumarin, belongs to the Apiaceae family. A high-quality assembled genome of P. praeruptorum is lacking, which has posed obstacles to functional identification and molecular evolution studies of genes associated with coumarin production. Here, a chromosome-scale reference genome of P. praeruptorum, an important medicinal and aromatic plant, was first sequenced and assembled using Oxford Nanopore Technologies and Hi-C sequencing. The final assembled genome size was 1.83 Gb, with a contig N50 of 11.12 Mb. The entire BUSCO evaluation and second-generation read comparability rates were 96.0 % and 99.31 %, respectively. Furthermore, 99.91 % of the genome was anchored to 11 pseudochromosomes. The comparative genomic study revealed the presence of 18,593 orthogroups, which included 476 species-specific orthogroups and 1211 expanded gene families. Two whole-genome duplication (WGD) events and one whole-genome triplication (WGT) event occurred in P. praeruptorum. In addition to the γ-WGT shared by core eudicots or most eudicots, the first WGD was shared by Apiales, while the most recent WGD was unique to Apiaceae. Our study demonstrated that WGD events that occurred in Apioideae highlighted the important role of tandem duplication in the biosynthesis of coumarins and terpenes in P. praeruptorum. Additionally, the expansion of the cytochrome P450 monooxygenase, O-methyltransferase, ATP-binding cassette (ABC) transporter, and terpene synthase families may be associated with the abundance of coumarins and terpenoids. Moreover, we identified >170 UDP-glucosyltransferase members that may be involved in the glycosylation post-modification of coumarins. Significant gene expansion was observed in the ABCG, ABCB, and ABCC subgroups of the ABC transporter family, potentially facilitating the transmembrane transport of coumarins after bolting. The P. praeruptorum genome provides valuable insights into the machinery of coumarin biosynthesis and enhances our understanding of Apiaceae evolution.
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Affiliation(s)
- Cheng Song
- Anhui Dabieshan Academy of Traditional Chinese Medicine, Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, College of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an 237012, China
| | - Yingyu Zhang
- Henan Key Laboratory of Rare Diseases, Endocrinology and Metabolism Center, The First Affiliated Hospital, College of Clinical Medicine of Henan University of Science and Technology, Luoyang 471003, China
| | - Muhammad Aamir Manzoor
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 201109, China
| | - Peipei Wei
- Anhui Dabieshan Academy of Traditional Chinese Medicine, Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, College of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an 237012, China
| | - Shanyong Yi
- Anhui Dabieshan Academy of Traditional Chinese Medicine, Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, College of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an 237012, China
| | - Shanshan Chu
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China
| | - Zhenzhen Tong
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China
| | - Xiangwen Song
- Anhui Dabieshan Academy of Traditional Chinese Medicine, Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, College of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an 237012, China
| | - Tao Xu
- Anhui Dabieshan Academy of Traditional Chinese Medicine, Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, College of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an 237012, China
| | - Fang Wang
- Anhui Dabieshan Academy of Traditional Chinese Medicine, Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, College of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an 237012, China
| | - Huasheng Peng
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China; State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Cunwu Chen
- Anhui Dabieshan Academy of Traditional Chinese Medicine, Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, College of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an 237012, China.
| | - Bangxing Han
- Anhui Dabieshan Academy of Traditional Chinese Medicine, Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, College of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an 237012, China.
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11
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Mall MS, Shah S, Singh S, Singh N, Singh N, Vaish S, Gupta D. Genome-wide identification and characterization of ABC transporter superfamily in the legume Cajanus cajan. J Appl Genet 2023; 64:615-644. [PMID: 37624461 DOI: 10.1007/s13353-023-00774-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 07/17/2023] [Accepted: 08/01/2023] [Indexed: 08/26/2023]
Abstract
Plant ATP-binding cassette (ABC) protein family is the largest multifunctional highly conserved protein superfamily that transports diverse substrates across biological membranes by the hydrolysis of ATP and is also the part of the several other biological processes like cellular detoxification, growth and development, stress biology, and signaling processes. In the agriculturally important legume crop Cajanus cajan, a genome-wide identification and characterization of the ABC gene family was carried out. A total of 159 ABC genes were identified that belong to eight canonical classes CcABCA to CcABCG and CcABCI based on the phylogenetic analysis. The number of genes was highest in CcABCG followed by CcABCC and CcABCB class. A total of 85 CcABC genes were found on 11 chromosomes and 74 were found on scaffold. Tandem duplication was the major driver of CcABC gene family expansion. The dN/dS ratio revealed the purifying selection. The phylogenetic analysis revealed class-specific eight superclades which reflect their functional importance. The largest clade was found to be CcABCG which reflects their functional significance. CcABC proteins were mainly basic in nature and found to be localized in the plasma membrane. The secondary structure prediction revealed the dominance of α-helix. The canonical transmembrane and nucleotide binding domain, signature motif LSSGQ, Walker A, Walker B region, and Q loop were also identified. A class-specific exon-intron pattern was also observed. In addition to core elements, different cis-acting regulatory elements like stress, hormone, and cellular responsive were also identified. Expression profiling of CcABC genes at various developmental stages of different anatomical tissues was performed and it was noticed that CcABCF3, CcABCF4, CcABCF5, CcABCG66, and CcABCI3 had the highest expression. The results of the current study endow us with the further functional analysis of Cajanus ABC in the future.
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Affiliation(s)
- Mridula Sanjana Mall
- Faculty of Biosciences, Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, -Deva Road, Barabanki, Lucknow, Uttar Pradesh, 225003, India
| | - Shreya Shah
- Faculty of Biosciences, Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, -Deva Road, Barabanki, Lucknow, Uttar Pradesh, 225003, India
| | - Shivani Singh
- Experiome Biotech Private Limited, B1-517, Vijaypur Colony, DLF MyPAD, Vibhutikhand, Gomtinagar, Lucknow, Uttar Pradesh, 226010, India
| | - Namita Singh
- Experiome Biotech Private Limited, B1-517, Vijaypur Colony, DLF MyPAD, Vibhutikhand, Gomtinagar, Lucknow, Uttar Pradesh, 226010, India
| | - Nootan Singh
- Faculty of Biosciences, Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, -Deva Road, Barabanki, Lucknow, Uttar Pradesh, 225003, India
| | - Swati Vaish
- Faculty of Biosciences, Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, -Deva Road, Barabanki, Lucknow, Uttar Pradesh, 225003, India
| | - Divya Gupta
- Faculty of Biosciences, Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, -Deva Road, Barabanki, Lucknow, Uttar Pradesh, 225003, India.
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12
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Wu M, Tu A, Feng H, Guo Y, Xu G, Shi J, Chen J, Yang J, Zhong K. Genome-Wide Identification and Analysis of the ABCF Gene Family in Triticum aestivum. Int J Mol Sci 2023; 24:16478. [PMID: 38003668 PMCID: PMC10671407 DOI: 10.3390/ijms242216478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/08/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
The ATP-binding cassette (ABC) superfamily of proteins is a group of evolutionarily conserved proteins. The ABCF subfamily is involved in ribosomal synthesis, antibiotic resistance, and transcriptional regulation. However, few studies have investigated the role of ABCF in wheat (Triticum aestivum) immunity. Here, we identified 18 TaABCFs and classified them into four categories based on their domain characteristics. Functional similarity between Arabidopsis and wheat ABCF genes was predicted using phylogenetic analysis. A comprehensive genome-wide analysis of gene structure, protein motifs, chromosomal location, and cis-acting elements was also performed. Tissue-specific analysis and expression profiling under temperature, hormonal, and viral stresses were performed using real-time quantitative reverse transcription polymerase chain reaction after randomly selecting one gene from each group. The results revealed that all TaABCF genes had the highest expression at 25 °C and responded to methyl jasmonate induction. Notably, TaABCF2 was highly expressed in all tissues except the roots, and silencing it significantly increased the accumulation of Chinese wheat mosaic virus or wheat yellow mosaic virus in wheat leaves. These results indicated that TaABCF may function in response to viral infection, laying the foundation for further studies on the mechanisms of this protein family in plant defence.
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Affiliation(s)
| | | | | | | | | | | | | | - Jian Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Rural Affairs and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Kaili Zhong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Rural Affairs and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
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13
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Xu Y, Li Y, Li Y, Zhai C, Zhang K. Transcriptome Analysis Reveals the Stress Tolerance Mechanisms of Cadmium in Zoysia japonica. PLANTS (BASEL, SWITZERLAND) 2023; 12:3833. [PMID: 38005730 PMCID: PMC10674853 DOI: 10.3390/plants12223833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/09/2023] [Accepted: 11/10/2023] [Indexed: 11/26/2023]
Abstract
Cadmium (Cd) is a severe heavy metal pollutant globally. Zoysia japonica is an important perennial warm-season turf grass that potentially plays a role in phytoremediation in Cd-polluted soil areas; however, the molecular mechanisms underlying its Cd stress response are unknown. To further investigate the early gene response pattern in Z. japonica under Cd stress, plant leaves were harvested 0, 6, 12, and 24 h after Cd stress (400 μM CdCl2) treatment and used for a time-course RNA-sequencing analysis. Twelve cDNA libraries were constructed and sequenced, and high-quality data were obtained, whose mapped rates were all higher than 94%, and more than 601 million bp of sequence were generated. A total of 5321, 6526, and 4016 differentially expressed genes were identified 6, 12, and 24 h after Cd stress treatment, respectively. A total of 1660 genes were differentially expressed at the three time points, and their gene expression profiles over time were elucidated. Based on the analysis of these genes, the important mechanisms for the Cd stress response in Z. japonica were identified. Specific genes participating in glutathione metabolism, plant hormone signal and transduction, members of protein processing in the endoplasmic reticulum, transporter proteins, transcription factors, and carbohydrate metabolism pathways were further analyzed in detail. These genes may contribute to the improvement of Cd tolerance in Z. japonica. In addition, some candidate genes were highlighted for future studies on Cd stress resistance in Z. japonica and other plants. Our results illustrate the early gene expression response of Z. japonica leaves to Cd and provide some new understanding of the molecular mechanisms of Cd stress in Zosia and Gramineae species.
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Affiliation(s)
- Yi Xu
- College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China; (Y.X.); (Y.L.); (Y.L.); (C.Z.)
- College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Yonglong Li
- College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China; (Y.X.); (Y.L.); (Y.L.); (C.Z.)
| | - Yan Li
- College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China; (Y.X.); (Y.L.); (Y.L.); (C.Z.)
| | - Chenyuan Zhai
- College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China; (Y.X.); (Y.L.); (Y.L.); (C.Z.)
| | - Kun Zhang
- College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China; (Y.X.); (Y.L.); (Y.L.); (C.Z.)
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14
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Flores-Iga G, Lopez-Ortiz C, Gracia-Rodriguez C, Almeida A, Nimmakayala P, Reddy UK, Balagurusamy N. A Genome-Wide Identification and Comparative Analysis of the Heavy-Metal-Associated Gene Family in Cucurbitaceae Species and Their Role in Cucurbita pepo under Arsenic Stress. Genes (Basel) 2023; 14:1877. [PMID: 37895226 PMCID: PMC10606463 DOI: 10.3390/genes14101877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 09/21/2023] [Accepted: 09/25/2023] [Indexed: 10/29/2023] Open
Abstract
The heavy-metal-associated (HMA) proteins are a class of PB1-type ATPases related to the intracellular transport and detoxification of metals. However, due to a lack of information regarding the HMA gene family in the Cucurbitaceae family, a comprehensive genome-wide analysis of the HMA family was performed in ten Cucurbitaceae species: Citrullus amarus, Citrullus colocynthis, Citrullus lanatus, Citrullus mucosospermus, Cucumis melo, Cucumis sativus, Cucurbita maxima, Cucurbita moschata, Cucurbita pepo, and Legenaria siceraria. We identified 103 Cucurbit HMA proteins with various members, ranging from 8 (Legenaria siceraria) to 14 (Cucurbita pepo) across species. The phylogenetic and structural analysis confirmed that the Cucurbitaceae HMA protein family could be further classified into two major clades: Zn/Co/Cd/Pb and Cu/Ag. The GO-annotation-based subcellular localization analysis predicted that all HMA gene family members were localized on membranes. Moreover, the analysis of conserved motifs and gene structure (intron/exon) revealed the functional divergence between clades. The interspecies microsynteny analysis demonstrated that maximum orthologous genes were found between species of the Citrullus genera. Finally, nine candidate HMA genes were selected, and their expression analysis was carried out via qRT-PCR in root, leaf, flower, and fruit tissues of C. pepo under arsenic stress. The expression pattern of the CpeHMA genes showed a distinct pattern of expression in root and shoot tissues, with a remarkable expression of CpeHMA6 and CpeHMA3 genes from the Cu/Ag clade. Overall, this study provides insights into the functional analysis of the HMA gene family in Cucurbitaceae species and lays down the basic knowledge to explore the role and mechanism of the HMA gene family to cope with arsenic stress conditions.
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Affiliation(s)
- Gerardo Flores-Iga
- Laboratorio de Biorremediación, Facultad de Ciencias Biológicas, Universidad Autónoma de Coahuila, Torreón 27275, Coahuila, México; (G.F.-I.); (C.G.-R.)
- Gus R. Douglass Institute, Department of Biology, West Virginia State University, Institute, WV 25112-1000, USA; (C.L.-O.); (P.N.)
| | - Carlos Lopez-Ortiz
- Gus R. Douglass Institute, Department of Biology, West Virginia State University, Institute, WV 25112-1000, USA; (C.L.-O.); (P.N.)
| | - Celeste Gracia-Rodriguez
- Laboratorio de Biorremediación, Facultad de Ciencias Biológicas, Universidad Autónoma de Coahuila, Torreón 27275, Coahuila, México; (G.F.-I.); (C.G.-R.)
- Gus R. Douglass Institute, Department of Biology, West Virginia State University, Institute, WV 25112-1000, USA; (C.L.-O.); (P.N.)
| | - Aldo Almeida
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark;
| | - Padma Nimmakayala
- Gus R. Douglass Institute, Department of Biology, West Virginia State University, Institute, WV 25112-1000, USA; (C.L.-O.); (P.N.)
| | - Umesh K. Reddy
- Gus R. Douglass Institute, Department of Biology, West Virginia State University, Institute, WV 25112-1000, USA; (C.L.-O.); (P.N.)
| | - Nagamani Balagurusamy
- Laboratorio de Biorremediación, Facultad de Ciencias Biológicas, Universidad Autónoma de Coahuila, Torreón 27275, Coahuila, México; (G.F.-I.); (C.G.-R.)
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15
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Shen C, Li X. Genome-wide identification and expression pattern profiling of the ATP-binding cassette gene family in tea plant (Camelliasinensis). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 202:107930. [PMID: 37552927 DOI: 10.1016/j.plaphy.2023.107930] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 07/28/2023] [Accepted: 08/01/2023] [Indexed: 08/10/2023]
Abstract
The ATP-binding cassette (ABC) gene family is one of the largest and oldest protein families, consisting of ATP-driven transporters facilitating substrate transportation across cell membranes. However, little is known about the evolution and biological function of the ABC gene family in tea plants. In this study, we performed a genome-wide identification and expression analysis of genes encoding ABC transporter proteins in Camellia sinensis. Our analysis of 170 ABC genes revealed that CsABCs were unevenly distributed across 15 chromosomes, with an amino acid length ranging from 188 to 2489 aa, molecular weight ranging from 20.29 to 277.34 kDa, and an isoelectric point ranging from 4.89 to 10.63. Phylogenetic analysis showed that CsABCs were divided into eight subfamilies, among which the ABCG subfamily was the most abundant. Furthermore, the subcellular localization of CsABCs indicated that they were present in various organelles. Collinearity analysis between the tea plant and Arabidopsis thaliana genomes revealed that the CsABC genes were homologous to the AtABC genes. Large gene fragment duplication analysis identified ten gene pairs as tandem repeats, and interaction network analysis demonstrated that CsABCs interacted with various types of target genes, with protein interactions also occurring within the family. Tissue expression analysis indicated that CsABCs were highly expressed in roots, stems, and leaves and were easily induced by drought and cold stress. Moreover, qRT-PCR analysis of the relative expression level of the gene under drought and cold stress correlated with the sequencing results. Identifying ABC genes in tea plants lays a foundation for the classification and functional analysis of ABC family genes, which can facilitate molecular breeding and the development of new tea varieties.
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Affiliation(s)
- Chuan Shen
- Shaannan Eco-economy Research Center, Ankang University, 725000, Ankang, China.
| | - Xia Li
- Department of Electronic and Information Engineering, Ankang University, 725000, Ankang, China
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16
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Chen X, Zhao Y, Zhong Y, Chen J, Qi X. Deciphering the functional roles of transporter proteins in subcellular metal transportation of plants. PLANTA 2023; 258:17. [PMID: 37314548 DOI: 10.1007/s00425-023-04170-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 05/31/2023] [Indexed: 06/15/2023]
Abstract
MAIN CONCLUSION The role of transporters in subcellular metal transport is of great significance for plants in coping with heavy metal stress and maintaining their proper growth and development. Heavy metal toxicity is a serious long-term threat to plant growth and agricultural production, becoming a global environmental concern. Excessive heavy metal accumulation not only damages the biochemical and physiological functions of plants but also causes chronic health hazard to human beings through the food chain. To deal with heavy metal stress, plants have evolved a series of elaborate mechanisms, especially a variety of spatially distributed transporters, to strictly regulate heavy metal uptake and distribution. Deciphering the subcellular role of transporter proteins in controlling metal absorption, transport and separation is of great significance for understanding how plants cope with heavy metal stress and improving their adaptability to environmental changes. Hence, we herein introduce the detrimental effects of excessive common essential and non-essential heavy metals on plant growth, and describe the structural and functional characteristics of transporter family members, with a particular emphasis on their roles in maintaining heavy metal homeostasis in various organelles. Besides, we discuss the potential of controlling transporter gene expression by transgenic approaches in response to heavy metal stress. This review will be valuable to researchers and breeders for enhancing plant tolerance to heavy metal contamination.
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Affiliation(s)
- Xingqi Chen
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou, 215011, China
| | - Yuanchun Zhao
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou, 215011, China
| | - Yuqing Zhong
- Environmental Monitoring Station of Suzhou City, Suzhou, 215004, China
| | - Jiajia Chen
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou, 215011, China
| | - Xin Qi
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou, 215011, China.
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17
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Fan P, Wu L, Wang Q, Wang Y, Luo H, Song J, Yang M, Yao H, Chen S. Physiological and molecular mechanisms of medicinal plants in response to cadmium stress: Current status and future perspective. JOURNAL OF HAZARDOUS MATERIALS 2023; 450:131008. [PMID: 36842201 DOI: 10.1016/j.jhazmat.2023.131008] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 02/08/2023] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
Medicinal plants have a wide range of uses worldwide. However, the quality of medicinal plants is affected by severe cadmium pollution. Cadmium can reduce photosynthetic capacity, lead to plant growth retardation and oxidative stress, and affect secondary metabolism. Medicinal plants have complex mechanisms to cope with cadmium stress. On the one hand, an antioxidant system can effectively scavenge excess reactive oxygen species produced by cadmium stress. On the other hand, cadmium chelates are formed by chelating peptides and then sequestered through vacuolar compartmentalization. Cadmium has no specific transporter in plants and is generally transferred to plant tissues through competition for the transporters of divalent metal ions, such as zinc, iron, and manganese. In recent years, progress has been achieved in exploring the physiological mechanisms by which medicinal plants responding to cadmium stress. The exogenous regulation of cadmium accumulation in medicinal plants has been studied, and the aim is reducing the toxicity of cadmium. However, research into molecular mechanisms is still lagging. In this paper, we review the physiological and molecular mechanisms and regulatory networks of medicinal plants exposed to cadmium, providing a reference for the study on the responses of medicinal plants to cadmium stress.
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Affiliation(s)
- Panhui Fan
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Liwei Wu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Qing Wang
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Yu Wang
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Hongmei Luo
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Jingyuan Song
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Meihua Yang
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Hui Yao
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China; Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing 100193, China.
| | - Shilin Chen
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China.
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18
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Zhang B, Tang Y, Yu F, Peng Z, Yao S, Deng X, Long H, Wang X, Huang K. Translatomics and physiological analyses of the detoxification mechanism of green alga Chlamydomonas reinhardtii to cadmium toxicity. JOURNAL OF HAZARDOUS MATERIALS 2023; 448:130990. [PMID: 36860060 DOI: 10.1016/j.jhazmat.2023.130990] [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: 10/24/2022] [Revised: 02/02/2023] [Accepted: 02/09/2023] [Indexed: 06/18/2023]
Abstract
Cadmium (Cd) is one of the most toxic pollutants found in aquatic ecosystems. Although gene expression in algae exposed to Cd has been studied at the transcriptional level, little is known about Cd impacts at the translational level. Ribosome profiling is a novel translatomics method that can directly monitor RNA translation in vivo. Here, we analyzed the translatome of the green alga Chlamydomonas reinhardtii following treatment with Cd to identify the cellular and physiological responses to Cd stress. Interestingly, we found that the cell morphology and cell wall structure were altered, and starch and high-electron-density particles accumulated in the cytoplasm. Several ATP-binding cassette transporters that responded to Cd exposure were identified. Redox homeostasis was adjusted to adapt to Cd toxicity, and GDP-L-galactose phosphorylase (VTC2), glutathione peroxidase (GPX5), and ascorbate were found to play important roles in maintaining reactive oxygen species homeostasis. Moreover, we found that the key enzyme of flavonoid metabolism, i.e., hydroxyisoflavone reductase (IFR1), is also involved in the detoxification of Cd. Thus, in this study, translatome and physiological analyses provided a complete picture of the molecular mechanisms of green algae cell responses to Cd.
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Affiliation(s)
- Baolong Zhang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, China
| | - Yuxin Tang
- School of Urban Construction, Wuhan University of Science and Technology, Wuhan 430065, Hubei, China
| | - Fei Yu
- School of Urban Construction, Wuhan University of Science and Technology, Wuhan 430065, Hubei, China
| | - Zhao Peng
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, Hubei, China
| | - Sheng Yao
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, Hubei, China
| | - Xuan Deng
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, China
| | - Huan Long
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, China
| | - Xun Wang
- School of Urban Construction, Wuhan University of Science and Technology, Wuhan 430065, Hubei, China
| | - Kaiyao Huang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, China.
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19
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Perlein A, Bert V, de Souza MF, Papin A, Meers E. Field evaluation of industrial non-food crops for phytomanaging a metal-contaminated dredged sediment. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:44963-44984. [PMID: 36701059 DOI: 10.1007/s11356-022-24964-9] [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: 05/24/2022] [Accepted: 12/20/2022] [Indexed: 06/17/2023]
Abstract
Phytomanagement is a concept fit for a bio-based circular economy that combines phytotechnologies and biomass production for non-food purposes. Here, ten annual and perennial industrial non-food crops (Sorghum Biomass 133, Sorghum Santa Fe red, Linum usitatissimum L., Eucalyptus sp., Salix Inger, Salix Tordis, Beta vulgaris L., Phacelia tanacetifolia Benth., Malva sylvestris L., and Chenopodium album L.) were studied under field conditions for phytomanaging a metal (Cd, Cu, Pb, and Zn)-contaminated dredged sediment in the North of France. The crops were selected according to their relevance to pedoclimatic and future climatic conditions, and one or more non-food end-products were proposed for each plant part collected, such as biogas, bioethanol, compost, natural dye, ecocatalyst, and fiber. Based on the soil-plant transfer of metals, eight out of the crops cultivated on field plots exhibited an excluder behavior (bioconcentration factor, BCF < 1), a trait suitable for phytostabilization. However, these crops did not change the metal mobilities in the dredged sediment. The BCF < 1 was not sufficient to characterize the excluder behavior of crops as this factor depended on the total dredged-sediment contaminant. Therefore, a BCF group ranking method was proposed accounting for metal phytotoxicity levels or yield decrease as a complemental way to discuss the crop behavior. The feasibility of the biomass-processing chains was discussed based on these results and according to a survey of available legislation in standard and scientific literature.
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Affiliation(s)
- Alexandre Perlein
- Laboratory for Bioresource Recovery, Ghent University Campus Coupure, B6, Coupure Links 653, 9000, Ghent, Belgium.
- Clean Technologies and Circular Economy, INERIS, Parc Technologique Alata, BP2, 60550, Verneuil-en-Halatte, France.
| | - Valérie Bert
- Clean Technologies and Circular Economy, INERIS, Parc Technologique Alata, BP2, 60550, Verneuil-en-Halatte, France
| | - Marcella Fernandes de Souza
- Laboratory for Bioresource Recovery, Ghent University Campus Coupure, B6, Coupure Links 653, 9000, Ghent, Belgium
| | - Arnaud Papin
- Analytical Methods and Developments for the Environment, INERIS, Parc Technologique Alata, BP2, 60550, Verneuil-en-Halatte, France
| | - Erik Meers
- Laboratory for Bioresource Recovery, Ghent University Campus Coupure, B6, Coupure Links 653, 9000, Ghent, Belgium
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Zang H, He J, Zhang Q, Li X, Wang T, Bi X, Zhang Y. Ectopic Expression of PvHMA2.1 Enhances Cadmium Tolerance in Arabidopsis thaliana. Int J Mol Sci 2023; 24:ijms24043544. [PMID: 36834955 PMCID: PMC9966247 DOI: 10.3390/ijms24043544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 02/06/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023] Open
Abstract
Cadmium (Cd) in soil inhibits plant growth and development and even harms human health through food chain transmission. Switchgrass (Panicum virgatum L.), a perennial C4 biofuel crop, is considered an ideal plant for phytoremediation due to its high efficiency in removing Cd and other heavy metals from contaminated soil. The key to understanding the mechanisms of switchgrass Cd tolerance is to identify the genes involved in Cd transport. Heavy-metal ATPases (HMAs) play pivotal roles in heavy metal transport, including Cd, in Arabidopsis thaliana and Oryza sativa, but little is known about the functions of their orthologs in switchgrass. Therefore, we identified 22 HMAs in switchgrass, which were distributed on 12 chromosomes and divided into 4 groups using a phylogenetic analysis. Then, we focused on PvHMA2.1, which is one of the orthologs of the rice Cd transporter OsHMA2. We found that PvHMA2.1 was widely expressed in roots, internodes, leaves, spikelets, and inflorescences, and was significantly induced in the shoots of switchgrass under Cd treatment. Moreover, PvHMA2.1 was found to have seven transmembrane domains and localized at the cell plasma membrane, indicating that it is a potential transporter. The ectopic expression of PvHMA2.1 alleviated the reduction in primary root length and the loss of fresh weight of Arabidopsis seedlings under Cd treatment, suggesting that PvHMA2.1 enhanced Cd tolerance in Arabidopsis. The higher levels of relative water content and chlorophyll content of the transgenic lines under Cd treatment reflected that PvHMA2.1 maintained water retention capacity and alleviated photosynthesis inhibition under Cd stress in Arabidopsis. The roots of the PvHMA2.1 ectopically expressed lines accumulated less Cd compared to the WT, while no significant differences were found in the Cd contents of the shoots between the transgenic lines and the WT under Cd treatment, suggesting that PvHMA2.1 reduced Cd absorption from the environment through the roots in Arabidopsis. Taken together, our results showed that PvHMA2.1 enhanced Cd tolerance in Arabidopsis, providing a promising target that could be engineered in switchgrass to repair Cd-contaminated soil.
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Liu Q, Sui X, Wang Y, Zhu M, Zhou Y, Gao F. Genome-Wide Analyses of Thaumatin-like Protein Family Genes Reveal the Involvement in the Response to Low-Temperature Stress in Ammopiptanthus nanus. Int J Mol Sci 2023; 24:ijms24032209. [PMID: 36768531 PMCID: PMC9917035 DOI: 10.3390/ijms24032209] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/15/2023] [Accepted: 01/20/2023] [Indexed: 01/25/2023] Open
Abstract
Thaumatin-like proteins (TLPs), a family of proteins with high sequence similarity to thaumatin, are shown to be involved in plant defense, and are thus classified into the pathogenesis related protein family 5. Ammopiptanthus nanus is a rare evergreen broad-leaved shrub distributed in the temperate zone of Central Asia, which has a high tolerance to low-temperature stress. To characterize A. nanus TLPs and understand their roles in low-temperature response in A. nanus, a comprehensive analysis of the structure, evolution, and expression of TLP family proteins was performed. A total of 31 TLP genes were detected in the A. nanus genome, and they were divided into four groups based on their phylogenetic positions. The majority of the AnTLPs contained the conserved cysteine residues and were predicted to have the typical three-dimensional structure of plant TLPs. The primary modes of gene duplication of the AnTLP family genes were segmental duplication. The promoter regions of most AnTLP genes contain multiple cis-acting elements related to environmental stress response. Gene expression analysis based on transcriptome data and fluorescence quantitative PCR analysis revealed that several AnTLP genes were involved in cold-stress response. We further showed that a cold-induced AnTLP gene, AnTLP13, was localized in apoplast, and heterologous expression of the AnTLP13 in Escherichia coli and yeast cells and tobacco leaves enhanced low-temperature stress tolerance when compared with the control cells or seedlings. Our study provided important data for understanding the roles of TLPs in plant response to abiotic stress.
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Affiliation(s)
- Qi Liu
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China
- Key Laboratory of Ecology and Environment in Minority Areas, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Xiangyu Sui
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Ying Wang
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China
- Key Laboratory of Ecology and Environment in Minority Areas, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Ming Zhu
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China
- Key Laboratory of Ecology and Environment in Minority Areas, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Yijun Zhou
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China
- Key Laboratory of Ecology and Environment in Minority Areas, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
- Correspondence: (Y.Z.); (F.G.); Tel.: +86-68932633 (Y.Z. & F.G.)
| | - Fei Gao
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China
- Key Laboratory of Ecology and Environment in Minority Areas, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
- Correspondence: (Y.Z.); (F.G.); Tel.: +86-68932633 (Y.Z. & F.G.)
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Al-Khayri JM, Banadka A, Rashmi R, Nagella P, Alessa FM, Almaghasla MI. Cadmium toxicity in medicinal plants: An overview of the tolerance strategies, biotechnological and omics approaches to alleviate metal stress. FRONTIERS IN PLANT SCIENCE 2023; 13:1047410. [PMID: 36733604 PMCID: PMC9887195 DOI: 10.3389/fpls.2022.1047410] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 12/05/2022] [Indexed: 06/18/2023]
Abstract
Medicinal plants, an important source of herbal medicine, are gaining more demand with the growing human needs in recent times. However, these medicinal plants have been recognized as one of the possible sources of heavy metal toxicity in humans as these medicinal plants are exposed to cadmium-rich soil and water because of extensive industrial and agricultural operations. Cadmium (Cd) is an extremely hazardous metal that has a deleterious impact on plant development and productivity. These plants uptake Cd by symplastic, apoplastic, or via specialized transporters such as HMA, MTPs, NRAMP, ZIP, and ZRT-IRT-like proteins. Cd exerts its effect by producing reactive oxygen species (ROS) and interfere with a range of metabolic and physiological pathways. Studies have shown that it has detrimental effects on various plant growth stages like germination, vegetative and reproductive stages by analyzing the anatomical, morphological and biochemical changes (changes in photosynthetic machinery and membrane permeability). Also, plants respond to Cd toxicity by using various enzymatic and non-enzymatic antioxidant systems. Furthermore, the ROS generated due to the heavy metal stress alters the genes that are actively involved in signal transduction. Thus, the biosynthetic pathway of the important secondary metabolite is altered thereby affecting the synthesis of secondary metabolites either by enhancing or suppressing the metabolite production. The present review discusses the abundance of Cd and its incorporation, accumulation and translocation by plants, phytotoxic implications, and morphological, physiological, biochemical and molecular responses of medicinal plants to Cd toxicity. It explains the Cd detoxification mechanisms exhibited by the medicinal plants and further discusses the omics and biotechnological strategies such as genetic engineering and gene editing CRISPR- Cas 9 approach to ameliorate the Cd stress.
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Affiliation(s)
- Jameel M. Al-Khayri
- Department of Agricultural Biotechnology, College of Agriculture and Food Sciences, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Akshatha Banadka
- Department of Life Sciences, CHRIST (Deemed to be University), Bangalore, Karnataka, India
| | - R Rashmi
- Department of Life Sciences, CHRIST (Deemed to be University), Bangalore, Karnataka, India
| | - Praveen Nagella
- Department of Life Sciences, CHRIST (Deemed to be University), Bangalore, Karnataka, India
| | - Fatima M. Alessa
- Department of Food Science and Nutrition, College of Agriculture and Food Sciences, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Mustafa I. Almaghasla
- Department of Arid Land Agriculture, College of Agriculture and Food Sciences, King Faisal University, Al-Ahsa, Saudi Arabia
- Plant Pests, and Diseases Unit, College of Agriculture and Food Sciences, King Faisal University, Al-Ahsa, Saudi Arabia
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23
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Liao J, Huang X, Jiang Y, Pu X, Zhang Y, Deng X, Yang R, Zhang L. Identification of Salvia miltiorrhiza Bunge with high and low cadmium accumulation and insight into the mechanisms of cadmium accumulation. CHEMOSPHERE 2022; 307:135978. [PMID: 35961456 DOI: 10.1016/j.chemosphere.2022.135978] [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: 06/30/2022] [Revised: 07/30/2022] [Accepted: 08/04/2022] [Indexed: 06/15/2023]
Abstract
Salvia miltiorrhiza Bunge is used as a Chinese herbal medicine (CHM) particularly its roots. No relevant reports at home and abroad have been made on the mechanism of cadmium (Cd) accumulation in S. miltiorrhiza. The Cd accumulation characteristics of S. miltiorrhiza from main cultivation areas in China were evaluated for the first time to obtain high and low Cd accumulation in S. miltiorrhiza roots. Results showed obvious differences in the Cd enrichment capacity of S. miltiorrhiza from different cultivation areas. We took the lead in identifying the germplasm resources of S. miltiorrhiza with high and low Cd accumulation, that is, S. miltiorrhiza roots from Pingyi Shangdong (SDPY) belongs to the resource with high Cd accumulation (SDPY-H) and that from Zhongjiang Sichuan (SCZJ) is the resources with low Cd accumulation (SCZJ-L) based on relevant physiological and biochemical indexes. Although the Cd content of SDPY-H was apparently higher than that from SCZJ-L, its translocation factor from root to aboveground part is significantly lower than that in SCZJ-L. Therefore, planting SCZJ-L is not only an economic and effective way to use Cd in slightly and moderately polluted soil, but also its aboveground part can be used for phytoremediation. Changes in Cd content before and after the use of transpiration inhibitor indicate that SDPY-H enriched Cd through the symplastic pathway, whereas SCZJ-L mainly enriched Cd through the apoplastic pathways. In addition, the role of the symplastic pathway in SCZJ-L is weaker than that in SDPY-H, which were preliminarily revealed by fluorescent quantitative polymerase chain reaction. The significant reduction of the SmNramps transcription expression amount is one of the reasons for the low Cd accumulation of SCZJ-L.
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Affiliation(s)
- Jinqiu Liao
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China; Featured Medicinal Plants Sharing and Service Platform of Sichuan Province, Sichuan Agricultural University, Ya'an 625014, China; Sichuan Provincial Engineering Research Center for Breeding Technology of Authentic Traditional Chinese Medicine, Sichuan Agricultural University, Ya'an 625014, China
| | - Xianhao Huang
- College of Science, Sichuan Agricultural University, Ya'an 625014, China; Featured Medicinal Plants Sharing and Service Platform of Sichuan Province, Sichuan Agricultural University, Ya'an 625014, China; Sichuan Provincial Engineering Research Center for Breeding Technology of Authentic Traditional Chinese Medicine, Sichuan Agricultural University, Ya'an 625014, China
| | - Yuanyuan Jiang
- College of Science, Sichuan Agricultural University, Ya'an 625014, China; Featured Medicinal Plants Sharing and Service Platform of Sichuan Province, Sichuan Agricultural University, Ya'an 625014, China; Sichuan Provincial Engineering Research Center for Breeding Technology of Authentic Traditional Chinese Medicine, Sichuan Agricultural University, Ya'an 625014, China
| | - Xiang Pu
- College of Science, Sichuan Agricultural University, Ya'an 625014, China; Featured Medicinal Plants Sharing and Service Platform of Sichuan Province, Sichuan Agricultural University, Ya'an 625014, China; Sichuan Provincial Engineering Research Center for Breeding Technology of Authentic Traditional Chinese Medicine, Sichuan Agricultural University, Ya'an 625014, China
| | - Yunsong Zhang
- College of Science, Sichuan Agricultural University, Ya'an 625014, China; Featured Medicinal Plants Sharing and Service Platform of Sichuan Province, Sichuan Agricultural University, Ya'an 625014, China; Sichuan Provincial Engineering Research Center for Breeding Technology of Authentic Traditional Chinese Medicine, Sichuan Agricultural University, Ya'an 625014, China
| | - Xuexue Deng
- College of Science, Sichuan Agricultural University, Ya'an 625014, China; Featured Medicinal Plants Sharing and Service Platform of Sichuan Province, Sichuan Agricultural University, Ya'an 625014, China; Sichuan Provincial Engineering Research Center for Breeding Technology of Authentic Traditional Chinese Medicine, Sichuan Agricultural University, Ya'an 625014, China
| | - Ruiwu Yang
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China; Featured Medicinal Plants Sharing and Service Platform of Sichuan Province, Sichuan Agricultural University, Ya'an 625014, China; Sichuan Provincial Engineering Research Center for Breeding Technology of Authentic Traditional Chinese Medicine, Sichuan Agricultural University, Ya'an 625014, China
| | - Li Zhang
- College of Science, Sichuan Agricultural University, Ya'an 625014, China; Featured Medicinal Plants Sharing and Service Platform of Sichuan Province, Sichuan Agricultural University, Ya'an 625014, China; Sichuan Provincial Engineering Research Center for Breeding Technology of Authentic Traditional Chinese Medicine, Sichuan Agricultural University, Ya'an 625014, China.
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24
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Liu L, Zhang L, Zhao L, Chen Q, Zhang Q, Cao D, Liu Z. Differential Gene Expression and Metabolic Pathway Analysis of Cladophora rupestris under Pb Stress Conditions. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:13910. [PMID: 36360789 PMCID: PMC9656615 DOI: 10.3390/ijerph192113910] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/19/2022] [Accepted: 10/21/2022] [Indexed: 06/16/2023]
Abstract
This study aimed to analyze the transcriptome of C. rupestris under Pb2+ stress by using high-throughput sequencing technology, observe the changes of gene expression and metabolic pathway after three and five days under 1.0 and 5.0 mg/L of Pb2+ treatment, and analyze the differentially expressed genes (DEGs) and related functional genes after Pb2+ treatment. Metabolic pathways were revealed through Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Results show that DEGs increased significantly with the increase of Pb2+ concentration and stress time. A total of 32 genes were closely related to Pb2+ stress response. GO analysis identified two major transporter proteins, namely, ATP-binding transport protein-related (ABC transporters) and zinc finger CCHC domain containing protein (Zfp) in C. rupestris. Pthr19248, pthr19211, Zfp pthr23002, Zfp p48znf pthr12681, Zfp 294 pthr12389, and Zfp pthr23067 played important roles against Pb2+ toxicity and its absorption in C. rupestris. KEGG pathway analysis suggested that ABCA1, ATM, and ABCD3 were closely related to Pb2+ absorption. Pb2+ stress was mainly involved in metallothionein (MT), plant hormone signal transduction, ABC transporters, and glutathione (GSH) metabolism.
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Affiliation(s)
- Lei Liu
- Anhui Province Key Laboratory of Farmland Ecological Conservation and Pollution Prevention, School of Resources and Environment, Anhui Agricultural University, Hefei 230036, China
| | - Lusheng Zhang
- Anhui Province Key Laboratory of Farmland Ecological Conservation and Pollution Prevention, School of Resources and Environment, Anhui Agricultural University, Hefei 230036, China
| | - Lingyun Zhao
- Anhui Province Key Laboratory of Farmland Ecological Conservation and Pollution Prevention, School of Resources and Environment, Anhui Agricultural University, Hefei 230036, China
| | - Qiuyu Chen
- Anhui Province Key Laboratory of Farmland Ecological Conservation and Pollution Prevention, School of Resources and Environment, Anhui Agricultural University, Hefei 230036, China
| | - Qian Zhang
- Anhui Province Key Laboratory of Farmland Ecological Conservation and Pollution Prevention, School of Resources and Environment, Anhui Agricultural University, Hefei 230036, China
| | - Deju Cao
- Anhui Province Key Laboratory of Farmland Ecological Conservation and Pollution Prevention, School of Resources and Environment, Anhui Agricultural University, Hefei 230036, China
| | - Zhaowen Liu
- Anhui Province Key Laboratory of Farmland Ecological Conservation and Pollution Prevention, School of Resources and Environment, Anhui Agricultural University, Hefei 230036, China
- School of Materials and Environmental Engineering, Chizhou University, Chizhou 247000, China
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25
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Song C, Li X, Jia B, Liu L, Wei P, Manzoor MA, Wang F, Li BY, Wang G, Chen C, Han B. Comparative Transcriptomics Unveil the Crucial Genes Involved in Coumarin Biosynthesis in Peucedanum praeruptorum Dunn. FRONTIERS IN PLANT SCIENCE 2022; 13:899819. [PMID: 35656010 PMCID: PMC9152428 DOI: 10.3389/fpls.2022.899819] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 04/29/2022] [Indexed: 06/15/2023]
Abstract
Peucedanum praeruptorum Dunn is a commonly used traditional Chinese medicine that is abundant in furano- and dihydropyrano coumarins. When P. praeruptorum reaches the bolting stage, the roots gradually lignified, and the content of coumarins declines rapidly. Non-bolting has always been a decisive factor for harvesting the P. praeruptorum materials. To evaluate the amount of coumarin components in unbolted and bolted P. praeruptorum, the variations of praeruptorin A, praeruptorin B, praeruptorin E, peucedanocoumarin I, and peucedanocoumarin II were determined. Additionally, 336,505 transcripts were obtained from the comparative transcriptome data. Among them, a total of 1,573 differentially expressed genes were screened out. To identify the critical genes involved in coumarin biosynthesis, comparative transcriptomics coupled with co-expression associated analysis was conducted. Finally, coumarin biosynthesis-related eighteen candidate genes were selected for the validation of qPCR. Additionally, a phylogenetic tree and the expression profile of ATP-binding cassette (ABC) transporters were constructed. To clarify the main genes in the regulation of coumarin biosynthesis, the interaction network of the co-expression genes from thirteen modules was constructed. Current results exhibited the significant increment of praeruptorin A, praeruptorin B and praeruptorin E in the bolted P. praeruptorum. Although, peucedanocoumarin I and peucedanocoumarin II were slightly increased. Besides the content of coumarins, the essential genes involved in the coumarin biosynthesis also exhibited an overall downward trend after bolting. Three peroxidases (PRXs) involved in the production of lignin monomers had been demonstrated to be downregulated. PAL, C4H, HCT, COMT, CCoAOMT, and some ABC transporters were dramatically downregulated at the bolting stage. These results indicated that the downregulation of coumarin biosynthetic genes in the bolted P. praeruptorum ultimately reduced the formation of coumarins. However, the mechanism through which bolting indirectly affects the formation of coumarin still needs extra functional verification.
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Affiliation(s)
- Cheng Song
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, Lu’an, China
| | - Xiaoli Li
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, Lu’an, China
| | - Bin Jia
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, Lu’an, China
| | - Li Liu
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, Lu’an, China
| | - Peipei Wei
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, Lu’an, China
| | | | - Fang Wang
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, Lu’an, China
| | - Biqi Yao Li
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, Lu’an, China
| | - Guanglin Wang
- Analytical and Testing Center, West Anhui University, Lu’an, China
| | - Cunwu Chen
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, Lu’an, China
| | - Bangxing Han
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, Lu’an, China
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26
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Banasiak J, Jasiński M. ATP-binding cassette transporters in nonmodel plants. THE NEW PHYTOLOGIST 2022; 233:1597-1612. [PMID: 34614235 DOI: 10.1111/nph.17779] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 09/21/2021] [Indexed: 06/13/2023]
Abstract
Knowledge about plant ATP-binding cassette (ABC) proteins is of great value for sustainable agriculture, economic yield, and the generation of high-quality products, especially under unfavorable growth conditions. We have learned much about ABC proteins in model organisms, notably Arabidopsis thaliana; however, the importance of research dedicated to these transporters extends far beyond Arabidopsis biology. Recent progress in genomic and transcriptomic approaches for nonmodel and noncanonical model plants allows us to look at ABC transporters from a wider perspective and consider chemodiversity and functionally driven adaptation as distinctive mechanisms during their evolution. Here, by considering several representatives from agriculturally important families and recent progress in functional characterization of nonArabidopsis ABC proteins, we aim to bring attention to understanding the evolutionary background, distribution among lineages and possible mechanisms underlying the adaptation of this versatile transport system for plant needs. Increasing the knowledge of ABC proteins in nonmodel plants will facilitate breeding and development of new varieties based on, for example, genetic variations of endogenous genes and/or genome editing, representing an alternative to transgenic approaches.
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Affiliation(s)
- Joanna Banasiak
- Department of Plant Molecular Physiology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704, Poznań, Poland
| | - Michał Jasiński
- Department of Plant Molecular Physiology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704, Poznań, Poland
- Department of Biochemistry and Biotechnology, Poznań University of Life Sciences, Dojazd 11, 60-632, Poznań, Poland
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Ma Y, Wei N, Wang Q, Liu Z, Liu W. Genome-wide identification and characterization of the heavy metal ATPase (HMA) gene family in Medicago truncatula under copper stress. Int J Biol Macromol 2021; 193:893-902. [PMID: 34728304 DOI: 10.1016/j.ijbiomac.2021.10.197] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 08/08/2021] [Accepted: 10/26/2021] [Indexed: 10/19/2022]
Abstract
In nature, the normal growth, development, and quality of plants are significantly affected by many abiotic stresses, such as drought, salinity, low temperature, and heavy metals. Among heavy metals, copper is an essential element for plant growth and development but also has a toxic effect on plants when its concentration is excessive. Therefore, plants have evolved a complex regulatory network to regulate the balance of copper ions in cells. Heavy metal ATPases (HMAs), which transport heavy metals to intracellular compartments or detoxify heavy metals present at excessive concentrations, have been extensively studied in model plant species. However, no comprehensive and systematic surveys of members of the HMA gene family have been conducted in the model legume species Medicago truncatula. Here, nine putative MtHMAs were identified in the M. truncatula genome. These MtHMAs were phylogenetically divided into two distinct groups. The members in each group had a relatively conserved gene structure and motif composition. The number of introns in the MtHMAs varied from 5 to 16, with the majority of these genes containing 8 introns. The expression patterns showed that MtHMAs exhibit preferential or distinct expression patterns among different tissues. Finally, the expression patterns of the members of this gene family were verified in the leaves and roots of plants under Cu stress. Our findings will be valuable for the functional investigation and application of members of this gene family in M. truncatula and other related legume species.
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Affiliation(s)
- Yitong Ma
- State Key Laboratory of Grassland Agro-ecosystems, Lanzhou University, China; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, China; Western China Technology Innovation Center for Grassland Industry, Gansu Province, China; Engineering Research Center of Grassland Industry, Ministry of Education, China; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China
| | - Na Wei
- State Key Laboratory of Grassland Agro-ecosystems, Lanzhou University, China; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, China; Western China Technology Innovation Center for Grassland Industry, Gansu Province, China; Engineering Research Center of Grassland Industry, Ministry of Education, China; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China
| | - Qiuxia Wang
- State Key Laboratory of Grassland Agro-ecosystems, Lanzhou University, China; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, China; Western China Technology Innovation Center for Grassland Industry, Gansu Province, China; Engineering Research Center of Grassland Industry, Ministry of Education, China; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China
| | - Zhipeng Liu
- State Key Laboratory of Grassland Agro-ecosystems, Lanzhou University, China; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, China; Western China Technology Innovation Center for Grassland Industry, Gansu Province, China; Engineering Research Center of Grassland Industry, Ministry of Education, China; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China.
| | - Wenxian Liu
- State Key Laboratory of Grassland Agro-ecosystems, Lanzhou University, China; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, China; Western China Technology Innovation Center for Grassland Industry, Gansu Province, China; Engineering Research Center of Grassland Industry, Ministry of Education, China; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China.
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28
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Wei W, Peng H, Xie Y, Wang X, Huang R, Chen H, Ji X. The role of silicon in cadmium alleviation by rice root cell wall retention and vacuole compartmentalization under different durations of Cd exposure. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 226:112810. [PMID: 34571424 DOI: 10.1016/j.ecoenv.2021.112810] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/16/2021] [Accepted: 09/18/2021] [Indexed: 05/22/2023]
Abstract
Silicon (Si) plays a pivotal role in mitigating phytotoxicity caused by cadmium (Cd). However, few former reports focused on the internal mechanism how Si assisted in alleviating Cd stress in rice under different durations of Cd exposure. Herein, the effects of Si on subcellular distribution of Cd in rice roots under short-term (12 h) and long-term (20 d) Cd exposure were explored. Results showed that Si decreased shoot Cd concentration but had little impact on root Cd levels. Under short-term Cd exposure, subcellular distribution analysis showed that Si increased the ratio of Cd in root cell wall by 23.2~24.0%, and decreased the ratio of Cd in root soluble fraction by 20.6~21.5%. This suggested that Si supply improved root retention of Cd by fixing it on the cell wall and thus restricted intracellular transportation of Cd. Further analysis unraveled that pectin (especially ionic-soluble pectin) of the cell wall was the main binding component, and Si supply induced more Cd accumulation in covalent-soluble pectin and hemicellulose. Moreover, the overexpression of germin-like proteins (GLPs) proved the role of cell wall in moderating Cd toxicity. Under long-term Cd exposure, Si promoted phytochelatin 2 (PC2) and phytochelatin 3 (PC3) synthesis in cytosol, at the same time, Si down-regulated the expression of the Cd efflux-related protein multidrug resistance-associated protein-like ATP-binding cassette transporters (MRP-like ABC transporters) and limited Cd transportation from vacuole to cytosol. Taken together, Si rather predominates in limiting Cd translocation by the cell wall of root under short-term Cd exposure and promoting vacuole compartmentalization to mitigate the Cd toxicity under long-term exposure, instead of reducing the absorption of Cd in rice roots, thereby decreasing Cd delivery into shoots.
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Affiliation(s)
- Wei Wei
- Long Ping Branch, Graduate School of Hunan University, Changsha 410125, China
| | - Hua Peng
- Institute of Agro-Environment and Ecology, Hunan Academy of Agricultural, Science (HAAS), Changsha 410125, China
| | - Yunhe Xie
- Institute of Agro-Environment and Ecology, Hunan Academy of Agricultural, Science (HAAS), Changsha 410125, China
| | - Xin Wang
- School of Geographic Sciences, Hunan Normal University, Changsha, Hunan 410081, China
| | - Rui Huang
- Long Ping Branch, Graduate School of Hunan University, Changsha 410125, China
| | - Haoyu Chen
- Long Ping Branch, Graduate School of Hunan University, Changsha 410125, China
| | - Xionghui Ji
- Long Ping Branch, Graduate School of Hunan University, Changsha 410125, China; Institute of Agro-Environment and Ecology, Hunan Academy of Agricultural, Science (HAAS), Changsha 410125, China.
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Cao H, Zhang X, Wang S, Liu J, Han D, Zhao B, Wang H. Insights Into Mechanism of the Naphthalene-Enhanced Biodegradation of Phenanthrene by Pseudomonas sp. SL-6 Based on Omics Analysis. Front Microbiol 2021; 12:761216. [PMID: 34867892 PMCID: PMC8635735 DOI: 10.3389/fmicb.2021.761216] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 10/18/2021] [Indexed: 12/04/2022] Open
Abstract
The existence of polycyclic aromatic hydrocarbons (PAHs) in contaminated environment is multifarious. At present, studies of metabolic regulation focus on the degradation process of single PAH. The global metabolic regulatory mechanisms of microorganisms facing coexisting PAHs are poorly understood, which is the major bottleneck for efficient bioremediation of PAHs pollution. Naphthalene (NAP) significantly enhanced the biodegradation of phenanthrene (PHE) by Pseudomonas sp. SL-6. To explore the underlying mechanism, isobaric tags for relative and absolute quantification (iTRAQ) labeled quantitative proteomics was used to characterize the differentially expressed proteins of SL-6 cultured with PHE or NAP + PHE as carbon source. Through joint analysis of proteome and genome, unique proteins were identified and quantified. The up-regulated proteins mainly concentrated in PAH catabolism, Transporters and Electron transfer carriers. In the process, the regulator NahR, activated by salicylate (intermediate of NAP-biodegradation), up-regulates degradation enzymes (NahABCDE and SalABCDEFGH), which enhances the biodegradation of PHE and accumulation of toxic intermediate–1-hydroxy-2-naphthoic acid (1H2Na); 1H2Na stimulates the expression of ABC transporter, which maintains intracellular physiological activity by excreting 1H2Na; the up-regulation of cytochrome C promotes the above process running smoothly. Salicylate works as a trigger that stimulates cell to respond globally. The conjecture was verified at transcriptional and metabolic levels. These new insights contribute to improving the overall understanding of PAHs-biodegradation processes under complex natural conditions, and promoting the application of microbial remediation technology for PAHs pollution.
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Affiliation(s)
- Hao Cao
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xinyu Zhang
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shuangyan Wang
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiading Liu
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dongfei Han
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Baisuo Zhao
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Haisheng Wang
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing, China
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Povkhova LV, Melnikova NV, Rozhmina TA, Novakovskiy RO, Pushkova EN, Dvorianinova EM, Zhuchenko AA, Kamionskaya AM, Krasnov GS, Dmitriev AA. Genes Associated with the Flax Plant Type (Oil or Fiber) Identified Based on Genome and Transcriptome Sequencing Data. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10122616. [PMID: 34961087 PMCID: PMC8707629 DOI: 10.3390/plants10122616] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 11/25/2021] [Accepted: 11/26/2021] [Indexed: 06/14/2023]
Abstract
As a result of the breeding process, there are two main types of flax (Linum usitatissimum L.) plants. Linseed is used for obtaining seeds, while fiber flax is used for fiber production. We aimed to identify the genes associated with the flax plant type, which could be important for the formation of agronomically valuable traits. A search for polymorphisms was performed in genes involved in the biosynthesis of cell wall components, lignans, fatty acids, and ion transport based on genome sequencing data for 191 flax varieties. For 143 of the 424 studied genes (4CL, C3'H, C4H, CAD, CCR, CCoAOMT, COMT, F5H, HCT, PAL, CTL, BGAL, ABC, HMA, DIR, PLR, UGT, TUB, CESA, RGL, FAD, SAD, and ACT families), one or more polymorphisms had a strong correlation with the flax type. Based on the transcriptome sequencing data, we evaluated the expression levels for each flax type-associated gene in a wide range of tissues and suggested genes that are important for the formation of linseed or fiber flax traits. Such genes were probably subjected to the selection press and can determine not only the traits of seeds and stems but also the characteristics of the root system or resistance to stresses at a particular stage of development, which indirectly affects the ability of flax plants to produce seeds or fiber.
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Affiliation(s)
- Liubov V. Povkhova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (L.V.P.); (N.V.M.); (R.O.N.); (E.N.P.); (E.M.D.); (G.S.K.)
- Moscow Institute of Physics and Technology, 141701 Moscow, Russia
| | - Nataliya V. Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (L.V.P.); (N.V.M.); (R.O.N.); (E.N.P.); (E.M.D.); (G.S.K.)
| | - Tatiana A. Rozhmina
- Federal Research Center for Bast Fiber Crops, 172002 Torzhok, Russia; (T.A.R.); (A.A.Z.)
| | - Roman O. Novakovskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (L.V.P.); (N.V.M.); (R.O.N.); (E.N.P.); (E.M.D.); (G.S.K.)
| | - Elena N. Pushkova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (L.V.P.); (N.V.M.); (R.O.N.); (E.N.P.); (E.M.D.); (G.S.K.)
| | - Ekaterina M. Dvorianinova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (L.V.P.); (N.V.M.); (R.O.N.); (E.N.P.); (E.M.D.); (G.S.K.)
- Moscow Institute of Physics and Technology, 141701 Moscow, Russia
| | - Alexander A. Zhuchenko
- Federal Research Center for Bast Fiber Crops, 172002 Torzhok, Russia; (T.A.R.); (A.A.Z.)
- All-Russian Horticultural Institute for Breeding, Agrotechnology and Nursery, 115598 Moscow, Russia
| | - Anastasia M. Kamionskaya
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia;
| | - George S. Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (L.V.P.); (N.V.M.); (R.O.N.); (E.N.P.); (E.M.D.); (G.S.K.)
| | - Alexey A. Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (L.V.P.); (N.V.M.); (R.O.N.); (E.N.P.); (E.M.D.); (G.S.K.)
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Meng X, Liu J, Zhao M. Genome-wide identification of RING finger genes in flax ( Linum usitatissimum) and analyses of their evolution. PeerJ 2021; 9:e12491. [PMID: 34820204 PMCID: PMC8601054 DOI: 10.7717/peerj.12491] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 10/25/2021] [Indexed: 01/05/2023] Open
Abstract
Background Flax (Linum usitatissimum) is an important crop for its seed oil and stem fiber. Really Interesting New Gene (RING) finger genes play essential roles in growth, development, and biotic and abiotic stress responses in plants. However, little is known about these genes in flax. Methods Here, we performed a systematic genome-wide analysis to identify RING finger genes in flax. Results We identified 587 RING domains in 574 proteins and classified them into RING-H2 (292), RING-HCa (181), RING-HCb (23), RING-v (53), RING-C2 (31), RING-D (2), RING-S/T (3), and RING-G (2). These proteins were further divided into 45 groups according to domain organization. These genes were located in 15 chromosomes and clustered into three clades according to their phylogenetic relationships. A total of 312 segmental duplicated gene pairs were inferred from 411 RING finger genes, indicating a major contribution of segmental duplications to the RING finger gene family expansion. The non-synonymous/synonymous substitution ratio of the segmentally duplicated gene pairs was less than 1, suggesting that the gene family was under negative selection since duplication. Further, most RING genes in flax were differentially expressed during seed development or in the shoot apex. This study provides useful information for further functional analysis of RING finger genes in flax and to develop gene-derived molecular markers in flax breeding.
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Affiliation(s)
- Xianwen Meng
- The College of Ecological Environmental and Resources, Qinghai Provincial Key Laboratory of High Value Utilization of Characteristic Economic Plants, Qinghai Tibet Alpine Wetland Restoration Engineering Technology Research Center, Qinghai Minzu University, Xining, China
| | - Jing Liu
- The College of Ecological Environmental and Resources, Qinghai Provincial Key Laboratory of High Value Utilization of Characteristic Economic Plants, Qinghai Tibet Alpine Wetland Restoration Engineering Technology Research Center, Qinghai Minzu University, Xining, China
| | - Mingde Zhao
- The College of Ecological Environmental and Resources, Qinghai Provincial Key Laboratory of High Value Utilization of Characteristic Economic Plants, Qinghai Tibet Alpine Wetland Restoration Engineering Technology Research Center, Qinghai Minzu University, Xining, China
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Sun W, Zhan J, Zheng T, Wu G, Xu H, Chen Y, Yao M, Zeng J, Yan J, Chen H. Involvement of several putative transporters of different families in β-cyclocitral-induced alleviation of cadmium toxicity in quinoa (Chenopodium quinoa) seedlings. JOURNAL OF HAZARDOUS MATERIALS 2021; 419:126474. [PMID: 34186425 DOI: 10.1016/j.jhazmat.2021.126474] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 06/17/2021] [Accepted: 06/21/2021] [Indexed: 06/13/2023]
Abstract
Cadmium (Cd) has a serious negative impact on crop growth and human food security. This study investigated the alleviating effect of β-cyclocitral, a potential heavy metal barrier, on Cd stress in quinoa seedlings and the associated mechanisms. Our results showed that β-cyclocitral alleviated Cd stress-induced growth inhibition in quinoa seedlings and promoted quinoa seedling root development under Cd stress. Moreover, it maintained the antioxidant system of quinoa seedlings, including the enzymatic, i.e., superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), ascorbate peroxidase (APX), and nonenzymatic, i.e., reduced glutathione (GSH) and ascorbic acid (ASA), antioxidants, which eliminate the damage from excessive reactive oxygen species (ROS). Our results showed that β-cyclocitral could reduce the amount of Cd absorbed by roots. Furthermore, we systematically identified five transporter families from the quinoa genome, and the RT-qPCR results showed that ZIP, Nramp and YSL gene families were downregulated by β-cyclocitral to reduce Cd uptake by roots. Thus, β-cyclocitral promoted the growth, photosynthetic capacity and antioxidant capacity of the aboveground parts of quinoa seedlings. Taken together, these results suggested that the β-cyclocitral-induced decrease in Cd uptake may be caused by the downregulation of several selected transporter genes.
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Affiliation(s)
- Wenjun Sun
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China.
| | - Junyi Zhan
- College of Life Science, Nanjing Agricultural University, Nanjing 210032, China.
| | - Tianrun Zheng
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China.
| | - Guoming Wu
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China.
| | - Haishen Xu
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China.
| | - Ying Chen
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China.
| | - Min Yao
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China.
| | - Jing Zeng
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China.
| | - Jun Yan
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture Rural Affairs, School of Pharmacy and Bioengineering, Chengdu University, Chengdu 610106, China.
| | - Hui Chen
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China.
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Xie X, Cao P, Wang Z, Gao J, Wu M, Li X, Zhang J, Wang Y, Gong D, Yang J. Genome-wide characterization and expression profiling of the PDR gene family in tobacco (Nicotiana tabacum). Gene 2021; 788:145637. [PMID: 33848571 DOI: 10.1016/j.gene.2021.145637] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 03/13/2021] [Accepted: 04/07/2021] [Indexed: 11/18/2022]
Abstract
The pleiotropic drug resistance (PDR) proteins of the ATP-binding cassette (ABC) family play essential roles in physiological processes and have been characterized in many plant species. However, no comprehensive investigation of tobacco (Nicotiana tabacum), an important economic crop and a useful model plant for scientific research, has been presented. We identified 32 PDR genes in the tobacco genome and explored their domain organization, chromosomal distribution and evolution, promoter cis-elements, and expression profiles. A phylogenetic analysis revealed that tobacco has a significantly expanded number of PDR genes involved in plant defense. It also revealed that two tobacco PDR proteins may function as strigolactone transporters to regulate shoot branching, and several NtPDR genes may be involved in cadmium transport. Moreover, tissue expression profiles of NtPDR genes and their responses to several hormones and abiotic stresses were assessed using quantitative real-time PCR. Most of the NtPDR genes were regulated by jasmonate or salicylic acid, suggesting the important regulatory roles of NtPDRs in plant defense and secondary metabolism. They were also responsive to abiotic stresses, like drought and cold, and there was a strong correlation between the presence of promoter cis-elements and abiotic/biotic stress responses. These results provide useful clues for further in-depth studies on the functions of the tobacco PDR genes.
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Affiliation(s)
- Xiaodong Xie
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China
| | - Peijian Cao
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China
| | - Zhong Wang
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China
| | - Junping Gao
- China Tobacco Hunan Industrial Co., Ltd., Changsha 410007, China
| | - Mingzhu Wu
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China
| | - Xiaoxu Li
- China Tobacco Hunan Industrial Co., Ltd., Changsha 410007, China
| | - Jianfeng Zhang
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China
| | - Yaofu Wang
- China Tobacco Hunan Industrial Co., Ltd., Changsha 410007, China
| | - Daping Gong
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China.
| | - Jun Yang
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China.
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Huang J, Li X, Chen X, Guo Y, Liang W, Wang H. Genome-Wide Identification of Soybean ABC Transporters Relate to Aluminum Toxicity. Int J Mol Sci 2021; 22:6556. [PMID: 34207256 PMCID: PMC8234336 DOI: 10.3390/ijms22126556] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/13/2021] [Accepted: 06/15/2021] [Indexed: 11/17/2022] Open
Abstract
ATP-binding cassette (ABC) transporter proteins are a gene super-family in plants and play vital roles in growth, development, and response to abiotic and biotic stresses. The ABC transporters have been identified in crop plants such as rice and buckwheat, but little is known about them in soybean. Soybean is an important oil crop and is one of the five major crops in the world. In this study, 255 ABC genes that putatively encode ABC transporters were identified from soybean through bioinformatics and then categorized into eight subfamilies, including 7 ABCAs, 52 ABCBs, 48 ABCCs, 5 ABCDs, 1 ABCEs, 10 ABCFs, 111 ABCGs, and 21 ABCIs. Their phylogenetic relationships, gene structure, and gene expression profiles were characterized. Segmental duplication was the main reason for the expansion of the GmABC genes. Ka/Ks analysis suggested that intense purifying selection was accompanied by the evolution of GmABC genes. The genome-wide collinearity of soybean with other species showed that GmABCs were relatively conserved and that collinear ABCs between species may have originated from the same ancestor. Gene expression analysis of GmABCs revealed the distinct expression pattern in different tissues and diverse developmental stages. The candidate genes GmABCB23, GmABCB25, GmABCB48, GmABCB52, GmABCI1, GmABCI5, and GmABCI13 were responsive to Al toxicity. This work on the GmABC gene family provides useful information for future studies on ABC transporters in soybean and potential targets for the cultivation of new germplasm resources of aluminum-tolerant soybean.
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Affiliation(s)
| | | | | | | | | | - Huahua Wang
- College of Life Science, Henan Normal University, Xinxiang 453007, China; (J.H.); (X.L.); (X.C.); (Y.G.); (W.L.)
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