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Raza A, Salehi H, Bashir S, Tabassum J, Jamla M, Charagh S, Barmukh R, Mir RA, Bhat BA, Javed MA, Guan DX, Mir RR, Siddique KHM, Varshney RK. Transcriptomics, proteomics, and metabolomics interventions prompt crop improvement against metal(loid) toxicity. PLANT CELL REPORTS 2024; 43:80. [PMID: 38411713 PMCID: PMC10899315 DOI: 10.1007/s00299-024-03153-7] [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: 11/23/2023] [Accepted: 01/05/2024] [Indexed: 02/28/2024]
Abstract
The escalating challenges posed by metal(loid) toxicity in agricultural ecosystems, exacerbated by rapid climate change and anthropogenic pressures, demand urgent attention. Soil contamination is a critical issue because it significantly impacts crop productivity. The widespread threat of metal(loid) toxicity can jeopardize global food security due to contaminated food supplies and pose environmental risks, contributing to soil and water pollution and thus impacting the whole ecosystem. In this context, plants have evolved complex mechanisms to combat metal(loid) stress. Amid the array of innovative approaches, omics, notably transcriptomics, proteomics, and metabolomics, have emerged as transformative tools, shedding light on the genes, proteins, and key metabolites involved in metal(loid) stress responses and tolerance mechanisms. These identified candidates hold promise for developing high-yielding crops with desirable agronomic traits. Computational biology tools like bioinformatics, biological databases, and analytical pipelines support these omics approaches by harnessing diverse information and facilitating the mapping of genotype-to-phenotype relationships under stress conditions. This review explores: (1) the multifaceted strategies that plants use to adapt to metal(loid) toxicity in their environment; (2) the latest findings in metal(loid)-mediated transcriptomics, proteomics, and metabolomics studies across various plant species; (3) the integration of omics data with artificial intelligence and high-throughput phenotyping; (4) the latest bioinformatics databases, tools and pipelines for single and/or multi-omics data integration; (5) the latest insights into stress adaptations and tolerance mechanisms for future outlooks; and (6) the capacity of omics advances for creating sustainable and resilient crop plants that can thrive in metal(loid)-contaminated environments.
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Affiliation(s)
- Ali Raza
- Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Hajar Salehi
- Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122, Piacenza, Italy
| | - Shanza Bashir
- Institute of Environmental Sciences and Engineering, School of Civil and Environmental Engineering, National University of Sciences and Technology, Islamabad, Pakistan
| | - Javaria Tabassum
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
| | - Monica Jamla
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune University, Ganeshkhind, Pune, 411016, India
| | - Sidra Charagh
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Hangzhou, China
| | - Rutwik Barmukh
- WA State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, 6150, Australia
| | - Rakeeb Ahmad Mir
- Department of Biotechnology, School of Life Sciences, Central University of Kashmir, Ganderbal, India
| | - Basharat Ahmad Bhat
- Department of Bio-Resources, Amar Singh College Campus, Cluster University Srinagar, Srinagar, JK, India
| | - Muhammad Arshad Javed
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
| | - Dong-Xing Guan
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Reyazul Rouf Mir
- Division of Genetics and Plant Breeding, Faculty of Agriculture, Sher-e-Kashmir University of Agricultural Sciences and Technology (SKUAST), Srinagar, Kashmir, India
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia.
| | - Rajeev K Varshney
- WA State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, 6150, Australia.
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Wan L, Huo J, Huang Q, Ji X, Song L, Zhang Z, Pan L, Fu J, Abd Elhamid MA, Soaud SA, Heakel RMY, Gao J, Wei S, El-Sappah AH. Genetics and metabolic responses of Artemisia annua L to the lake of phosphorus under the sparingly soluble phosphorus fertilizer: evidence from transcriptomics analysis. Funct Integr Genomics 2024; 24:26. [PMID: 38329581 DOI: 10.1007/s10142-024-01301-6] [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: 08/02/2023] [Revised: 01/14/2024] [Accepted: 01/16/2024] [Indexed: 02/09/2024]
Abstract
The medicinal herb Artemisia annua L. is prized for its capacity to generate artemisinin, which is used to cure malaria. Potentially influencing the biomass and secondary metabolite synthesis of A. annua is plant nutrition, particularly phosphorus (P). However, most soil P exist as insoluble inorganic and organic phosphates, which results to low P availability limiting plant growth and development. Although plants have developed several adaptation strategies to low P levels, genetics and metabolic responses to P status remain largely unknown. In a controlled greenhouse experiment, the sparingly soluble P form, hydroxyapatite (Ca5OH(PO4)3/CaP) was used to simulate calcareous soils with low P availability. In contrast, the soluble P form KH2PO4/KP was used as a control. A. annua's morphological traits, growth, and artemisinin concentration were determined, and RNA sequencing was used to identify the differentially expressed genes (DEGs) under two different P forms. Total biomass, plant height, leaf number, and stem diameter, as well as leaf area, decreased by 64.83%, 27.49%, 30.47%, 38.70%, and 54.64% in CaP compared to KP; however, LC-MS tests showed an outstanding 37.97% rise in artemisinin content per unit biomass in CaP contrary to KP. Transcriptome analysis showed 2015 DEGs (1084 up-regulated and 931 down-regulated) between two P forms, including 39 transcription factor (TF) families. Further analysis showed that DEGs were mainly enriched in carbohydrate metabolism, secondary metabolites biosynthesis, enzyme catalytic activity, signal transduction, and so on, such as tricarboxylic acid (TCA) cycle, glycolysis, starch and sucrose metabolism, flavonoid biosynthesis, P metabolism, and plant hormone signal transduction. Meanwhile, several artemisinin biosynthesis genes were up-regulated, including DXS, GPPS, GGPS, MVD, and ALDH, potentially increasing artemisinin accumulation. Furthermore, 21 TF families, including WRKY, MYB, bHLH, and ERF, were up-regulated in reaction to CaP, confirming their importance in P absorption, internal P cycling, and artemisinin biosynthesis regulation. Our results will enable us to comprehend how low P availability impacts the parallel transcriptional control of plant development, growth, and artemisinin production in A. annua. This study could lay the groundwork for future research into the molecular mechanisms underlying A. annua's low P adaptation.
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Affiliation(s)
- Lingyun Wan
- Guangxi Key Laboratory of High-Quality Formation and Utilization of Dao-di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Juan Huo
- Guangxi Key Laboratory of High-Quality Formation and Utilization of Dao-di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Qiulan Huang
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
| | - Xiaowen Ji
- Guangxi Key Laboratory of High-Quality Formation and Utilization of Dao-di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Lisha Song
- Guangxi Key Laboratory of High-Quality Formation and Utilization of Dao-di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Zhanjiang Zhang
- Guangxi Key Laboratory of High-Quality Formation and Utilization of Dao-di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Limei Pan
- Guangxi Key Laboratory of High-Quality Formation and Utilization of Dao-di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Jine Fu
- Guangxi Key Laboratory of High-Quality Formation and Utilization of Dao-di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | | | - Salma A Soaud
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Rania M Y Heakel
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Jihai Gao
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Shugen Wei
- Guangxi Key Laboratory of High-Quality Formation and Utilization of Dao-di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, China.
| | - Ahmed H El-Sappah
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China.
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt.
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Gou C, Huang Q, Rady MM, Wang L, Ihtisham M, El-Awady HH, Seif M, Alazizi EMY, Eid RSM, Yan K, Tahri W, Li J, Desoky ESM, El-Sappah AH. Integrative application of silicon and/or proline improves Sweet corn (Zea mays L. saccharata) production and antioxidant defense system under salt stress condition. Sci Rep 2023; 13:18315. [PMID: 37880216 PMCID: PMC10600099 DOI: 10.1038/s41598-023-45003-8] [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: 07/13/2023] [Accepted: 10/14/2023] [Indexed: 10/27/2023] Open
Abstract
Silicon (Si) and/or proline (Pro) are natural supplements that are considered to induce plants' stress tolerance against various abiotic stresses. Sweet corn (Zea mays L. saccharata) production is severely afflicted by salinity stress. Therefore, two field tests were conducted to evaluate the potential effects of Si and/or Pro (6mM) used as seed soaking (SS) and/or foliar spray (FS) on Sweet corn plant growth and yield, physio-biochemical attributes, and antioxidant defense systems grown in a saline (EC = 7.14dS m-1) soil. The Si and/or Pro significantly increased growth and yield, photosynthetic pigments, free proline, total soluble sugars (TSS), K+/Na+ratios, relative water content (RWC), membrane stability index (MSI), α-Tocopherol (α-TOC), Ascorbate (AsA), glutathione (GSH), enzymatic antioxidants activities and other anatomical features as compared to controls. In contrast, electrolytes, such as SS and/or FS under salt stress compared to controls (SS and FS using tap water) were significantly decreased. The best results were obtained when SS was combined with FS via Si or Pro. These alterations are brought about by the exogenous application of Si and/or Pro rendering these elements potentially useful in aiding sweet corn plants to acclimate successfully to saline soil.
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Affiliation(s)
- Caiming Gou
- College of Agriculture, Forestry, and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Qiulan Huang
- College of Agriculture, Forestry, and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Mostafa M Rady
- Botany Department, Faculty of Agriculture, Fayoum University, Fayoum, 63514, Egypt
| | - Linghui Wang
- College of Agriculture, Forestry, and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Muhammad Ihtisham
- College of Agriculture, Forestry, and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Hamada H El-Awady
- College of Horticulture, Northwest A&F University, Xianyang, 712100, China
| | - Mohamed Seif
- Toxicology and Food Contaminants Department, Food Industries and Nutrition Research Institute, National Research Centre, Dokki, Giza, 12622, Egypt
| | - Esmail M Y Alazizi
- Sichuan University of Science and Engineering, Yibin, 643000, Sichuan, China
| | - Rania S M Eid
- Agricultural Botany Department, Faculty of Agriculture, Benha University, Banha, 13518, Egypt
| | - Kuan Yan
- College of Agriculture, Forestry, and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Walid Tahri
- International Faculty of Applied Technology, Yibin University, Yibin, 644000, Sichuan, China
| | - Jia Li
- College of Agriculture, Forestry, and Food Engineering, Yibin University, Yibin, Sichuan, China.
| | - El-Sayed M Desoky
- Botany Department, Faculty of Agriculture, Zagazig University, Zagazig, 44511, Egypt.
| | - Ahmed H El-Sappah
- College of Agriculture, Forestry, and Food Engineering, Yibin University, Yibin, Sichuan, China.
- Department of Genetics, Faculty of Agriculture, Zagazig University, Zagazig, 44511, Egypt.
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Li J, Abbas M, Desoky ESM, Zafar S, Soaud SA, Hussain SS, Abbas S, Hussain A, Ihtisham M, Ragauskas AJ, Wafa HA, El-Sappah AH. Analysis of metal tolerance protein (MTP) family in sunflower (Helianthus annus L.) and role of HaMTP10 as Cadmium antiporter under moringa seed extract. INDUSTRIAL CROPS AND PRODUCTS 2023; 202:117023. [DOI: 10.1016/j.indcrop.2023.117023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
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Yilmaz H, Özer G, Baloch FS, Çiftçi V, Chung YS, Sun HJ. Genome-Wide Identification and Expression Analysis of MTP (Metal Ion Transport Proteins) Genes in the Common Bean. PLANTS (BASEL, SWITZERLAND) 2023; 12:3218. [PMID: 37765382 PMCID: PMC10535811 DOI: 10.3390/plants12183218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/01/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023]
Abstract
MTP/CDF carriers, called metal ion transport proteins, act as substrates for the transmission of micronutrients such as iron (Fe), zinc (Zn), and manganese (Mn) to membrane carriers in plants. In this study, genome-wide analysis of the MTP gene family in the common bean genome, expression analysis of the PvMTP4, PvMTP5, and PvMTP12 genes after Fe and Zn treatments, and the effects of Fe and Zn applications on iron and zinc content were investigated. This study used common bean genotypes assumed to have high or low Fe and Zn accumulation ability. PvMTP genes were defined as containing conserved catalytic domains with molecular weights and protein lengths ranging from 41.35 to 91.05 kDa and from 369 to 813 amino acids (aa), respectively. As a result of the phylogenetic analysis, three main clusters containing seven subgroups were formed. In this study, the first characterization of the MTP gene family of beans was performed, and the responses of three different PvMTP genes in the Zn-CDF group to Fe and Zn applications were revealed. The obtained findings are thought to constitute pioneering resources for future research on common bean biofortification studies, plant breeding related to Fe and Zn, and the functional characterization of the MTP gene family.
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Affiliation(s)
- Hilal Yilmaz
- Plant and Animal Production Program, Izmit Vocational School, Kocaeli University, Kocaeli 41285, Türkiye;
- Department of Field Crops, Faculty of Agriculture, Bolu Abant Izzet Baysal University, Bolu 14030, Türkiye;
| | - Göksel Özer
- Department of Plant Protection, Faculty of Agriculture, Bolu Abant Izzet Baysal University, Bolu 14030, Türkiye;
| | - Faheem Shehzad Baloch
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas 58140, Türkiye
| | - Vahdettin Çiftçi
- Department of Field Crops, Faculty of Agriculture, Bolu Abant Izzet Baysal University, Bolu 14030, Türkiye;
| | - Yong Suk Chung
- Department of Plant Resources and Environment, Jeju National University, Jeju 63243, Republic of Korea;
| | - Hyeon-Jin Sun
- Subtropical Horticulture Research Institute, Jeju National University, Jeju 63243, Republic of Korea;
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Shirazi Z, Khakdan F, Rafiei F, Balalami MY, Ranjbar M. Genome-wide identification and expression profile analysis of metal tolerance protein gene family in Eucalyptus grandis under metal stresses. BMC PLANT BIOLOGY 2023; 23:240. [PMID: 37149585 PMCID: PMC10163719 DOI: 10.1186/s12870-023-04240-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 04/21/2023] [Indexed: 05/08/2023]
Abstract
Metal tolerance proteins (MTPs) as Me2+/H+(K+) antiporters participate in the transport of divalent cations, leading to heavy metal stress resistance and mineral utilization in plants. In the present study, to obtain better knowledge of the biological functions of the MTPs family, 20 potential EgMTPs genes were identified in Eucalyptus grandis and classified into seven groups belonging to three cation diffusion facilitator groups (Mn-CDFs, Zn/Fe-CDFs, and Zn-CDFs) and seven groups. EgMTP-encoded amino acids ranged from 315 to 884, and most of them contained 4-6 recognized transmembrane domains and were clearly prognosticated to localize into the cell vacuole. Almost all EgMTP genes experienced gene duplication events, in which some might be uniformly distributed in the genome. The numbers of cation efflux and the zinc transporter dimerization domain were highest in EgMTP proteins. The promoter regions of EgMTP genes have different cis-regulatory elements, indicating that the transcription rate of EgMTP genes can be a controlled response to different stimuli in multiple pathways. Our findings provide accurate perception on the role of the predicted miRNAs and the presence of SSR marker in the Eucalyptus genome and clarify their functions in metal tolerance regulation and marker-assisted selection, respectively. Gene expression profiling based on previous RNA-seq data indicates a probable function for EgMTP genes during development and responses to biotic stress. Additionally, the upregulation of EgMTP6, EgMTP5, and EgMTP11.1 to excess Cd2+ and Cu2+ exposure might be responsible for metal translocation from roots to leaves.
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Affiliation(s)
- Zahra Shirazi
- Department of Biotechnology Research, Research Institute of Forests and Rangelands, Agricultural Research, Education and Extension Organization (AREEO), National Botanical Garden, Tehran Karaj Freeway, P.O. Box 13185-116, Tehran, Iran.
| | | | - Fariba Rafiei
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA
| | - Mahdi Yahyazadeh Balalami
- Department of Medicinal Plant Research, Research Institute of Forests and Rangelands, Agricultural Research, Education and Extension Organization (AREEO), National Botanical Garden, Tehran Karaj Freeway, P.O. Box 13185-116, Tehran, Iran
| | - Mojtaba Ranjbar
- Microbial Biotechnology Department, College of Biotechnology, University of Special Modern Technologies, Amol, Iran
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Wan L, Huang Q, Ji X, Song L, Zhang Z, Pan L, Fu J, Elbaiomy RG, Eldomiaty AS, Rather SA, Elashtokhy MMA, Gao J, Guan L, Wei S, El-Sappah AH. RNA sequencing in Artemisia annua L explored the genetic and metabolic responses to hardly soluble aluminum phosphate treatment. Funct Integr Genomics 2023; 23:141. [PMID: 37118364 DOI: 10.1007/s10142-023-01067-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 04/18/2023] [Accepted: 04/21/2023] [Indexed: 04/30/2023]
Abstract
Artemisia annua L. is a medicinal plant valued for its ability to produce artemisinin, a molecule used to treat malaria. Plant nutrients, especially phosphorus (P), can potentially influence plant biomass and secondary metabolite production. Our work aimed to explore the genetic and metabolic response of A. annua to hardly soluble aluminum phosphate (AlPO4, AlP), using soluble monopotassium phosphate (KH2PO4, KP) as a control. Liquid chromatography-mass spectrometry (LC-MS) was used to analyze artemisinin. RNA sequencing, gene ontology (GO), and the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were applied to analyze the differentially expressed genes (DEGs) under poor P conditions. Results showed a significant reduction in plant growth parameters, such as plant height, stem diameter, number of leaves, leaf areas, and total biomass of A. annua. Conversely, LC-MS analysis revealed a significant increase in artemisinin concentration under the AlP compared to the KP. Transcriptome analysis revealed 762 differentially expressed genes (DEGs) between the AlP and the KP. GH3, SAUR, CRE1, and PYL, all involved in plant hormone signal transduction, showed differential expression. Furthermore, despite the downregulation of HMGR in the artemisinin biosynthesis pathway, the majority of genes (ACAT, FPS, CYP71AV1, and ALDH1) were upregulated, resulting in increased artemisinin accumulation in the AlP. In addition, 12 transcription factors, including GATA and MYB, were upregulated in response to AlP, confirming their importance in regulating artemisinin biosynthesis. Overall, our findings could contribute to a better understanding the parallel transcriptional regulation of plant hormone transduction and artemisinin biosynthesis in A. annua L. in response to hardly soluble phosphorus fertilizer.
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Affiliation(s)
- Lingyun Wan
- Key Laboratory of Guangxi for High-Quality Formation and Utilization of Dao-Di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Qiulan Huang
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China.
| | - Xiaowen Ji
- Key Laboratory of Guangxi for High-Quality Formation and Utilization of Dao-Di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Lisha Song
- Key Laboratory of Guangxi for High-Quality Formation and Utilization of Dao-Di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Zhanjiang Zhang
- Key Laboratory of Guangxi for High-Quality Formation and Utilization of Dao-Di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Limei Pan
- Key Laboratory of Guangxi for High-Quality Formation and Utilization of Dao-Di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Jine Fu
- Key Laboratory of Guangxi for High-Quality Formation and Utilization of Dao-Di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Rania G Elbaiomy
- Faculty of Pharmacy, Ahram Canadian University, 6 October, Giza, Egypt
| | - Ahmed S Eldomiaty
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Shabir A Rather
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Yunnan, China
| | | | - Jihai Gao
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Lingliang Guan
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Shugen Wei
- Key Laboratory of Guangxi for High-Quality Formation and Utilization of Dao-Di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, China.
| | - Ahmed H El-Sappah
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China.
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt.
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Ihtisham M, Hasanuzzaman M, El-Sappah AH, Zaman F, Khan N, Raza A, Sarraf M, Khan S, Abbas M, Hassan MJ, Li J, Zhao X, Zhao X. Primary plant nutrients modulate the reactive oxygen species metabolism and mitigate the impact of cold stress in overseeded perennial ryegrass. FRONTIERS IN PLANT SCIENCE 2023; 14:1149832. [PMID: 37063220 PMCID: PMC10103648 DOI: 10.3389/fpls.2023.1149832] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 03/06/2023] [Indexed: 06/08/2023]
Abstract
Overseeded perennial ryegrass (Lolium perenne L.) turf on dormant bermudagrass (Cynodon dactylon Pers. L) in transitional climatic zones (TCZ) experience a severe reduction in its growth due to cold stress. Primary plant nutrients play an important role in the cold stress tolerance of plants. To better understand the cold stress tolerance of overseeded perennial ryegrass under TCZ, a three-factor and five-level central composite rotatable design (CCRD) with a regression model was used to study the interactive effects of nitrogen (N), phosphorus (P), and potassium (K) fertilization on lipid peroxidation, electrolyte leakage, reactive oxygen species (ROS) production, and their detoxification by the photosynthetic pigments, enzymatic and non-enzymatic antioxidants. The study demonstrated substantial effects of N, P, and K fertilization on ROS production and their detoxification through enzymatic and non-enzymatic pathways in overseeded perennial ryegrass under cold stress. Our results demonstrated that the cold stress significantly enhanced malondialdehyde, electrolyte leakage, and hydrogen peroxide contents, while simultaneously decreasing ROS-scavenging enzymes, antioxidants, and photosynthetic pigments in overseeded perennial ryegrass. However, N, P, and K application mitigated cold stress-provoked adversities by enhancing soluble protein, superoxide dismutase, peroxide dismutase, catalase, and proline contents as compared to the control conditions. Moreover, N, P, and, K application enhanced chlorophyll a, chlorophyll b, total chlorophyll, and carotenoids in overseeded perennial ryegrass under cold stress as compared to the control treatments. Collectively, this 2-years study indicated that N, P, and K fertilization mitigated cold stress by activating enzymatic and non-enzymatic antioxidants defense systems, thereby concluding that efficient nutrient management is the key to enhanced cold stress tolerance of overseeded perennial ryegrass in a transitional climate. These findings revealed that turfgrass management will not only rely on breeding new varieties but also on the development of nutrient management strategies for coping cold stress.
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Affiliation(s)
- Muhammad Ihtisham
- College of Agriculture, Forestry, and Food Engineering, Yibin University, Yibin, Sichuan, China
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, China
| | - Mirza Hasanuzzaman
- Department of Agronomy, Faculty of Agriculture, Sher-e-Bangla Agricultural University, Dhaka, Bangladesh
| | - Ahmed H. El-Sappah
- College of Agriculture, Forestry, and Food Engineering, Yibin University, Yibin, Sichuan, China
- Department of Genetics, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Fawad Zaman
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, China
| | - Nawab Khan
- College of Management, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Ali Raza
- Chengdu Institute of Biology, University of Chinese Academy of Sciences, Beijing, China
| | - Mohammad Sarraf
- Department of Horticultural Sciences, Faculty of Agriculture, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Shamshad Khan
- School of Geography and Resources Science, Neijiang Normal University, Neijiang, China
| | - Manzar Abbas
- College of Agriculture, Forestry, and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Muhammad Jawad Hassan
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jia Li
- College of Agriculture, Forestry, and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Xianming Zhao
- College of Agriculture, Forestry, and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Xin Zhao
- College of Agriculture, Forestry, and Food Engineering, Yibin University, Yibin, Sichuan, China
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Genome-wide identification and expression analysis of metal tolerance protein (MTP) gene family in soybean (Glycine max) under heavy metal stress. Mol Biol Rep 2023; 50:2975-2990. [PMID: 36653731 DOI: 10.1007/s11033-022-08100-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 11/08/2022] [Indexed: 01/19/2023]
Abstract
AIM Plant metal tolerance proteins (MTPs) are plant membrane divalent cation transporters that specifically contribute to heavy metal stress resistance and mineral uptake. However, little is known about this family's molecular behaviors and biological activities in soybean. METHODS AND RESULTS A total of 20 potential MTP candidate genes were identified and studied in the soybean genome for phylogenetic relationships, chromosomal distributions, gene structures, gene ontology, cis-elements, and previous gene expression. Furthermore, the expression of MTPs has been investigated under different heavy metals treatments. All identified soybean MTPs (GmaMTPs) contain a cation efflux domain or a ZT dimer and are further divided into three primary cation diffusion facilitator (CDF) groups: Mn-CDFs, Zn-CDFs, and Fe/Zn-CDFs. The developmental analysis reveals that segmental duplication contributes to the GmaMTP family's expansion. Tissue-specific expression profiling revealed comparative expression profiling in similar groups, although gene expression differed between groups. GmaMTP genes displayed biased responses in either plant leaves or roots when treated with heavy metal. In the leaves and roots, nine and ten GmaMTPs responded to at least one metal ion treatment. Furthermore, in most heavy metal treatments, GmaMTP1.1, GmaMTP1.2, GmaMTP3.1, GmaMTP3.2, GmaMTP4.1, and GmaMTP4.3 exhibited significant expression responses. CONCLUSION Our findings provided insight into the evolution of MTPs in soybean. Overall, our findings shed light on the evolution of the MTP gene family in soybean and pave the path for further functional characterization of this gene family.
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El-Sappah AH, Metwally MAS, Rady MM, Ali HM, Wang L, Maitra P, Ihtisham M, Yan K, Zhao X, Li J, Desoky ESM. Interplay of silymarin and clove fruit extract effectively enhances cadmium stress tolerance in wheat ( Triticum aestivum). FRONTIERS IN PLANT SCIENCE 2023; 14:1144319. [PMID: 37123831 PMCID: PMC10140571 DOI: 10.3389/fpls.2023.1144319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 02/27/2023] [Indexed: 05/03/2023]
Abstract
Introduction Osmoprotectant supplementation can be used as a useful approach to enhance plant stress tolerance. However, the effect of silymarin and clove fruit extract (CFE) on wheat plants grown under cadmium (Cd) stress has not been studied. Methods Wheat seeds were planted in plastic pots filled with ions-free sand. A ½-strength Hoagland's nutrient solution was used for irrigation. Pots were treated with eight treatments thirteen days after sowing: 1) Control, 2) 0.5 mM silymarin foliar application [silymarin], 3) 2% CFE foliar application [CFE], 4) CFE enriched with silymarin (0.24 g silymarin L-1 of CFE) [CFE-silymarin], 5) Watering wheat seedlings with a nutritious solution of 2 mM Cd [Cd]. 6) Cadmium + silymarin, 7) Cadmium + CFE, and 8) Cadmium + CFE-silymarin. The experimental design was a completely randomized design with nine replicates. Results and discussion The Cd stress decreased grain yield, shoot dry weight, leaf area, carotenoids, chlorophylls, stomatal conductance, net photosynthetic rate, transpiration rate, membrane stability index, nitrogen, phosphorus, and potassium content by 66.9, 60.6, 56.7, 23.8, 33.5, 48.1, 41.2, 48.7, 42.5, 24.1, 39.9, and 24.1%, respectively. On the other hand, Cd has an Application of CFE, silymarin, or CEF-silymarin for wheat plants grown under Cd stress, significantly improved all investigated biochemical, morphological, and physiological variables and enhanced the antioxidant enzyme activities. Applying CFE and/or silymarin enhanced plant tolerance to Cd stress more efficiently. Our findings suggest using CFE-silymarin as a meaningful biostimulator for wheat plants to increase wheat plants' tolerance to Cd stress via enhancing various metabolic and physiological processes.
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Affiliation(s)
- Ahmed H. El-Sappah
- School of Agriculture, Forestry, and Food Engineering, Yibin University, Yibin, Sichuan, China
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | | | - Mostafa M. Rady
- Botany Department, Faculty of Agriculture, Fayoum University, Fayoum, Egypt
| | - Hayssam M. Ali
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Linghui Wang
- School of Agriculture, Forestry, and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Pulak Maitra
- Institute of Dendrology, Polish Academy of Sciences, Kórnik, Poland
| | - Muhammad Ihtisham
- School of Agriculture, Forestry, and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Kuan Yan
- School of Agriculture, Forestry, and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Xin Zhao
- School of Agriculture, Forestry, and Food Engineering, Yibin University, Yibin, Sichuan, China
- *Correspondence: Jia Li, ; El-Sayed M. Desoky, ; Xin Zhao,
| | - Jia Li
- School of Agriculture, Forestry, and Food Engineering, Yibin University, Yibin, Sichuan, China
- *Correspondence: Jia Li, ; El-Sayed M. Desoky, ; Xin Zhao,
| | - El-Sayed M. Desoky
- Botany Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
- *Correspondence: Jia Li, ; El-Sayed M. Desoky, ; Xin Zhao,
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11
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Feng YX, Tian P, Li CZ, Zhang Q, Trapp S, Yu XZ. Individual and mutual effects of elevated carbon dioxide and temperature on salt and cadmium uptake and translocation by rice seedlings. FRONTIERS IN PLANT SCIENCE 2023; 14:1161334. [PMID: 37089641 PMCID: PMC10113512 DOI: 10.3389/fpls.2023.1161334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 03/23/2023] [Indexed: 05/03/2023]
Abstract
Plant kingdoms are facing increasingly harsh environmental challenges marked by the coexposure of salinity and pollution in the pedosphere and elevated CO2 and temperature in the atmosphere due to the rapid acceleration of industrialization and global climate change. In this study, we deployed a hydroponics-based experiment to explore the individual and mutual effects of different temperatures (low temperature, T1: 23°C; high temperature, T2: 27°C) and CO2 concentrations (ambient CO2: 360 ppm; medium CO2: 450 ppm; high CO2: 700 ppm) on the uptake and translocation of sodium chloride (NaCl, 0.0, 0.2, 0.6, and 1.1 g Na/L) and cadmium nitrate (Cd(NO3)2·4H2O, 0.0, 0.2, 1.8, and 5.4 mg Cd/L) by rice seedlings. The results indicated that Cd and Na exposure significantly (P< 0.05) inhibited plant growth, but T2 and medium/high CO2 alleviated the effects of Cd and Na on plant growth. Neither significant synergistic nor antagonistic effects of Cd and Na were observed, particularly not at T1 or high CO2. At increasing temperatures, relative growth rates increased despite higher concentrations of Cd and Na in both rice roots and shoots. Similarly, higher CO2 stimulated the growth rate but resulted in significantly lower concentrations of Na, while the Cd concentration was highest at medium CO2. Coexposure experiments suggested that the concentration of Cd in roots slightly declined with additional Na and more at T2. Overall, our preliminary study suggested that global climate change may alter the distribution of mineral and toxic elements in rice plants as well as the tolerance of the plants.
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Affiliation(s)
- Yu-Xi Feng
- College of Environmental Science & Engineering, Guilin University of Technology, Guilin, China
| | - Peng Tian
- College of Environmental Science & Engineering, Guilin University of Technology, Guilin, China
| | - Cheng-Zhi Li
- College of Environmental Science & Engineering, Guilin University of Technology, Guilin, China
| | - Qing Zhang
- College of Environmental Science & Engineering, Guilin University of Technology, Guilin, China
| | - Stefan Trapp
- Department of Environmental and Resource Engineering, Technical University of Denmark, Kongens Lyngby, Denmark
- *Correspondence: Stefan Trapp, ; Xiao-Zhang Yu,
| | - Xiao-Zhang Yu
- College of Environmental Science & Engineering, Guilin University of Technology, Guilin, China
- *Correspondence: Stefan Trapp, ; Xiao-Zhang Yu,
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Hussain SS, Abbas M, Abbas S, Wei M, El-Sappah AH, Sun Y, Li Y, Ragauskas AJ, Li Q. Alternative splicing: transcriptional regulatory network in agroforestry. FRONTIERS IN PLANT SCIENCE 2023; 14:1158965. [PMID: 37123829 PMCID: PMC10132464 DOI: 10.3389/fpls.2023.1158965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 03/13/2023] [Indexed: 05/03/2023]
Abstract
Alternative splicing (AS) in plants plays a key role in regulating the expression of numerous transcripts from a single gene in a regulatory pathway. Variable concentrations of growth regulatory hormones and external stimuli trigger alternative splicing to switch among different growth stages and adapt to environmental stresses. In the AS phenomenon, a spliceosome causes differential transcriptional modifications in messenger RNA (mRNAs), resulting in partial or complete retention of one or more introns as compared to fully spliced mRNA. Differentially expressed proteins translated from intron-retaining messenger RNA (mRNAir) perform vital functions in the feedback mechanism. At the post-transcriptional level, AS causes the remodeling of transcription factors (TFs) by the addition or deletion of binding domains to activate and/or repress transcription. In this study, we have summarized the specific role of AS in the regulation of gene expression through repression and activation of the transcriptional regulatory network under external stimuli and switch among developmental stages.
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Affiliation(s)
- Syed Sarfaraz Hussain
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
| | - Manzar Abbas
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Sammar Abbas
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Mingke Wei
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
| | - Ahmed H. El-Sappah
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Yuhan Sun
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Yun Li
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- *Correspondence: Yun Li, ; Arthur J. Ragauskas, ; Quanzi Li,
| | - Arthur J. Ragauskas
- Department of Forestry, Wildlife, and Fisheries, Center for Renewable Carbon, University of Tennessee Institute of Agriculture, Knoxville, TN, United States
- Joint Institute for Biological Science, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Department of Chemical and Biomolecular Engineering, The University of Tennessee-Knoxville, Knoxville, TN, United States
- *Correspondence: Yun Li, ; Arthur J. Ragauskas, ; Quanzi Li,
| | - Quanzi Li
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- *Correspondence: Yun Li, ; Arthur J. Ragauskas, ; Quanzi Li,
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Ebrahim A, Alfwuaires MA, Abukhalil MH, Alasmari F, Ahmad F, Yao R, Luo Y, Huang Y. Schizosaccharomyces pombe Grx4, Fep1, and Php4: In silico analysis and expression response to different iron concentrations. Front Genet 2022; 13:1069068. [PMID: 36568394 PMCID: PMC9768344 DOI: 10.3389/fgene.2022.1069068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 11/16/2022] [Indexed: 12/12/2022] Open
Abstract
Due to iron's essential role in cellular metabolism, most organisms must maintain their homeostasis. In this regard, the fission yeast Schizosaccharomyces pombe (sp) uses two transcription factors to regulate intracellular iron levels: spFep1 under iron-rich conditions and spPhp4 under iron-deficient conditions, which are controlled by spGrx4. However, bioinformatics analysis to understand the role of the spGrx4/spFep1/spPhp4 axis in maintaining iron homeostasis in S. pombe is still lacking. Our study aimed to perform bioinformatics analysis on S. pombe proteins and their sequence homologs in Aspergillus flavus (af), Saccharomyces cerevisiae (sc), and Homo sapiens (hs) to understand the role of spGrx4, spFep1, and spPhp4 in maintaining iron homeostasis. The three genes' expression patterns were also examined at various iron concentrations. A multiple sequence alignment analysis of spGrx4 and its sequence homologs revealed a conserved cysteine residue in each PF00085 domain. Blast results showed that hsGLRX3 is most similar to spGrx4. In addition, spFep1 is most closely related in sequence to scDal80, whereas scHap4 is most similar to spFep1. We also found two highly conserved motifs in spFep1 and its sequence homologs that are significant for iron transport systems because they contain residues involved in iron homeostasis. The scHap4 is most similar to spPhp4. Using STRING to analyze protein-protein interactions, we found that spGrx4 interacts strongly with spPhp4 and spFep1. Furthermore, spGrx4, spPhp4, and spFep1 interact with spPhp2, spPhp3, and spPhp5, indicating that the three proteins play cooperative roles in iron homeostasis. At the highest level of Fe, spgrx4 had the highest expression, followed by spfep1, while spphp4 had the lowest expression; a contrast occurred at the lowest level of Fe, where spgrx4 expression remained constant. Our findings support the notion that organisms develop diverse strategies to maintain iron homeostasis.
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Affiliation(s)
- Alia Ebrahim
- Jiangsu Key Laboratory for Microbes and Genomics, School of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Manal A. Alfwuaires
- Department of Biological Sciences, Faculty of Science, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Mohammad H. Abukhalil
- Department of Medical Analysis, Princess Aisha Bint Al-Hussein College of Nursing and Health Sciences, Al-Hussein Bin Talal University, Ma’an, Jordan,Department of Biology, College of Science, Al-Hussein Bin Talal University, Ma’an, Jordan
| | - Fawaz Alasmari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Fawad Ahmad
- Jiangsu Key Laboratory for Microbes and Genomics, School of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Rui Yao
- Jiangsu Key Laboratory for Microbes and Genomics, School of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Ying Luo
- Jiangsu Key Laboratory for Microbes and Genomics, School of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Ying Huang
- Jiangsu Key Laboratory for Microbes and Genomics, School of Life Sciences, Nanjing Normal University, Nanjing, China,*Correspondence: Ying Huang,
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El-Sappah AH, Seif MM, Abdel-Kader HH, Soaud SA, Elhamid MAA, Abdelghaffar AM, El-Sappah HH, Sarwar H, Yadav V, Maitra P, Zhao X, Yan K, Li J, Abbas M. Genotoxicity and Trace Elements Contents Analysis in Nile Tilapia (Oreochromis niloticus) Indicated the Levels of Aquatic Contamination at Three Egyptian Areas. Front Vet Sci 2022; 9:818866. [PMID: 35478598 PMCID: PMC9038200 DOI: 10.3389/fvets.2022.818866] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 02/02/2022] [Indexed: 11/30/2022] Open
Abstract
The toxic waste and pollutants of heavy metals continuously pollute freshwater aquatic reservoirs, which have severe implications on aquatic life and human health. The present work aims to evaluate trace elements (Zn, Mn, Cu, Cd, and Pb) along with three sites, Mariout Lake, Abbassa, and River Nile Aswan in Egypt, using Nile tilapia (Oreochromis niloticus) as bioindicator. The quality assurance, health-risk assessment, sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), quantitative polymerase chain reaction (qPCR), and micronucleus test were performed to investigate the effect of different trace elements on Hsp70 gene level and micronuclei formation. We observed the highest expression of Hsp70 protein band of 70 KD and stress-responsive Hsp70 gene in the liver followed by gills of Nile tilapia caught from Mariout and Abbassa, but the lowest expression was in Nile tilapia caught from Aswan. Obvious micronuclei were observed under the microscope in erythrocytes, and their number was gradually decreased in the following manner: Mariout > Abbassa > Aswan. Noticeably, Cu, Zn, and Mn contents were low. Still, Pb and Cd contents were higher than the toxicity level recommended by the Food and Agriculture Organization (FAO), The World Health Organization (WHO), and the European Commission (EC). These results showed that Hsp70's appearance at the two levels of mRNA and protein is an effective indicator for aquatic pollution besides the aberration at the chromosome level represented in the micronucleus test. Furthermore, these results showed that Nile tilapia of the Aswan region had comparatively low trace elements contamination and were suitable for consumption.
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Affiliation(s)
- Ahmed H. El-Sappah
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Mohamed M. Seif
- Toxicology and Food Contaminants Department, Food Industries and Nutrition Research Institute, National Research Centre, Giza, Egypt
| | | | - Salma A. Soaud
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | | | | | | | - Huda Sarwar
- Department of Bioscience, University of Wah, Wah Cantt, Pakistan
| | - Vivek Yadav
- College of Horticulture, Northwest A&F University, Xianyang, China
| | - Pulak Maitra
- Institute of Dendrology, Polish Academy of Sciences, Kórnik, Poland
| | - Xianming Zhao
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
| | - Kuan Yan
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
- Kuan Yan
| | - Jia Li
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
- Jia Li
| | - Manzar Abbas
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
- *Correspondence: Manzar Abbas
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Li J, Zhang L, G. Elbaiomy R, Chen L, Wang Z, Jiao J, Zhu J, Zhou W, Chen B, Soaud SA, Abbas M, Lin N, El-Sappah AH. Evolution analysis of FRIZZY PANICLE ( FZP) orthologs explored the mutations in DNA coding sequences in the grass family (Poaceae). PeerJ 2022; 10:e12880. [PMID: 35295554 PMCID: PMC8919851 DOI: 10.7717/peerj.12880] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 01/13/2022] [Indexed: 01/11/2023] Open
Abstract
FRIZZY PANICLE (FZP), an essential gene that controls spikelet differentiation and development in the grass family (Poaceae), prevents the formation of axillary bud meristems and is closely associated with crop yields. It is unclear whether the FZP gene or its orthologs were selected during the evolutionary process of grass species, which possess diverse spike morphologies. In the present study, we adopted bioinformatics methods for the evolutionary analysis of FZP orthologs in species of the grass family. Thirty-five orthologs with protein sequences identical to that of the FZP gene were identified from 29 grass species. Analysis of conserved domains revealed that the AP2/ERF domains were highly conserved with almost no amino acid mutations. However, species of the tribe Triticeae, genus Oryza, and C4 plants exhibited more significant amino acid mutations in the acidic C-terminus region. Results of the phylogenetic analysis showed that the 29 grass species could be classified into three groups, namely, Triticeae, Oryza, and C4 plants. Within the Triticeae group, the FZP genes originating from the same genome were classified into the same sub-group. When selection pressure analysis was performed, significant positive selection sites were detected in species of the Triticeae and Oryza groups. Our results show that the FZP gene was selected during the grass family's evolutionary process, and functional divergence may have already occurred among the various species. Therefore, researchers investigating the FZP gene's functions should take note of the possible presence of various roles in other grass species.
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Affiliation(s)
- Jia Li
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Litian Zhang
- Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, Qinghai, China,State Key Laboratory of Plateau Ecology and Agriculture, Xining, Qinghai, China
| | | | - Lilan Chen
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Zhenrong Wang
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Jie Jiao
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Jiliang Zhu
- Agriculture and Rural Bureau of Zhongjiang County, Deyang, Sichuan, China
| | - Wanhai Zhou
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Bo Chen
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Salma A. Soaud
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Manzar Abbas
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Na Lin
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Ahmed H. El-Sappah
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China,Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
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Li J, Zhang L, Yuan Y, Wang Q, Elbaiomy RG, Zhou W, Wu H, Soaud SA, Abbas M, Chen B, Zhao D, El-Sappah AH. In Silico Functional Prediction and Expression Analysis of C2H2 Zinc-Finger Family Transcription Factor Revealed Regulatory Role of ZmZFP126 in Maize Growth. Front Genet 2021; 12:770427. [PMID: 34804129 PMCID: PMC8602080 DOI: 10.3389/fgene.2021.770427] [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: 09/03/2021] [Accepted: 10/21/2021] [Indexed: 11/16/2022] Open
Abstract
The C2H2-zinc finger proteins (ZFP) comprise a large family of transcription factors with various functions in biological processes. In maize, the function regulation of C2H2- zine finger (ZF) genes are poorly understood. We conducted an evolution analysis and functional prediction of the maize C2H2-ZF gene family. Furthermore, the ZmZFP126 gene has been cloned and sequenced for further favorable allelic variation discovery. The phylogenetic analysis of the C2H2-ZF domain indicated that the position and sequence of the C2H2-ZF domain of the poly-zinc finger gene are relatively conserved during evolution, and the C2H2-ZF domain with the same position is highly conserved. The expression analysis of the C2H2-ZF gene family in 11 tissues at different growth stages of B73 inbred lines showed that genes with multiple transcripts were endowed with more functions. The expression analysis of the C2H2-ZF gene in P1 and P2 inbred lines under drought conditions showed that the C2H2-ZF genes were mainly subjected to negative regulation under drought stress. Functional prediction indicated that the maize C2H2-ZF gene is mainly involved in reproduction and development, especially concerning the formation of important agronomic traits in maize yield. Furthermore, sequencing and correlation analysis of the ZmZFP126 gene indicated that this gene was significantly associated with the SDW-NAP and TDW-NAP. The analysis of the relationship between maize C2H2-ZF genes and C2H2-ZF genes with known functions indicated that the functions of some C2H2-ZF genes are relatively conservative, and the functions of homologous genes in different species are similar.
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Affiliation(s)
- Jia Li
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
| | - Litian Zhang
- State Key Laboratory of Plateau Ecology and Agriculture, Academy of Animal Science and Veterinary Medicine of Qinghai University, Xining, China
| | - Yibing Yuan
- Maize Research Institute, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, China
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, China
| | - Qi Wang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, China
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, China
| | | | - Wanhai Zhou
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
| | - Hui Wu
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
| | - Salma A. Soaud
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Manzar Abbas
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
| | - Bo Chen
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
| | - Deming Zhao
- Yibin Academy of Agricultural Sciences, Yibin, China
| | - Ahmed H. El-Sappah
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
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