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Xie M, Zhu Y, Zhao K, Zhao L, Gong Y, Wang Y, Wang Y, Zhu M, Ran W, Cai M, Du S. R-Napropamide Potentially Regulates Cadmium Accumulation in Arabidopsis Shoots through Transport Channel Modulation. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024. [PMID: 38842427 DOI: 10.1021/acs.jafc.4c03404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
Heavy metal contamination in soils poses a significant environmental threat to human health. This study examines the effects of the chiral herbicide napropamide (NAP) on Arabidopsis thaliana, focusing on growth metrics and cadmium (Cd) accumulation. R-NAP does not adversely affect plant growth compared to the control, whereas S-NAP significantly reduces root length and fresh weight. Notably, R-NAP markedly increases Cd accumulation in the shoots, exceeding levels observed in the control and S-NAP. This increase coincides with reduced photosynthetic efficiency. Noninvasive electrode techniques reveal a higher net Cd absorption flux in the root mature zone under R-NAP than S-NAP, although similar to the control. Transcriptomic analysis highlights significant stereoisomer differences in Cd transporters, predominantly under R-NAP treatment. SEM and molecular docking simulations support that R-NAP primarily upregulates transporters such as HMA4. The results suggest careful management of herbicides like R-NAP in contaminated fields to avoid excessive heavy metal buildup in crops.
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Affiliation(s)
- Minghui Xie
- College of Geography and Environmental Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Yaxin Zhu
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Interdisciplinary Research Academy (IRA), Zhejiang Shuren University, Hangzhou 310015, China
| | - Kai Zhao
- Zhejiang Zhongyi Testing Research Institute Co., Ltd, Ningbo 315040, China
| | - Lu Zhao
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Interdisciplinary Research Academy (IRA), Zhejiang Shuren University, Hangzhou 310015, China
| | - Yanxia Gong
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Yin Wang
- College of Geography and Environmental Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Yuying Wang
- College of Geography and Environmental Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Mengfei Zhu
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Interdisciplinary Research Academy (IRA), Zhejiang Shuren University, Hangzhou 310015, China
| | - Wu Ran
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Interdisciplinary Research Academy (IRA), Zhejiang Shuren University, Hangzhou 310015, China
| | - Miaozhen Cai
- College of Geography and Environmental Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Shaoting Du
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Interdisciplinary Research Academy (IRA), Zhejiang Shuren University, Hangzhou 310015, China
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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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Ding M, Zhou D, Ye Y, Wen S, Zhang X, Tian Q, Zhang X, Mou W, Dang C, Fang Y, Xue D. Genome-Wide Identification and Expression Analysis of the Stearoyl-Acyl Carrier Protein Δ9 Desaturase Gene Family under Abiotic Stress in Barley. Int J Mol Sci 2023; 25:113. [PMID: 38203283 PMCID: PMC10778905 DOI: 10.3390/ijms25010113] [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: 10/24/2023] [Revised: 12/11/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024] Open
Abstract
Stearoyl-acyl carrier protein (ACP) Δ9 desaturase (SAD) is a critical fatty acid dehydrogenase in plants, playing a prominent role in regulating the synthesis of unsaturated fatty acids (UFAs) and having a significant impact on plant growth and development. In this study, we conducted a comprehensive genomic analysis of the SAD family in barley (Hordeum vulgare L.), identifying 14 HvSADs with the FA_desaturase_2 domain, which were divided into four subgroups based on sequence composition and phylogenetic analysis, with members of the same subgroup possessing similar genes and motif structures. Gene replication analysis suggested that tandem and segmental duplication may be the major reasons for the expansion of the SAD family in barley. The promoters of HvSADs contained various cis-regulatory elements (CREs) related to light, abscisic acid (ABA), and methyl jasmonate (MeJA). In addition, expression analysis indicated that HvSADs exhibit multiple tissue expression patterns in barley as well as different response characteristics under three abiotic stresses: salt, drought, and cold. Briefly, this evolutionary and expression analysis of HvSADs provides insight into the biological functions of barley, supporting a comprehensive analysis of the regulatory mechanisms of oil biosynthesis and metabolism in plants under abiotic stress.
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Affiliation(s)
- Mingyu Ding
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China; (M.D.); (D.Z.); (Y.Y.); (S.W.); (X.Z.); (Q.T.); (X.Z.); (W.M.); (C.D.); (Y.F.)
| | - Danni Zhou
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China; (M.D.); (D.Z.); (Y.Y.); (S.W.); (X.Z.); (Q.T.); (X.Z.); (W.M.); (C.D.); (Y.F.)
| | - Yichen Ye
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China; (M.D.); (D.Z.); (Y.Y.); (S.W.); (X.Z.); (Q.T.); (X.Z.); (W.M.); (C.D.); (Y.F.)
| | - Shuting Wen
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China; (M.D.); (D.Z.); (Y.Y.); (S.W.); (X.Z.); (Q.T.); (X.Z.); (W.M.); (C.D.); (Y.F.)
| | - Xian Zhang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China; (M.D.); (D.Z.); (Y.Y.); (S.W.); (X.Z.); (Q.T.); (X.Z.); (W.M.); (C.D.); (Y.F.)
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 311121, China
| | - Quanxiang Tian
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China; (M.D.); (D.Z.); (Y.Y.); (S.W.); (X.Z.); (Q.T.); (X.Z.); (W.M.); (C.D.); (Y.F.)
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 311121, China
| | - Xiaoqin Zhang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China; (M.D.); (D.Z.); (Y.Y.); (S.W.); (X.Z.); (Q.T.); (X.Z.); (W.M.); (C.D.); (Y.F.)
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 311121, China
| | - Wangshu Mou
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China; (M.D.); (D.Z.); (Y.Y.); (S.W.); (X.Z.); (Q.T.); (X.Z.); (W.M.); (C.D.); (Y.F.)
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 311121, China
| | - Cong Dang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China; (M.D.); (D.Z.); (Y.Y.); (S.W.); (X.Z.); (Q.T.); (X.Z.); (W.M.); (C.D.); (Y.F.)
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 311121, China
| | - Yunxia Fang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China; (M.D.); (D.Z.); (Y.Y.); (S.W.); (X.Z.); (Q.T.); (X.Z.); (W.M.); (C.D.); (Y.F.)
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 311121, China
| | - Dawei Xue
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China; (M.D.); (D.Z.); (Y.Y.); (S.W.); (X.Z.); (Q.T.); (X.Z.); (W.M.); (C.D.); (Y.F.)
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 311121, China
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Xu W, Huang H, Li X, Yang M, Chi S, Pan Y, Li N, Paterson AH, Chai Y, Lu K. CaHMA1 promotes Cd accumulation in pepper fruit. JOURNAL OF HAZARDOUS MATERIALS 2023; 460:132480. [PMID: 37683343 DOI: 10.1016/j.jhazmat.2023.132480] [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: 04/30/2023] [Revised: 08/30/2023] [Accepted: 09/03/2023] [Indexed: 09/10/2023]
Abstract
The main planting areas for pepper (Capsicum sp.) are high in cadmium (Cd), which is the most prevalent heavy metal pollutant worldwide. Breeding pepper cultivars with low Cd levels can promote sustainable agricultural production and ensure the safety of pepper products. To identify breeding targets for reducing Cd accumulation in pepper fruits, we performed a genome-wide association study on 186 accessions. Polymorphisms were associated with fruit Cd content in a genomic region containing a homolog of Arabidopsis (Arabidopsis thaliana) Heavy metal-transporting ATPase 1 (HMA1) encoding a P-type ATPase. In two cultivars with contrasting Cd accumulation, transcriptome analysis revealed differentially expressed genes enriched for carbohydrate metabolism and photosynthesis in fruits with high Cd accumulation, and a Cd2+/Zn2+-exporting ATPase gene (HMA). Heterologous expression of CaHMA1 in yeast increases Cd sensitivity. Overexpression of CaHMA1 conferred a severe increase in Cd content in Arabidopsis plants, whereas reduced CaHMA1 expression in pepper fruits decreased Cd content. We propose that CaHMA1 expression may be an important component of the high Cd accumulation in pepper plants.
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Affiliation(s)
- Weihong Xu
- College of Resources and Environmental Sciences, Southwest University, Chongqing 400715, China
| | - He Huang
- College of Resources and Environmental Sciences, Southwest University, Chongqing 400715, China
| | - Xiaodong Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Mei Yang
- College of Resources and Environmental Sciences, Southwest University, Chongqing 400715, China
| | - Sunlin Chi
- College of Resources and Environmental Sciences, Southwest University, Chongqing 400715, China
| | - Yu Pan
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China
| | - Nannan Li
- College of Resources and Environmental Sciences, Southwest University, Chongqing 400715, China
| | - Andrew H Paterson
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30605, USA.
| | - Yourong Chai
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China.
| | - Kun Lu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China.
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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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Moravčíková D, Žiarovská J. The Effect of Cadmium on Plants in Terms of the Response of Gene Expression Level and Activity. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091848. [PMID: 37176906 PMCID: PMC10181241 DOI: 10.3390/plants12091848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/27/2023] [Accepted: 04/28/2023] [Indexed: 05/15/2023]
Abstract
Cadmium (Cd) is a heavy metal that can cause damage to living organisms at different levels. Even at low concentrations, Cd can be toxic to plants, causing harm at multiple levels. As they are unable to move away from areas contaminated by Cd, plants have developed various defence mechanisms to protect themselves. Hyperaccumulators, which can accumulate and detoxify heavy metals more efficiently, are highly valued by scientists studying plant accumulation and detoxification mechanisms, as they provide a promising source of genes for developing plants suitable for phytoremediation techniques. So far, several genes have been identified as being upregulated when plants are exposed to Cd. These genes include genes encoding transcription factors such as iron-regulated transporter-like protein (ZIP), natural resistance associated macrophage protein (NRAMP) gene family, genes encoding phytochelatin synthases (PCs), superoxide dismutase (SOD) genes, heavy metal ATPase (HMA), cation diffusion facilitator gene family (CDF), Cd resistance gene family (PCR), ATP-binding cassette transporter gene family (ABC), the precursor 1-aminocyclopropane-1-carboxylic acid synthase (ACS) and precursor 1-aminocyclopropane-1-carboxylic acid oxidase (ACO) multigene family are also influenced. Thanks to advances in omics sciences and transcriptome analysis, we are gaining more insights into the genes involved in Cd stress response. Recent studies have also shown that Cd can affect the expression of genes related to antioxidant enzymes, hormonal pathways, and energy metabolism.
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Affiliation(s)
- Dagmar Moravčíková
- Faculty of Agrobiology and Food Resources, Institute of Plant and Environmental Sciences, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 949 76 Nitra, Slovakia
| | - Jana Žiarovská
- Faculty of Agrobiology and Food Resources, Institute of Plant and Environmental Sciences, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 949 76 Nitra, Slovakia
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Zahra S, Shaheen T, Qasim M, Mahmood-Ur-Rahman, Hussain M, Zulfiqar S, Shaukat K, Mehboob-Ur-Rahman. Genome-wide survey of HMA gene family and its characterization in wheat ( Triticum aestivum). PeerJ 2023; 11:e14920. [PMID: 36890869 PMCID: PMC9987320 DOI: 10.7717/peerj.14920] [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: 11/16/2022] [Accepted: 01/27/2023] [Indexed: 03/06/2023] Open
Abstract
Background Abiotic stresses, particularly drought and heavy metal toxicity, have presented a significant risk to long-term agricultural output around the world. Although the heavy-metal-associated domain (HMA) gene family has been widely explored in Arabidopsis and other plants, it has not been thoroughly studied in wheat (Triticum aestivum). This study was proposed to investigate the HMA gene family in wheat. Methods To analyze the phylogenetic relationships, gene structure, gene ontology, and conserved motifs, a comparative study of wheat HMA genes with the Arabidopsis genome was performed. Results A total of 27 T. aestivum proteins belonging to the HMA gene family were identified in this study, with amino acid counts ranging from 262 to 1,071. HMA proteins were found to be grouped into three subgroups in a phylogenetic tree, and closely related proteins in the tree showed the same expression patterns as motifs found in distinct subgroups. Gene structural study elucidated that intron and exon arrangement differed by family. Conclusion As a result, the current work offered important information regarding HMA family genes in the T. aestivum genome, which will be valuable in understanding their putative functions in other wheat species.
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Affiliation(s)
- Sadaf Zahra
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Tayyaba Shaheen
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Muhammad Qasim
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Mahmood-Ur-Rahman
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Momina Hussain
- Department of Biotechnology, Faculty of Life Sciences, University of Okara, Okara, Pakistan
| | - Sana Zulfiqar
- Plant Genomics and Molecular Breeding Laboratory, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, Pakistan
| | - Kanval Shaukat
- Department of Botany, University of Balochistan, Quetta, Pakistan
| | - Mehboob-Ur-Rahman
- Plant Genomics and Molecular Breeding Laboratory, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, Pakistan
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Tanwar UK, Stolarska E, Rudy E, Paluch-Lubawa E, Grabsztunowicz M, Arasimowicz-Jelonek M, Sobieszczuk-Nowicka E. Metal tolerance gene family in barley: an in silico comprehensive analysis. J Appl Genet 2022; 64:197-215. [PMID: 36586056 PMCID: PMC10076399 DOI: 10.1007/s13353-022-00744-6] [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: 10/28/2022] [Revised: 12/20/2022] [Accepted: 12/21/2022] [Indexed: 01/01/2023]
Abstract
Metal-tolerance proteins (MTPs) are divalent cation transporters that play critical roles in metal tolerance and ion homeostasis in plants. However, a comprehensive study of MTPs is still lacking in crop plants. The current study aimed to comprehensively identify and characterize the MTP gene family in barley (Hordeum vulgare, Hv), an important crop. In total, 12 HvMTPs were identified in the barley genome in this study. They were divided into three phylogenetic groups (Zn-cation diffusion facilitator proteins [CDFs], Fe/Zn-CDFs, and Mn-CDFs) and further subdivided into seven groups (G1, G5, G6, G7, G8, G9, and G12). The majority of MTPs were hydrophobic proteins found in the vacuolar membrane. Gene duplication analysis of HvMTPs revealed one pair of segmental-like duplications in the barley genome. Evolutionary analysis suggested that barley MTPs underwent purifying natural selection. Additionally, the HvMTPs were analyzed in the pan-genome sequences of barley (20 accessions), which suggests that HvMTPs are highly conserved in barley evolution. Cis-acting regulatory elements, microRNA target sites, and protein-protein interaction analysis indicated the role of HvMTPs in a variety of biological processes. Expression profiling suggests that HvMTPs play an active role in maintaining barley nutrient homeostasis throughout its life cycle, and their expression levels were not significantly altered by abiotic stresses like cold, drought, or heat. The expression of barley HvMTP genes in the presence of heavy metals such as Zn2+, Cu2+, As3+, and Cd2+ revealed that these MTPs were induced by at least one metal ion, implying their involvement in metal tolerance or transportation. The identification and comprehensive investigation of MTP gene family members will provide important gene resources for the genetic improvement of crops for metal tolerance, bioremediation, or biofortification of staple crops.
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Affiliation(s)
- Umesh Kumar Tanwar
- Department of Plant Physiology, Faculty of Biology, Adam Mickiewicz University, ul. Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland.
| | - Ewelina Stolarska
- Department of Plant Physiology, Faculty of Biology, Adam Mickiewicz University, ul. Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
| | - Elżbieta Rudy
- Department of Plant Physiology, Faculty of Biology, Adam Mickiewicz University, ul. Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
| | - Ewelina Paluch-Lubawa
- Department of Plant Physiology, Faculty of Biology, Adam Mickiewicz University, ul. Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
| | - Magda Grabsztunowicz
- Department of Plant Physiology, Faculty of Biology, Adam Mickiewicz University, ul. Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
| | - Magdalena Arasimowicz-Jelonek
- Department of Plant Ecophysiology, Faculty of Biology, Adam Mickiewicz University, ul. Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
| | - Ewa Sobieszczuk-Nowicka
- Department of Plant Physiology, Faculty of Biology, Adam Mickiewicz University, ul. Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland.
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Zhao Q, Li Q, Lin S, Hou R, Liu J, Tao Y, Li Y, Zhou Y, Ye Z, Yu X, Huang J. De Novo transcriptome combined with physiological analyses revealed key genes for cadmium accumulation in Zhe-Maidong ( Ophiopogon japonicus). FRONTIERS IN PLANT SCIENCE 2022; 13:1078330. [PMID: 36578338 PMCID: PMC9791205 DOI: 10.3389/fpls.2022.1078330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
INTRODUCTION Cadmium (Cd) is a toxic heavy metal that severely threatens safe food production. Zhe-Maidong, a well-known Chinese traditional herbal medicine, is susceptible to Cd stress. However, the characteristics of Cd transformation and migration, as well as the regulatory system for genes conferring Cd accumulation of Zhe-Maidong, remains an essential issue to be addressed. METHODS Zhe-Maidong seedling growth in Cd-contaminated and uncontaminated soil was conducted for 90 days. The Cd concentration was determined by inductively coupled plasma-mass spectrometry, and the Cd2+ fluorescence probe detected Cd distributions. The root transcriptome of Zhe-Maidong was then evaluated using various Cd stress hydroponic treatments designated Cd-0, Cd-M, and Cd-H. RESULTS AND DISCUSSION The enrichment factor (EF) value in the root was four times that of the leaves, indicating that the root has a high ability to absorb and accumulate Cd. The Cd2+ were mainly distributed in the root hair and the epidermis in both roots and leaves, revealing that the epidermal cells of roots may collect Cd2+ and also have an outstanding role in Cd2+ uptake. A total of 50 DEGs involved in Cd translocation and accumulation were identified. Among these DEGs, ANN, ABCC2/4, HMA1- 5, and CCX gene expression were positively correlated with EF-root, EF-leaf, EF-total, Cd-leaf, Cd-root, and Cd-plant, indicating their role in Cd transport and accumulation under Cd-stress. These data could be helpful in uncovering the Cd accumulation characteristics in Zhe-Maidong, as well as provide a bioinformatic foundation for investigations on finding gene functions and the screening of candidate genes related to Cd accumulation.
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Affiliation(s)
- Qian Zhao
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, China
| | - Qing Li
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, China
| | - Shuting Lin
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, China
| | - Ruijun Hou
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, China
| | - Jianying Liu
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, China
| | - Yachen Tao
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, China
| | - Ye Li
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, China
| | - Yifeng Zhou
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, China
| | - Zihong Ye
- College of Life Science, China Jiliang University, Hangzhou, China
| | - Xiaoping Yu
- College of Life Science, China Jiliang University, Hangzhou, China
| | - Jun Huang
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, China
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Genome-Wide Identification and Expression Analysis of the Zinc Finger Protein Gene Subfamilies under Drought Stress in Triticum aestivum. PLANTS 2022; 11:plants11192511. [PMID: 36235376 PMCID: PMC9572532 DOI: 10.3390/plants11192511] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/17/2022] [Accepted: 09/22/2022] [Indexed: 12/05/2022]
Abstract
The zinc finger protein (ZFP) family is one of plants’ most diverse family of transcription factors. These proteins with finger-like structural domains have been shown to play a critical role in plant responses to abiotic stresses such as drought. This study aimed to systematically characterize Triticum aestivum ZFPs (TaZFPs) and understand their roles under drought stress. A total of 9 TaC2H2, 38 TaC3HC4, 79 TaCCCH, and 143 TaPHD were identified, which were divided into 4, 7, 12, and 14 distinct subgroups based on their phylogenetic relationships, respectively. Segmental duplication dominated the evolution of four subfamilies and made important contributions to the large-scale amplification of gene families. Syntenic relationships, gene duplications, and Ka/Ks result consistently indicate a potential strong purifying selection on TaZFPs. Additionally, TaZFPs have various abiotic stress-associated cis-acting regulatory elements and have tissue-specific expression patterns showing different responses to drought and heat stress. Therefore, these genes may play multiple functions in plant growth and stress resistance responses. This is the first comprehensive genome-wide analysis of ZFP gene families in T. aestivum to elucidate the basis of their function and resistance mechanisms, providing a reference for precise manipulation of genetic engineering for drought resistance in T. aestivum.
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