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Tian L, Wu L, Zhong XF, Ma LH, Du GY. Genome-Wide Characterization of ABC Transporter Genes and Expression Profiles in Red Macroalga Pyropia yezoensis Expose to Low-Temperature. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2024:10.1007/s10126-024-10355-3. [PMID: 39269589 DOI: 10.1007/s10126-024-10355-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 08/05/2024] [Indexed: 09/15/2024]
Abstract
Pyropia yezoensis is an important economic macroalga widely cultivated in the East Asia countries of China, Korea, and Japan. The ATP-binding cassette (ABC) transporter gene family is one of the largest transporter families in all forms of life involved in various biological processes. The characteristics of ABC transporter genes in P. yezoensis (PyABC) and their functions in stress resistance, however, remain largely unknown. In this study, PyABCs were identified and characterized their expression patterns under low-temperature stress. A total of 48 PyABCs transporters were identified and divided into eight subfamilies, which are mostly predicted as membrane-binding proteins. The cis-elements of phytohormone and low-temperature response were distinguished in promoter sequences of PyABCs. Transcriptome analysis showed that PyABCs are involved in response to low-temperature stress. Among them, 12 PyABCs were significantly up-regulated after 24 h of exposure to low temperature (2 °C). Further quantitative RT-PCR analysis corroborated the highest expression happened at 24 for detected genes of PyABCC8, PyABCF3, and PyABCI1, extraordinarily for PyABCF3, and followed by decreased expression at 48 h. The expression of PyABCI1 was generally low in all tested strains. Whereas, in a strain of P. yezoensis with lower tolerance to low temperature, the expression was observed higher in PyABCC1, PyABCC8, and remarkably high in PyABCF3. This study provided valuable information on ABC gene families in P. yezoensis and their functional characteristics, especially on low-temperature resistance, and would help to understand the adaptive mechanisms of P. yezoensis to adverse environments.
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Affiliation(s)
- Lin Tian
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Science, Ocean University of China, Qingdao, 266003, China
| | - Lan Wu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Science, Ocean University of China, Qingdao, 266003, China
| | - Xue-Feng Zhong
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Science, Ocean University of China, Qingdao, 266003, China
| | - Li-Hong Ma
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Science, Ocean University of China, Qingdao, 266003, China
| | - Guo-Ying Du
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Science, Ocean University of China, Qingdao, 266003, China.
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Jackson AC, Carine MA, Chapman MA. Genomics of ecological adaptation in Canary Island Descurainia (Brassicaceae) and comparisons with other Brassicaceae. Ecol Evol 2024; 14:e70144. [PMID: 39119179 PMCID: PMC11307170 DOI: 10.1002/ece3.70144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 07/16/2024] [Accepted: 07/25/2024] [Indexed: 08/10/2024] Open
Abstract
Oceanic archipelagos provide striking examples of lineages that have radiated over pronounced ecological gradients. Accompanying this diversification, lineages have evolved adaptations allowing survival in extreme environments. Here, we investigate the genomic basis of ecological adaptation in Canary Island Descurainia (Brassicaceae), an island relative of Arabidopsis. The seven endemic species have diversified in situ along an elevational and ecological gradient, from low-elevation scrub to high-elevation sub-alpine desert. We first generated a reference genome for Descurainia millefolia, phylogenetic analysis of which placed it as sister to D. sophioides. Ninety-six gene families were found to be specific to D. millefolia and a further 1087 and 1469 gene families have expanded or contracted in size, respectively, along the D. millefolia branch. We then employed genome re-sequencing to sample 14 genomes across the seven species of Canary Island Descurainia and an outgroup. Phylogenomic analyses were consistent with previous reconstructions of Canary Island Descurainia in resolving low- and high-elevation clades. Using the branch-site dN/dS method, we detected positive selection for 275 genes on the branch separating the low- and high-elevation species and these positively selected genes (PSGs) were significantly enriched for functions related to reproduction and stress tolerance. Comparing PSGs to those in analyses of adaptation to elevation and/or latitude in other Brassicaceae, we found little evidence of widespread convergence and gene reuse, except for two examples, one of which was a significant overlap between Descurainia and Draba nivalis, a species restricted to high latitudes. The study of Canary Island Descurainia suggests that the transition to high-elevation environments such as that found in the high mountains of the Canary Islands involves selection on genes related to reproduction and stress tolerance but that repeated evolution across different lineages that have evolved into similar habitats is limited, indicating substantially different molecular trajectories to adaptation.
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Affiliation(s)
- Amy C. Jackson
- Biological SciencesUniversity of SouthamptonSouthamptonUK
- Algae, Fungi and Plants DivisionThe Natural History MuseumLondonUK
- Present address:
Royal Botanic Gardens, Kew, Kew GreenRichmondSurreyUK
| | - Mark A. Carine
- Algae, Fungi and Plants DivisionThe Natural History MuseumLondonUK
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Zeeshan M, Sun C, Wang X, Hu Y, Wu H, Li S, Salam A, Zhu S, Khan AH, Holford P, Ali MA, Elshikh MS, Zhang Z, Zhang P. Insights into the ameliorative effect of ZnONPs on arsenic toxicity in soybean mediated by hormonal regulation, transporter modulation, and stress responsive genes. FRONTIERS IN PLANT SCIENCE 2024; 15:1427367. [PMID: 39139724 PMCID: PMC11319271 DOI: 10.3389/fpls.2024.1427367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Accepted: 07/11/2024] [Indexed: 08/15/2024]
Abstract
Arsenic (As) contamination of agricultural soils poses a serious threat to crop productivity and food safety. Zinc oxide nanoparticles (ZnONPs) have emerged as a potential amendment for mitigating the adverse effects of As stress in plants. Soybean crop is mostly grown on marginalized land and is known for high accumulation of As in roots than others tissue. Therefore, this study aimed to elucidate the underlying mechanisms of ZnONPs in ameliorating arsenic toxicity in soybean. Our results demonstrated that ZnOB significantly improved the growth performance of soybean plants exposed to arsenic. This improvement was accompanied by a decrease (55%) in As accumulation and an increase in photosynthetic efficiency. ZnOB also modulated hormonal balance, with a significant increase in auxin (149%), abscisic acid (118%), gibberellin (160%) and jasmonic acid content (92%) under As(V) stress assuring that ZnONPs may enhance root growth and development by regulating hormonal signaling. We then conducted a transcriptomic analysis to understand further the molecular mechanisms underlying the NPs-induced As(V) tolerance. This analysis identified genes differentially expressed in response to ZnONPs supplementation, including those involved in auxin, abscisic acid, gibberellin, and jasmonic acid biosynthesis and signaling pathways. Weighted gene co-expression network analysis identified 37 potential hub genes encoding stress responders, transporters, and signal transducers across six modules potentially facilitated the efflux of arsenic from cells, reducing its toxicity. Our study provides valuable insights into the molecular mechanisms associated with metalloid tolerance in soybean and offers new avenues for improving As tolerance in contaminated soils.
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Affiliation(s)
- Muhammad Zeeshan
- National Key Laboratory of Green Pesticide, South China Agricultural University, Guangzhou, China
- Yingdong College of Biology and Agriculture, Shaoguan University, Shaoguan, China
| | - Chenyu Sun
- College of Natural Resources and Environment, Northwest A&F University, Yangling, China
| | - Xin Wang
- National Key Laboratory of Green Pesticide, South China Agricultural University, Guangzhou, China
| | - Yuxin Hu
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Hao Wu
- National Key Laboratory of Green Pesticide, South China Agricultural University, Guangzhou, China
| | - Shengnan Li
- National Key Laboratory of Green Pesticide, South China Agricultural University, Guangzhou, China
| | - Abdul Salam
- National Key Laboratory of Green Pesticide, South China Agricultural University, Guangzhou, China
| | - Shiqi Zhu
- National Key Laboratory of Green Pesticide, South China Agricultural University, Guangzhou, China
| | - Aamir Hamid Khan
- Faculty of Biology and Environmental Protection, Department of Biogeography, Paleoecology and Nature conservation, University of Lodz, Lodz, Poland
| | - Paul Holford
- School of Science, Western Sydney University, Penrith, NSW, Australia
| | - Mohammad Ajmal Ali
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohamed Soliman Elshikh
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Zhixiang Zhang
- National Key Laboratory of Green Pesticide, South China Agricultural University, Guangzhou, China
| | - Peiwen Zhang
- National Key Laboratory of Green Pesticide, South China Agricultural University, Guangzhou, China
- Yingdong College of Biology and Agriculture, Shaoguan University, Shaoguan, China
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Liu L, Yan W, Liu B, Qin W. Molecular Insights into Red Palm Weevil Resistance Mechanisms of Coconut ( Cocos nucifera) Leaves. PLANTS (BASEL, SWITZERLAND) 2024; 13:1928. [PMID: 39065455 PMCID: PMC11280253 DOI: 10.3390/plants13141928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2024] [Revised: 07/09/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024]
Abstract
Red palm weevil (RPW) (Rhynchophorus ferrugineus) threatens most palm species worldwide. This study investigated the molecular responses of coconut (Cocos nucifera) leaves to RPW infestation through metabolomics and transcriptomics analysis. An RPW insect attack model was developed by placing different RPW larval densitiesin coconut plants and measuring the relative chlorophyll content of different leaf positions and physiological indicators of dysfunction after RPW infestation. The metabolomic changes were detected in the leaves of 10, 20, 30, 40, and 50 days after infestation (DAI) using GC-MS. Certain metabolites (glycine, D-pinitol, lauric acid, allylmalonic acid, D-glucaro-1, 4-lactone, protocatechuic acid, alpha, and alpha-trehalose) were found to be possible indicators for distinct stages of infestation using metabolomics analysis. The influence on ABC transporters, glutathione, galactose, and glycolipid metabolism was emphasized by pathway analysis. Differentially expressed genes (DEGs) were identified at 5, 10, 15, and 20 DAI through transcriptomics analysis of infested coconut leaves, with altered expression levels under RPW infestation. The KEGG pathway and GO analysis revealed enrichment in pathways related to metabolism, stress response, and plant-pathogen interactions, shedding light on the intricate mechanisms underlying coconut-RPW interactions. The identified genes may serve as potential markers for tracking RPW infestation progression and could inform strategies for pest control and management.
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Affiliation(s)
- Li Liu
- Hainan Key Laboratory of Tropical Oil Crops Biology, Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China; (W.Y.); (B.L.); (W.Q.)
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Dölfors F, Ilbäck J, Bejai S, Fogelqvist J, Dixelius C. Nitrate transporter protein NPF5.12 and major latex-like protein MLP6 are important defense factors against Verticillium longisporum. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:4148-4164. [PMID: 38666306 PMCID: PMC11233413 DOI: 10.1093/jxb/erae185] [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: 07/17/2023] [Accepted: 04/23/2024] [Indexed: 07/11/2024]
Abstract
Plant defense responses to the soil-borne fungus Verticillium longisporum causing stem stripe disease on oilseed rape (Brassica napus) are poorly understood. In this study, a population of recombinant inbred lines (RILs) using the Arabidopsis accessions Sei-0 and Can-0 was established. Composite interval mapping, transcriptome data, and T-DNA mutant screening identified the NITRATE/PEPTIDE TRANSPORTER FAMILY 5.12 (AtNPF5.12) gene as being associated with disease susceptibility in Can-0. Co-immunoprecipitation revealed interaction between AtNPF5.12 and the MAJOR LATEX PROTEIN family member AtMLP6, and fluorescence microscopy confirmed this interaction in the plasma membrane and endoplasmic reticulum. CRISPR/Cas9 technology was applied to mutate the NPF5.12 and MLP6 genes in B. napus. Elevated fungal growth in the npf5.12 mlp6 double mutant of both oilseed rape and Arabidopsis demonstrated the importance of these genes in defense against V. longisporum. Colonization of this fungus depends also on available nitrates in the host root. Accordingly, the negative effect of nitrate depletion on fungal growth was less pronounced in Atnpf5.12 plants with impaired nitrate transport. In addition, suberin staining revealed involvement of the NPF5.12 and MLP6 genes in suberin barrier formation. Together, these results demonstrate a dependency on multiple plant factors that leads to successful V. longisporum root infection.
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Affiliation(s)
- Fredrik Dölfors
- Swedish University of Agricultural Sciences, Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, P.O. Box 7080, S-75007 Uppsala, Sweden
| | - Jonas Ilbäck
- Swedish University of Agricultural Sciences, Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, P.O. Box 7080, S-75007 Uppsala, Sweden
| | - Sarosh Bejai
- Swedish University of Agricultural Sciences, Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, P.O. Box 7080, S-75007 Uppsala, Sweden
| | - Johan Fogelqvist
- Swedish University of Agricultural Sciences, Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, P.O. Box 7080, S-75007 Uppsala, Sweden
| | - Christina Dixelius
- Swedish University of Agricultural Sciences, Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, P.O. Box 7080, S-75007 Uppsala, Sweden
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6
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Hammes UZ, Pedersen BP. Structure and Function of Auxin Transporters. ANNUAL REVIEW OF PLANT BIOLOGY 2024; 75:185-209. [PMID: 38211951 DOI: 10.1146/annurev-arplant-070523-034109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
Auxins, a group of central hormones in plant growth and development, are transported by a diverse range of transporters with distinct biochemical and structural properties. This review summarizes the current knowledge on all known auxin transporters with respect to their biochemical and biophysical properties and the methods used to characterize them. In particular, we focus on the recent advances that were made concerning the PIN-FORMED family of auxin exporters. Insights derived from solving their structures have improved our understanding of the auxin export process, and we discuss the current state of the art on PIN-mediated auxin transport, including the use of biophysical methods to examine their properties. Understanding the mechanisms of auxin transport is crucial for understanding plant growth and development, as well as for the development of more effective strategies for crop production and plant biotechnology.
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Affiliation(s)
- Ulrich Z Hammes
- School of Life Sciences, Plant Systems Biology, Technical University of Munich, Freising, Germany;
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7
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Florez-Rueda AM, Miguel CM, Figueiredo DD. Comparative transcriptomics of seed nourishing tissues: uncovering conserved and divergent pathways in seed plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:1134-1157. [PMID: 38709819 DOI: 10.1111/tpj.16786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 04/04/2024] [Accepted: 04/12/2024] [Indexed: 05/08/2024]
Abstract
The evolutionary and ecological success of spermatophytes is intrinsically linked to the seed habit, which provides a protective environment for the initial development of the new generation. This environment includes an ephemeral nourishing tissue that supports embryo growth. In gymnosperms this tissue originates from the asexual proliferation of the maternal megagametophyte, while in angiosperms it is a product of fertilization, and is called the endosperm. The emergence of these nourishing tissues is of profound evolutionary value, and they are also food staples for most of the world's population. Here, using Orthofinder to infer orthologue genes among newly generated and previously published datasets, we provide a comparative transcriptomic analysis of seed nourishing tissues from species of several angiosperm clades, including those of early diverging lineages, as well as of one gymnosperm. Our results show that, although the structure and composition of seed nourishing tissues has seen significant divergence along evolution, there are signatures that are conserved throughout the phylogeny. Conversely, we identified processes that are specific to species within the clades studied, and thus illustrate their functional divergence. With this, we aimed to provide a foundation for future studies on the evolutionary history of seed nourishing structures, as well as a resource for gene discovery in future functional studies.
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Affiliation(s)
- Ana Marcela Florez-Rueda
- Max Planck Institute of Molecular Plant Physiology, Potsdam Science Park, Am Mühlenberg 1, 14476, Potsdam, Germany
- University of Potsdam, Karl-Liebknechts-Str. 24-25, Haus 26, 14476, Potsdam, Germany
| | - Célia M Miguel
- Faculty of Sciences, Biosystems and Integrative Sciences Institute (BioISI), University of Lisbon, Lisboa, Portugal
| | - Duarte D Figueiredo
- Max Planck Institute of Molecular Plant Physiology, Potsdam Science Park, Am Mühlenberg 1, 14476, Potsdam, Germany
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8
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Thévenod F, Lee WK. Cadmium transport by mammalian ATP-binding cassette transporters. Biometals 2024; 37:697-719. [PMID: 38319451 PMCID: PMC11101381 DOI: 10.1007/s10534-024-00582-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 01/04/2024] [Indexed: 02/07/2024]
Abstract
Cellular responses to toxic metals depend on metal accessibility to intracellular targets, reaching interaction sites, and the intracellular metal concentration, which is mainly determined by uptake pathways, binding/sequestration and efflux pathways. ATP-binding cassette (ABC) transporters are ubiquitous in the human body-usually in epithelia-and are responsible for the transfer of indispensable physiological substrates (e.g. lipids and heme), protection against potentially toxic substances, maintenance of fluid composition, and excretion of metabolic waste products. Derailed regulation and gene variants of ABC transporters culminate in a wide array of pathophysiological disease states, such as oncogenic multidrug resistance or cystic fibrosis. Cadmium (Cd) has no known physiological role in mammalians and poses a health risk due to its release into the environment as a result of industrial activities, and eventually passes into the food chain. Epithelial cells, especially within the liver, lungs, gastrointestinal tract and kidneys, are particularly susceptible to the multifaceted effects of Cd because of the plethora of uptake pathways available. Pertinent to their broad substrate spectra, ABC transporters represent a major cellular efflux pathway for Cd and Cd complexes. In this review, we summarize current knowledge concerning transport of Cd and its complexes (mainly Cd bound to glutathione) by the ABC transporters ABCB1 (P-glycoprotein, MDR1), ABCB6, ABCC1 (multidrug resistance related protein 1, MRP1), ABCC7 (cystic fibrosis transmembrane regulator, CFTR), and ABCG2 (breast cancer related protein, BCRP). Potential detoxification strategies underlying ABC transporter-mediated efflux of Cd and Cd complexes are discussed.
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Affiliation(s)
- Frank Thévenod
- Institute for Physiology, Pathophysiology and Toxicology & ZBAF, Witten/Herdecke University, 58453, Witten, Germany
- Physiology and Pathophysiology of Cells and Membranes, Medical School OWL, Bielefeld University, Morgenbreede 1, 33615, Bielefeld, Germany
| | - Wing-Kee Lee
- Physiology and Pathophysiology of Cells and Membranes, Medical School OWL, Bielefeld University, Morgenbreede 1, 33615, Bielefeld, Germany.
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Xu SY, Mo YH, Liu YJ, Wang X, Li HY, Yang WD. Physiological and genetic responses of the benthic dinoflagellate Prorocentrum lima to polystyrene microplastics. HARMFUL ALGAE 2024; 136:102652. [PMID: 38876530 DOI: 10.1016/j.hal.2024.102652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 05/13/2024] [Accepted: 05/20/2024] [Indexed: 06/16/2024]
Abstract
Microplastics are well known as contaminants in marine environments. With the development of biofilms, most microplastics will eventually sink and deposit in benthic environment. However, little research has been done on benthic toxic dinoflagellates, and the effects of microplastics on benthic dinoflagellates are unknown. Prorocentrum lima is a cosmopolitan toxic benthic dinoflagellate, which can produce a range of polyether metabolites, such as diarrhetic shellfish poisoning (DSP) toxins. In order to explore the impact of microplastics on marine benthic dinoflagellates, in this paper, we studied the effects of polystyrene (PS) on the growth and toxin production of P. lima. The molecular response of P. lima to microplastic stress was analyzed by transcriptomics. We selected 100 nm, 10 μm and 100 μm PS, and set three concentrations of 1 mg L-1, 10 mg L-1 and 100 mg L-1. The results showed that PS exposure had limited effects on cell growth, but increased the OA and extracellular polysaccharide content at high concentrations. After exposure to PS MPs, genes associated with DSP toxins synthesis, carbohydrate synthesis and energy metabolism, such as glycolysis, TCA cycle and pyruvate metabolism, were significantly up-regulated. We speculated that after exposure to microplastics, P. lima may increase the synthesis of DSP toxins and extracellular polysaccharides, improve the level of energy metabolism and gene expression of ABC transporter, thereby protecting algal cells from damage. Our findings provide new insights into the effects of microplastics on toxic benthic dinoflagellates.
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Affiliation(s)
- Si-Yuan Xu
- Key Laboratory of Aquatic Eutrophication and Control of Harmful Algal Blooms of Guangdong Higher Education Institute, College of Life Science and Technology, Jinan University, Guangzhou 510632, PR China
| | - Yan-Hang Mo
- Key Laboratory of Aquatic Eutrophication and Control of Harmful Algal Blooms of Guangdong Higher Education Institute, College of Life Science and Technology, Jinan University, Guangzhou 510632, PR China
| | - Yu-Jie Liu
- Key Laboratory of Aquatic Eutrophication and Control of Harmful Algal Blooms of Guangdong Higher Education Institute, College of Life Science and Technology, Jinan University, Guangzhou 510632, PR China
| | - Xiang Wang
- Key Laboratory of Aquatic Eutrophication and Control of Harmful Algal Blooms of Guangdong Higher Education Institute, College of Life Science and Technology, Jinan University, Guangzhou 510632, PR China
| | - Hong-Ye Li
- Key Laboratory of Aquatic Eutrophication and Control of Harmful Algal Blooms of Guangdong Higher Education Institute, College of Life Science and Technology, Jinan University, Guangzhou 510632, PR China
| | - Wei-Dong Yang
- Key Laboratory of Aquatic Eutrophication and Control of Harmful Algal Blooms of Guangdong Higher Education Institute, College of Life Science and Technology, Jinan University, Guangzhou 510632, PR China.
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Singh D, Tripathi A, Bhati J, Taunk J, Singh D, Siddiqui MH, Singh MP. Genome wide identification and expression profiling of ATP binding cassette (ABC) transporters gene family in lentil (Lens culinaris Medikus) under aluminium stress condition. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 211:108710. [PMID: 38735154 DOI: 10.1016/j.plaphy.2024.108710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 04/22/2024] [Accepted: 05/06/2024] [Indexed: 05/14/2024]
Abstract
Adenosine triphosphate-binding cassette transporters (ABC transporters) are involved in regulating plant growth, development and tolerance to environmental stresses. In this study, a total of 138 ABC transporter genes were identified in the lentil genome that were classified into eight subfamilies. Four lentil ABC transporters from subfamily B and I were clustered together with the previously characterized ABC transporter proteins related to aluminium (Al) detoxification. Lentil ABC transporter genes were distributed across the chromosomes. Tandem duplication was the main driving force for expansion of the ABC gene family. Collinearity of lentil with soybean indicated that ABC gene family is closely linked to Glycine max. ABC genes in the same subfamily showed similar gene structure and conserved motifs. The ABC promoter regions harboured a large number of plant hormones and multiple stress responsive cis-regulatory elements. The qRT-PCR showed that ABC genes had varied expression in roots of lentil at different time points under Al stress. This is the first report on genome wide identification and expression analyses of genes encoding ABC transporter genes in lentil which has provided in-depth insight for future research on evolution and elucidation of molecular mechanisms for aluminium tolerance.
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Affiliation(s)
- Dharmendra Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
| | - Ankita Tripathi
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Jyotika Bhati
- ICAR-India Agricultural Statistics Research Institute, New Delhi, 110012, India
| | - Jyoti Taunk
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Deepti Singh
- Department of Botany, Meerut College, Meerut, 250001, India
| | - Manzer H Siddiqui
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Madan Pal Singh
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
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Zhang Z, Yu H, Tao M, Lv T, Li F, Yu D, Liu C. Mechanistic insight into the impact of polystyrene microparticle on submerged plant during asexual propagules germination to seedling: Internalization in functional organs and alterations of physiological phenotypes. JOURNAL OF HAZARDOUS MATERIALS 2024; 469:133929. [PMID: 38452672 DOI: 10.1016/j.jhazmat.2024.133929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 02/12/2024] [Accepted: 02/28/2024] [Indexed: 03/09/2024]
Abstract
Asexual reproduction is one of the most important propagations in aquatic plants. However, there is a lack of information about the growth-limiting mechanisms induced by microplastics on the submerged plant during asexual propagule germination to seedling. Hence, we investigated the effects of two sizes (2 µm, 0.2 µm) and three concentrations (0.5 mg/L, 5 mg/L, and 50 mg/L) of polystyrene microplastics (PSMPs) on Potamogeton crispus turion germination and seedling growth. Both PSMPs sizes were found in P. crispus seedling tissues. Metabolic profile alterations were observed in leaves, particularly affecting secondary metabolic pathways and ATP-binding cassette transporters. Metal elements are indispensable cofactors for photosynthesis; however, alterations in the metabolic profile led to varying degrees of reduced concentrations in magnesium, iron, copper, and zinc within P. crispus. Therefore, the maximum quantum yield of photosystem II significantly decreased in all concentrations with 0.2 µm-PSMPs, and at 50 mg/L with 2 µm-PSMPs. These findings reveal that internalization of microplastics, nutrient absorption inhibition, and metabolic changes contribute to the negative impact on P. crispus seedlings.
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Affiliation(s)
- Zhiqiang Zhang
- The National Field Station of Freshwater Ecosystem of Liangzi Lake, College of Life Science, Wuhan University, Wuhan, PR China
| | - Hongwei Yu
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China
| | - Min Tao
- The National Field Station of Freshwater Ecosystem of Liangzi Lake, College of Life Science, Wuhan University, Wuhan, PR China
| | - Tian Lv
- The National Field Station of Freshwater Ecosystem of Liangzi Lake, College of Life Science, Wuhan University, Wuhan, PR China
| | - Fuchao Li
- The National Field Station of Freshwater Ecosystem of Liangzi Lake, College of Life Science, Wuhan University, Wuhan, PR China
| | - Dan Yu
- The National Field Station of Freshwater Ecosystem of Liangzi Lake, College of Life Science, Wuhan University, Wuhan, PR China
| | - Chunhua Liu
- The National Field Station of Freshwater Ecosystem of Liangzi Lake, College of Life Science, Wuhan University, Wuhan, PR China.
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Ma B, Cao X, Li X, Bian Z, Zhang QQ, Fang Z, Liu J, Li Q, Liu Q, Zhang L, He Z. Two ABCI family transporters, OsABCI15 and OsABCI16, are involved in grain-filling in rice. J Genet Genomics 2024; 51:492-506. [PMID: 37913986 DOI: 10.1016/j.jgg.2023.10.007] [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: 10/07/2023] [Revised: 10/27/2023] [Accepted: 10/27/2023] [Indexed: 11/03/2023]
Abstract
Seed development is critical for plant reproduction and crop yield, with panicle seed-setting rate, grain-filling, and grain weight being key seed characteristics for yield improvement. However, few genes are known to regulate grain filling. Here, we identify two adenosine triphosphate (ATP)-binding cassette (ABC)I-type transporter genes, OsABCI15 and OsABCI16, involved in rice grain-filling. Both genes are highly expressed in developing seeds, and their proteins are localized to the plasma membrane and cytosol. Interestingly, knockout of OsABCI15 and OsABCI16 results in a significant reduction in seed-setting rate, caused predominantly by the severe empty pericarp phenotype, which differs from the previously reported low seed-setting phenotype resulting from failed pollination. Further analysis indicates that OsABCI15 and OsABCI16 participate in ion homeostasis and likely export ions between filial tissues and maternal tissues during grain filling. Importantly, overexpression of OsABCI15 and OsABCI16 enhances the seed-setting rate and grain yield in transgenic plants and decreases ion accumulation in brown rice. Moreover, the OsABCI15/16 orthologues in maize exhibit a similar role in kernel development, as demonstrated by their disruption in transgenic maize. Therefore, our findings reveal the important roles of two ABC transporters in cereal grain filling, highlighting their value in crop yield improvement.
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Affiliation(s)
- Bin Ma
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, Jiangsu 225009, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, Jiangsu 225009, China; National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai 200032, China.
| | - Xiubiao Cao
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, Jiangsu 225009, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Xiaoyuan Li
- Institute of Biotechnology, Hangzhou Academy of Agricultural Sciences, Hangzhou, Zhejiang 310024, China
| | - Zhong Bian
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, Jiangsu 225009, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Qi-Qi Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Zijun Fang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jiyun Liu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Qun Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Qiaoquan Liu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, Jiangsu 225009, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Lin Zhang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, Jiangsu 225009, China.
| | - Zuhua He
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai 200032, China.
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Devi R, Goyal P, Verma B, Hussain S, Chowdhary F, Arora P, Gupta S. A transcriptome-wide identification of ATP-binding cassette (ABC) transporters revealed participation of ABCB subfamily in abiotic stress management of Glycyrrhiza glabra L. BMC Genomics 2024; 25:315. [PMID: 38532362 DOI: 10.1186/s12864-024-10227-z] [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: 10/20/2023] [Accepted: 03/15/2024] [Indexed: 03/28/2024] Open
Abstract
Transcriptome-wide survey divulged a total of 181 ABC transporters in G. glabra which were phylogenetically classified into six subfamilies. Protein-Protein interactions revealed nine putative GgABCBs (-B6, -B14, -B15, -B25, -B26, -B31, -B40, -B42 &-B44) corresponding to five AtABCs orthologs (-B1, -B4, -B11, -B19, &-B21). Significant transcript accumulation of ABCB6 (31.8 folds), -B14 (147.5 folds), -B15 (17 folds), -B25 (19.7 folds), -B26 (18.31 folds), -B31 (61.89 folds), -B40 (1273 folds) and -B42 (51 folds) was observed under the influence of auxin. Auxin transport-specific inhibitor, N-1-naphthylphthalamic acid, showed its effectiveness only at higher (10 µM) concentration where it down regulated the expression of ABCBs, PINs (PIN FORMED) and TWD1 (TWISTED DWARF 1) genes in shoot tissues, while their expression was seen to enhance in the root tissues. Further, qRT-PCR analysis under various growth conditions (in-vitro, field and growth chamber), and subjected to abiotic stresses revealed differential expression implicating role of ABCBs in stress management. Seven of the nine genes were shown to be involved in the stress physiology of the plant. GgABCB6, 15, 25 and ABCB31 were induced in multiple stresses, while GgABCB26, 40 & 42 were exclusively triggered under drought stress. No study pertaining to the ABC transporters from G. glabra is available till date. The present investigation will give an insight to auxin transportation which has been found to be associated with plant growth architecture; the knowledge will help to understand the association between auxin transportation and plant responses under the influence of various conditions.
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Affiliation(s)
- Ritu Devi
- Plant Biotechnology Division, Jammu, India
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Pooja Goyal
- Plant Biotechnology Division, Jammu, India
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
- Registered from Guru Nanak Dev University, Amritsar, India
| | - Bhawna Verma
- Plant Biotechnology Division, Jammu, India
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Shahnawaz Hussain
- Plant Biotechnology Division, Jammu, India
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Fariha Chowdhary
- Plant Biotechnology Division, Jammu, India
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Palak Arora
- Plant Biotechnology Division, Jammu, India
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
| | - Suphla Gupta
- Plant Biotechnology Division, Jammu, India.
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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14
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Ibragimova NN, Mokshina NE. Expression of auxin transporter genes in flax (Linum usitatissimum) fibers during gravity response. Vavilovskii Zhurnal Genet Selektsii 2024; 28:33-43. [PMID: 38465245 PMCID: PMC10917669 DOI: 10.18699/vjgb-24-05] [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: 07/26/2023] [Revised: 10/15/2023] [Accepted: 10/16/2023] [Indexed: 03/12/2024] Open
Abstract
Gravitropism is an adaptive reaction of plants associated with the ability of various plant organs to be located and to grow in a certain direction relative to the gravity vector, while usually the asymmetric distribution of the phytohormone auxin is a necessary condition for the gravitropical bending of plant organs. Earlier, we described significant morphological changes in phloem fibers with a thickened cell wall located on different sides of the stem in the area of the gravitropic curvature. The present study is the first work devoted to the identification of genes encoding auxin transporters in cells at different stages of development and during gravity response. In this study, the flax genes encoding the AUX1/LAX, PIN-FORMED, PIN-LIKES, and ABCB auxin transporters were identified. A comparative analysis of the expression of these genes in flax phloem fibers at different stages of development revealed increased expression of some of these genes at the stage of intrusive growth (LusLAX2 (A, B), LuxPIN1-D, LusPILS7 (C, D)), at the early stage of tertiary cell wall formation (LusAUX1 (A, D), LusABCB1 (A, B), LusABCB15-A, LusPIN1 (A, B), LusPIN4-A, and LusPIN5-A), and at the late stage of tertiary cell wall development (LusLAX3 (A, B)). It was shown that in the course of gravitropism, the expression of many genes, including those responsible for the influx of auxin in cells (LusAUX1-D), in the studied families increased. Differential expression of auxin transporter genes was revealed during gravity response in fibers located on different sides of the stem (upper (PUL) and lower (OPP)). The difference was observed due to the expression of genes, the products of which are responsible for auxin intracellular transport (LusPILS3, LusPILS7-A) and its efflux (LusABCB15-B, LusABCB19-B). It was noted that the increased expression of PIN genes and ABCB genes was more typical of fibers on the opposite side. The results obtained allow us to make an assumption about the presence of differential auxin content in the fibers of different sides of gravistimulated flax plants, which may be determined by an uneven outflow of auxin. This study gives an idea of auxin carriers in flax and lays the foundation for further studies of their functions in the development of phloem fiber and in gravity response.
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Affiliation(s)
- N N Ibragimova
- Kazan Institute of Biochemistry and Biophysics of Kazan Scientific Center of the Russian Academy of Sciences, Kazan, Russia
| | - N E Mokshina
- Kazan Institute of Biochemistry and Biophysics of Kazan Scientific Center of the Russian Academy of Sciences, Kazan, Russia
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15
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Ding F, Zhang Y, Lin J, Zhong S, Li P, Li Y, Chen C, Jin S. Comparative transcriptome and metabolome analyses revealed quality difference between beauty tea processed through indoor withering and outdoor solar withering. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024; 104:1039-1050. [PMID: 37743412 DOI: 10.1002/jsfa.12990] [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: 05/25/2023] [Revised: 08/20/2023] [Accepted: 09/25/2023] [Indexed: 09/26/2023]
Abstract
BACKGROUND Withering is the first processing procedure of beauty tea, and there are few reports on the impact of withering methods on the quality of beauty tea and its regulatory mechanisms. RESULTS Through comparison of fresh tea leaves (FT) with the leaves after indoor natural withering for 18 h (IWT-18) and outdoor solar withering for 6 h (OWT-6), which were collected at the end of the two withering processes, 17 282 and 13 984 differentially expressed genes (DEGs) were respectively screened and 267 and 154 differential metabolites (DMs) were respectively identified. The coexpression network revealed that a large number of DEGs and DMs were enriched in phenylpropanoid, flavonoid, and adenosine triphosphate binding cassette (ABC) transporter pathways, and the number of DMs and DEGs in IWT-18 versus FT exceeded that in OWT-6 versus FT. Both withering methods promoted a significant increase in content of phenylalanine and upregulation of β-glucoside expression in the phenylpropanoid metabolism pathway. Five theaflavin-type proanthocyanidins in the flavonoid synthesis pathway were more significantly accumulated in FT versus IWT-18 than in FT versus OWT-6. Meanwhile, both withering methods can affect the ABC transporter pathway to promote the accumulation of amino acids and their derivatives, but different withering methods affect different ABC transporter families. Outdoor withering with more severe abiotic stress has a greater impact on the ABCG family, whereas indoor withering has a more significant effect on the ABCC family. Sensory evaluation results showed that the dry tea of IWT-18 was slightly better than that of OWT-6 because of the longer withering time and more thorough substance transformation. CONCLUSION In conclusion, the formation of honey flavor in beauty tea may be closely related to the DEGs and DMs in these three pathways. Our research provides theoretical data support for further revealing the mechanism of quality formation during the withering process of beauty tea. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Fengjiao Ding
- College of Horticulture, Fujian Agriculture and Forestry University/Fujian University Key Laboratory of Tea Science, Fuzhou, China
| | - Yunzhi Zhang
- College of Horticulture, Fujian Agriculture and Forestry University/Fujian University Key Laboratory of Tea Science, Fuzhou, China
| | - Jinlong Lin
- College of Horticulture, Fujian Agriculture and Forestry University/Fujian University Key Laboratory of Tea Science, Fuzhou, China
| | - Sitong Zhong
- College of Horticulture, Fujian Agriculture and Forestry University/Fujian University Key Laboratory of Tea Science, Fuzhou, China
| | - Pengchun Li
- Fujian Jiangshan Meiren Tea Co., Ltd, Sanming, China
| | - Yuanchao Li
- College of Horticulture, Fujian Agriculture and Forestry University/Fujian University Key Laboratory of Tea Science, Fuzhou, China
| | - Chunmei Chen
- Fujian Fengyuan Tea Industry Co., Ltd, Sanming, China
| | - Shan Jin
- College of Horticulture, Fujian Agriculture and Forestry University/Fujian University Key Laboratory of Tea Science, Fuzhou, China
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16
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Zhang D, Yu Z, Zeng B, Liu X. Genome-wide analysis of the ABC gene family in almond and functional predictions during flower development, freezing stress, and salt stress. BMC PLANT BIOLOGY 2024; 24:12. [PMID: 38163883 PMCID: PMC10759767 DOI: 10.1186/s12870-023-04698-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 12/18/2023] [Indexed: 01/03/2024]
Abstract
ABC (ATP-binding cassette) transporter proteins are one of the most extensive protein families known to date and are ubiquitously found in animals, plants, and microorganisms. ABCs have a variety of functions, such as plant tissue development regulation, hormone transport, and biotic and abiotic stress resistance. However, the gene characterization and function of the ABC gene family in almond (Prunus dulcis) have not been thoroughly studied. In this study, we identified 117 PdABC genes using the whole genome of 'Wanfeng' almond obtained by sequencing and explored their protein characterization. The PdABC family members were classified into eight subfamilies. The members of the same subfamily had conserved motifs but poorly conserved numbers of exons and introns and were unevenly distributed among the eight subfamilies and on the eight chromosomes. Expression patterns showed that PdABC family members were significantly differentially expressed during almond development, dormant freezing stress, and salt stress. We found that PdABC59 and PdABC77 had extremely high expression levels in pollen. PdABC63 and PdABC64 had high expression levels during almond petal development and multiple stages of flower development. PdABC98 was highly expressed in annual dormant branches after six temperature-freezing stress treatments. PdABC29, PdABC69, and PdABC98 were highly expressed under different concentrations of salt stress. This study preliminarily investigated the expression characteristics of ABC genes in different tissues of almond during flower development, freezing stress and salt stress, and the results will provide a reference for further in-depth research and breeding of almond in the future.
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Affiliation(s)
- Dongdong Zhang
- College of Horticulture, Xinjiang Agricultural University, Urumqi, 830000, China
| | - Zhenfan Yu
- College of Horticulture, Xinjiang Agricultural University, Urumqi, 830000, China
| | - Bin Zeng
- College of Horticulture, Xinjiang Agricultural University, Urumqi, 830000, China.
| | - Xingyue Liu
- College of Horticulture, Xinjiang Agricultural University, Urumqi, 830000, China
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17
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Li ZJ, Tang SY, Gao HS, Ren JY, Xu PL, Dong WP, Zheng Y, Yang W, Yu YY, Guo JH, Luo YM, Niu DD, Jiang CH. Plant growth-promoting rhizobacterium Bacillus cereus AR156 induced systemic resistance against multiple pathogens by priming of camalexin synthesis. PLANT, CELL & ENVIRONMENT 2024; 47:337-353. [PMID: 37775913 DOI: 10.1111/pce.14729] [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: 04/30/2023] [Revised: 09/04/2023] [Accepted: 09/17/2023] [Indexed: 10/01/2023]
Abstract
Phytoalexins play a crucial role in plant immunity. However, the mechanism of how phytoalexin is primed by beneficial microorganisms against broad-spectrum pathogens remains elusive. This study showed that Bacillus cereus AR156 could trigger ISR against broad-spectrum disease. RNA-sequencing and camalexin content assays showed that AR156-triggered ISR can prime the accumulation of camalexin synthesis and secretion-related genes. Moreover, it was found that AR156-triggered ISR elevates camalexin accumulation by increasing the expression of camalexin synthesis genes upon pathogen infection. We observed that the priming of camalexin accumulation by AR156 was abolished in cyp71a13 and pad3 mutants. Further investigations reveal that in the wrky33 mutant, the ability of AR156 to prime camalexin accumulation is abolished, and the mediated ISR against the three pathogens is significantly compromised. Furthermore, PEN3 and PDR12, acting as camalexin transporters, participate in AR156-induced ISR against broad-spectrum pathogens differently. In addition, salicylic acid and JA/ET signalling pathways participate in AR156-primed camalexin synthesis to resist pathogens in different forms depending on the pathogen. In summary, B. cereus AR156 triggers ISR against Botrytis cinerea, Pst DC3000 and Phytophthora capsici by priming camalexin synthesis. Our study provides deeper insights into the significant role of camalexin for AR156-induced ISR against broad-spectrum pathogens.
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Affiliation(s)
- Zi-Jie Li
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
- Engineering Center of Bioresource Pesticide in Jiangsu Province, Nanjing, China
- Key Laboratory of Integrated Management of Crop Disease and Pests, Nanjing Agricultural University, Nanjing, China
| | - Shu-Ya Tang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
- Engineering Center of Bioresource Pesticide in Jiangsu Province, Nanjing, China
- Key Laboratory of Integrated Management of Crop Disease and Pests, Nanjing Agricultural University, Nanjing, China
| | - Hong-Shan Gao
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
- Engineering Center of Bioresource Pesticide in Jiangsu Province, Nanjing, China
- Key Laboratory of Integrated Management of Crop Disease and Pests, Nanjing Agricultural University, Nanjing, China
| | - Jin-Yao Ren
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
- Engineering Center of Bioresource Pesticide in Jiangsu Province, Nanjing, China
- Key Laboratory of Integrated Management of Crop Disease and Pests, Nanjing Agricultural University, Nanjing, China
| | - Pei-Ling Xu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
- Engineering Center of Bioresource Pesticide in Jiangsu Province, Nanjing, China
- Key Laboratory of Integrated Management of Crop Disease and Pests, Nanjing Agricultural University, Nanjing, China
| | - Wen-Pan Dong
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
- Engineering Center of Bioresource Pesticide in Jiangsu Province, Nanjing, China
- Key Laboratory of Integrated Management of Crop Disease and Pests, Nanjing Agricultural University, Nanjing, China
| | - Ying Zheng
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
- Engineering Center of Bioresource Pesticide in Jiangsu Province, Nanjing, China
- Key Laboratory of Integrated Management of Crop Disease and Pests, Nanjing Agricultural University, Nanjing, China
| | - Wei Yang
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Huai'an, China
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology around Hongze Lake, Huaiyin Normal University, Huai'an, China
| | - Yi-Yang Yu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
- Engineering Center of Bioresource Pesticide in Jiangsu Province, Nanjing, China
- Key Laboratory of Integrated Management of Crop Disease and Pests, Nanjing Agricultural University, Nanjing, China
| | - Jian-Hua Guo
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
- Engineering Center of Bioresource Pesticide in Jiangsu Province, Nanjing, China
- Key Laboratory of Integrated Management of Crop Disease and Pests, Nanjing Agricultural University, Nanjing, China
| | - Yu-Ming Luo
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Huai'an, China
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology around Hongze Lake, Huaiyin Normal University, Huai'an, China
| | - Dong-Dong Niu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
- Engineering Center of Bioresource Pesticide in Jiangsu Province, Nanjing, China
- Key Laboratory of Integrated Management of Crop Disease and Pests, Nanjing Agricultural University, Nanjing, China
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Huai'an, China
| | - Chun-Hao Jiang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
- Engineering Center of Bioresource Pesticide in Jiangsu Province, Nanjing, China
- Key Laboratory of Integrated Management of Crop Disease and Pests, Nanjing Agricultural University, Nanjing, China
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Huai'an, China
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Yang W, Liu X, Yu S, Liu J, Jiang L, Lu X, Liu Y, Zhang J, Li X, Zhang S. The maize ATP-binding cassette (ABC) transporter ZmMRPA6 confers cold and salt stress tolerance in plants. PLANT CELL REPORTS 2023; 43:13. [PMID: 38135780 DOI: 10.1007/s00299-023-03094-7] [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: 08/03/2023] [Accepted: 11/10/2023] [Indexed: 12/24/2023]
Abstract
KEY MESSAGE ZmMRPA6 was cloned and characterized as the first ATP-binding cassette (ABC) transporter in maize to be proven to participate in cold and salt tolerance. Homologous genes AtABCC4 and AtABCC14 of ZmMRPA6 also responded to salt stress. ATP-binding cassette (ABC) proteins are major transmembrane transporters that play significant roles in plant development against various abiotic stresses. However, available information regarding stress-related ABC genes in maize is minimal. In this study, a maize ABC transporter gene, ZmMRPA6, was identified through genome-wide association analysis (GWAS) for cold tolerance in maize seeds germination and functionally characterized. During germination and seedling stages, the zmmrpa6 mutant exhibited enhanced resistance to cold or salt stress. Mutated of ZmMRPA6 did not affect the expression of downstream response genes related cold or salt response at the transcriptional level. Mass spectrometry analysis revealed that most of the differential proteins between zmmrpa6 and wild-type plants were involved in response to stress process including oxidative reduction, hydrolase activity, small molecule metabolism, and photosynthesis process. Meanwhile, the plants which lack the ZmMRPA6 homologous genes AtABCC4 or AtABCC14 were sensitive to salt stress in Arabidopsis. These results indicated that ZmMRPA6 and its homologous genes play a conserved role in cold and salt stress, and functional differentiation occurs in monocotyledonous and dicotyledonous plants. In summary, these findings dramatically improved our understanding of the function of ABC transporters resistance to abiotic stresses in plants.
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Affiliation(s)
- Wei Yang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Xiao Liu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Shaowei Yu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Jisheng Liu
- Institute of Molecular Breeding for Maize, Qilu Normal University, Jinan, 250200, Shandong, China
| | - Lijun Jiang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Xiaoduo Lu
- Institute of Molecular Breeding for Maize, Qilu Normal University, Jinan, 250200, Shandong, China
| | - Yinggao Liu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Jiedao Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Xiang Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China.
| | - Shuxin Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China.
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19
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Tamizhselvan P, Madhavan S, Constan-Aguilar C, Elrefaay ER, Liu J, Pěnčík A, Novák O, Cairó A, Hrtyan M, Geisler M, Tognetti VB. Chloroplast Auxin Efflux Mediated by ABCB28 and ABCB29 Fine-Tunes Salt and Drought Stress Responses in Arabidopsis. PLANTS (BASEL, SWITZERLAND) 2023; 13:7. [PMID: 38202315 PMCID: PMC10780339 DOI: 10.3390/plants13010007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 11/26/2023] [Accepted: 12/13/2023] [Indexed: 01/12/2024]
Abstract
Photosynthesis is among the first processes negatively affected by environmental cues and its performance directly determines plant cell fitness and ultimately crop yield. Primarily sites of photosynthesis, chloroplasts are unique sites also for the biosynthesis of precursors of the growth regulator auxin and for sensing environmental stress, but their role in intracellular auxin homeostasis, vital for plant growth and survival in changing environments, remains poorly understood. Here, we identified two ATP-binding cassette (ABC) subfamily B transporters, ABCB28 and ABCB29, which export auxin across the chloroplast envelope to the cytosol in a concerted action in vivo. Moreover, we provide evidence for an auxin biosynthesis pathway in Arabidopsis thaliana chloroplasts. The overexpression of ABCB28 and ABCB29 influenced stomatal regulation and resulted in significantly improved water use efficiency and survival rates during salt and drought stresses. Our results suggest that chloroplast auxin production and transport contribute to stomata regulation for conserving water upon salt stress. ABCB28 and ABCB29 integrate photosynthesis and auxin signals and as such hold great potential to improve the adaptation potential of crops to environmental cues.
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Affiliation(s)
- Prashanth Tamizhselvan
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic; (P.T.); (S.M.); (C.C.-A.); (E.R.E.); (A.C.); (M.H.)
| | - Sharmila Madhavan
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic; (P.T.); (S.M.); (C.C.-A.); (E.R.E.); (A.C.); (M.H.)
| | - Christian Constan-Aguilar
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic; (P.T.); (S.M.); (C.C.-A.); (E.R.E.); (A.C.); (M.H.)
| | - Eman Ryad Elrefaay
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic; (P.T.); (S.M.); (C.C.-A.); (E.R.E.); (A.C.); (M.H.)
| | - Jie Liu
- Department of Biology, University of Fribourg, CH-1700 Fribourg, Switzerland; (J.L.); (M.G.)
| | - Aleš Pěnčík
- Laboratory of Growth Regulators, Institute of Experimental Botany, The Czech Academy of Sciences, & Faculty of Science, Palacký University, Šlechtitelů 27, CZ-783 71 Olomouc, Czech Republic; (A.P.); (O.N.)
| | - Ondřej Novák
- Laboratory of Growth Regulators, Institute of Experimental Botany, The Czech Academy of Sciences, & Faculty of Science, Palacký University, Šlechtitelů 27, CZ-783 71 Olomouc, Czech Republic; (A.P.); (O.N.)
| | - Albert Cairó
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic; (P.T.); (S.M.); (C.C.-A.); (E.R.E.); (A.C.); (M.H.)
| | - Mónika Hrtyan
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic; (P.T.); (S.M.); (C.C.-A.); (E.R.E.); (A.C.); (M.H.)
| | - Markus Geisler
- Department of Biology, University of Fribourg, CH-1700 Fribourg, Switzerland; (J.L.); (M.G.)
| | - Vanesa Beatriz Tognetti
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic; (P.T.); (S.M.); (C.C.-A.); (E.R.E.); (A.C.); (M.H.)
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20
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Mall MS, Shah S, Singh S, Singh N, Singh N, Vaish S, Gupta D. Genome-wide identification and characterization of ABC transporter superfamily in the legume Cajanus cajan. J Appl Genet 2023; 64:615-644. [PMID: 37624461 DOI: 10.1007/s13353-023-00774-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 07/17/2023] [Accepted: 08/01/2023] [Indexed: 08/26/2023]
Abstract
Plant ATP-binding cassette (ABC) protein family is the largest multifunctional highly conserved protein superfamily that transports diverse substrates across biological membranes by the hydrolysis of ATP and is also the part of the several other biological processes like cellular detoxification, growth and development, stress biology, and signaling processes. In the agriculturally important legume crop Cajanus cajan, a genome-wide identification and characterization of the ABC gene family was carried out. A total of 159 ABC genes were identified that belong to eight canonical classes CcABCA to CcABCG and CcABCI based on the phylogenetic analysis. The number of genes was highest in CcABCG followed by CcABCC and CcABCB class. A total of 85 CcABC genes were found on 11 chromosomes and 74 were found on scaffold. Tandem duplication was the major driver of CcABC gene family expansion. The dN/dS ratio revealed the purifying selection. The phylogenetic analysis revealed class-specific eight superclades which reflect their functional importance. The largest clade was found to be CcABCG which reflects their functional significance. CcABC proteins were mainly basic in nature and found to be localized in the plasma membrane. The secondary structure prediction revealed the dominance of α-helix. The canonical transmembrane and nucleotide binding domain, signature motif LSSGQ, Walker A, Walker B region, and Q loop were also identified. A class-specific exon-intron pattern was also observed. In addition to core elements, different cis-acting regulatory elements like stress, hormone, and cellular responsive were also identified. Expression profiling of CcABC genes at various developmental stages of different anatomical tissues was performed and it was noticed that CcABCF3, CcABCF4, CcABCF5, CcABCG66, and CcABCI3 had the highest expression. The results of the current study endow us with the further functional analysis of Cajanus ABC in the future.
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Affiliation(s)
- Mridula Sanjana Mall
- Faculty of Biosciences, Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, -Deva Road, Barabanki, Lucknow, Uttar Pradesh, 225003, India
| | - Shreya Shah
- Faculty of Biosciences, Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, -Deva Road, Barabanki, Lucknow, Uttar Pradesh, 225003, India
| | - Shivani Singh
- Experiome Biotech Private Limited, B1-517, Vijaypur Colony, DLF MyPAD, Vibhutikhand, Gomtinagar, Lucknow, Uttar Pradesh, 226010, India
| | - Namita Singh
- Experiome Biotech Private Limited, B1-517, Vijaypur Colony, DLF MyPAD, Vibhutikhand, Gomtinagar, Lucknow, Uttar Pradesh, 226010, India
| | - Nootan Singh
- Faculty of Biosciences, Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, -Deva Road, Barabanki, Lucknow, Uttar Pradesh, 225003, India
| | - Swati Vaish
- Faculty of Biosciences, Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, -Deva Road, Barabanki, Lucknow, Uttar Pradesh, 225003, India
| | - Divya Gupta
- Faculty of Biosciences, Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, -Deva Road, Barabanki, Lucknow, Uttar Pradesh, 225003, India.
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21
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Pinto VB, Vidigal PMP, Dal-Bianco M, Almeida-Silva F, Venancio TM, Viana JMS. Transcriptome-based strategies for identifying aluminum tolerance genes in popcorn (Zea mays L. var. everta). Sci Rep 2023; 13:19400. [PMID: 37938583 PMCID: PMC10632369 DOI: 10.1038/s41598-023-46810-9] [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: 08/08/2023] [Accepted: 11/06/2023] [Indexed: 11/09/2023] Open
Abstract
Aluminum (Al) toxicity limits crop production worldwide. Although studies have identified genes associated with Al tolerance in crops, a large amount of data remains unexplored using other strategies. Here, we searched for single substitutions and InDels across differentially expressed genes (DEGs), linked DEGs to Al-tolerance QTLs reported in the literature for common maize, and investigated the alternative splicing regulated by Al3+ toxicity. We found 929 substitutions between DEGs in Al-tolerant and 464 in Al-sensitive inbred lines, of which 165 and 80 were non-synonymous, respectively. Only 12 NS variants had deleterious predicted effect on protein function in Al-tolerant and 13 in Al-sensitive. Moreover, 378 DEGs were mapped in Al-QTL regions for the Al-tolerant and 213 for the Al-sensitive. Furthermore, Al stress is primarily regulated at the transcriptional level in popcorn. Important genes identified, such as HDT1, SWEET4a, GSTs, SAD9, PIP2-2, CASP-like 5, and AGP, may benefit molecular assisted popcorn breeding or be useful in biotechnological approaches. These findings offer insights into the mechanisms of Al tolerance in popcorn and provide a 'hypothesis-free' strategy for identifying and prioritizing candidate genes that could be used to develop molecular markers or cultivars resilient to acidic soils.
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Affiliation(s)
- Vitor Batista Pinto
- Departamento de Biologia Geral, Universidade Federal de Viçosa (UFV), Viçosa, MG, 36570-000, Brazil.
- Laboratório de Biologia Celular e Tecidual, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, RJ, 28013-602, Brazil.
| | | | - Maximiller Dal-Bianco
- Laboratório de Bioquímica Genética de Plantas/BIOAGRO. UFV, Viçosa, MG, 36570-000, Brazil
| | - Fabricio Almeida-Silva
- Laboratório de Química e Função de Proteínas e Peptídeos, CBB. UENF, Campos dos Goytacazes, RJ, 28013-602, Brazil
| | - Thiago Motta Venancio
- Laboratório de Química e Função de Proteínas e Peptídeos, CBB. UENF, Campos dos Goytacazes, RJ, 28013-602, Brazil
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22
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Ruffinatti FA, Scarpellino G, Chinigò G, Visentin L, Munaron L. The Emerging Concept of Transportome: State of the Art. Physiology (Bethesda) 2023; 38:0. [PMID: 37668550 DOI: 10.1152/physiol.00010.2023] [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: 04/12/2023] [Revised: 09/01/2023] [Accepted: 09/01/2023] [Indexed: 09/06/2023] Open
Abstract
The array of ion channels and transporters expressed in cell membranes, collectively referred to as the transportome, is a complex and multifunctional molecular machinery; in particular, at the plasma membrane level it finely tunes the exchange of biomolecules and ions, acting as a functionally adaptive interface that accounts for dynamic plasticity in the response to environmental fluctuations and stressors. The transportome is responsible for the definition of membrane potential and its variations, participates in the transduction of extracellular signals, and acts as a filter for most of the substances entering and leaving the cell, thus enabling the homeostasis of many cellular parameters. For all these reasons, physiologists have long been interested in the expression and functionality of ion channels and transporters, in both physiological and pathological settings and across the different domains of life. Today, thanks to the high-throughput technologies of the postgenomic era, the omics approach to the study of the transportome is becoming increasingly popular in different areas of biomedical research, allowing for a more comprehensive, integrated, and functional perspective of this complex cellular apparatus. This article represents a first effort for a systematic review of the scientific literature on this topic. Here we provide a brief overview of all those studies, both primary and meta-analyses, that looked at the transportome as a whole, regardless of the biological problem or the models they used. A subsequent section is devoted to the methodological aspect by reviewing the most important public databases annotating ion channels and transporters, along with the tools they provide to retrieve such information. Before conclusions, limitations and future perspectives are also discussed.
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Affiliation(s)
- Federico Alessandro Ruffinatti
- Turin Cell Physiology Laboratory (TCP-Lab), Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Giorgia Scarpellino
- Turin Cell Physiology Laboratory (TCP-Lab), Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Giorgia Chinigò
- Turin Cell Physiology Laboratory (TCP-Lab), Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Luca Visentin
- Turin Cell Physiology Laboratory (TCP-Lab), Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Luca Munaron
- Turin Cell Physiology Laboratory (TCP-Lab), Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
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Shehzad J, Khan I, Zaheer S, Farooq A, Chaudhari SK, Mustafa G. Insights into heavy metal tolerance mechanisms of Brassica species: physiological, biochemical, and molecular interventions. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:108448-108476. [PMID: 37924172 DOI: 10.1007/s11356-023-29979-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 09/15/2023] [Indexed: 11/06/2023]
Abstract
Heavy metal (HM) contamination of soil due to anthropogenic activities has led to bioaccumulation and biomagnification, posing toxic effects on plants by interacting with vital cellular biomolecules such as DNA and proteins. Brassica species have developed complex physiological, biochemical, and molecular mechanisms for adaptability, tolerance, and survival under these conditions. This review summarizes the HM tolerance strategies of Brassica species, covering the role of root exudates, microorganisms, cell walls, cell membranes, and organelle-specific proteins. The first line of defence against HM stress in Brassica species is the avoidance strategy, which involves metal ion precipitation, root sorption, and metal exclusion. The use of plant growth-promoting microbes, Pseudomonas, Psychrobacter, and Rhizobium species effectively immobilizes HMs and reduces their uptake by Brassica roots. The roots of Brassica species efficiently detoxify metals, particularly by flavonoid glycoside exudation. The composition of the cell wall and callose deposition also plays a crucial role in enhancing HMs resistance in Brassica species. Furthermore, plasma membrane-associated transporters, BjCET, BjPCR, BjYSL, and BnMTP, reduce HM concentration by stimulating the efflux mechanism. Brassica species also respond to stress by up-regulating existing protein pools or synthesizing novel proteins associated with HM stress tolerance. This review provides new insights into the HM tolerance mechanisms of Brassica species, which are necessary for future development of HM-resistant crops.
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Affiliation(s)
- Junaid Shehzad
- Department of Plant Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Ilham Khan
- Department of Plant Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Saira Zaheer
- Department of Plant Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Atikah Farooq
- Department of Plant Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Sunbal Khalil Chaudhari
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Sargodha Campus, Sargodha, 42100, Pakistan
| | - Ghazala Mustafa
- Department of Plant Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan.
- Lishui Institute of Agriculture and Forestry Sciences, Lishui, 323000, China.
- State Agricultural Ministry Laboratory of Horticultural Crop growth and Development, Ministry of Agri-culture, Department of Horticulture, Zhejiang University, Hangzhou, 310058, China.
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24
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Caygill S, Dolan L. ATP binding cassette transporters and uridine diphosphate glycosyltransferases are ancient protein families that evolved roles in herbicide resistance through exaptation. PLoS One 2023; 18:e0287356. [PMID: 37733747 PMCID: PMC10513242 DOI: 10.1371/journal.pone.0287356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 08/25/2023] [Indexed: 09/23/2023] Open
Abstract
ATP-binding cassette (ABC) transporters actively transport various substances across membranes, while uridine diphosphate (UDP) glycosyltransferases (UGTs) are proteins that catalyse the chemical modification of various organic compounds. Both of these protein superfamilies have been associated with conferring herbicide resistance in weeds. Little is known about the evolutionary history of these protein families in the Archaeplastida. To infer the evolutionary histories of these protein superfamilies, we compared protein sequences collected from 10 species which represent distinct lineages of the Archaeplastida-the lineage including glaucophyte algae, rhodophyte algae, chlorophyte algae and the streptophytes-and generated phylogenetic trees. We show that ABC transporters were present in the last common ancestor of the Archaeplastida which lived 1.6 billion years ago, and the major clades identified in extant plants were already present then. Conversely, we only identified UGTs in members of the streptophyte lineage, which suggests a loss of these proteins in earlier diverging Archaeplastida lineages or arrival of UGTs into a common ancestor of the streptophyte lineage through horizontal gene transfer from a non-Archaeplastida eukaryote lineage. We found that within the streptophyte lineage, most diversification of the UGT protein family occurred in the vascular lineage, with 17 of the 20 clades identified in extant plants present only in vascular plants. Based on our findings, we conclude that ABC transporters and UGTs are ancient protein families which diversified during Archaeplastida evolution, which may have evolved for developmental functions as plants began to occupy new environmental niches and are now being selected to confer resistance to a diverse range of herbicides in weeds.
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Affiliation(s)
- Samuel Caygill
- Gregor Mendel Institute, Vienna, Austria
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Liam Dolan
- Gregor Mendel Institute, Vienna, Austria
- Department of Biology, University of Oxford, Oxford, United Kingdom
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25
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Lin HA, Coker HR, Howe JA, Tfaily MM, Nagy EM, Antony-Babu S, Hague S, Smith AP. Progressive drought alters the root exudate metabolome and differentially activates metabolic pathways in cotton ( Gossypium hirsutum). FRONTIERS IN PLANT SCIENCE 2023; 14:1244591. [PMID: 37711297 PMCID: PMC10499043 DOI: 10.3389/fpls.2023.1244591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 08/14/2023] [Indexed: 09/16/2023]
Abstract
Root exudates comprise various primary and secondary metabolites that are responsive to plant stressors, including drought. As increasing drought episodes are predicted with climate change, identifying shifts in the metabolome profile of drought-induced root exudation is necessary to understand the molecular interactions that govern the relationships between plants, microbiomes, and the environment, which will ultimately aid in developing strategies for sustainable agriculture management. This study utilized an aeroponic system to simulate progressive drought and recovery while non-destructively collecting cotton (Gossypium hirsutum) root exudates. The molecular composition of the collected root exudates was characterized by untargeted metabolomics using Fourier-Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR MS) and mapped to the Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Over 700 unique drought-induced metabolites were identified throughout the water-deficit phase. Potential KEGG pathways and KEGG modules associated with the biosynthesis of flavonoid compounds, plant hormones (abscisic acid and jasmonic acid), and other secondary metabolites were highly induced under severe drought, but not at the wilting point. Additionally, the associated precursors of these metabolites, such as amino acids (phenylalanine and tyrosine), phenylpropanoids, and carotenoids, were also mapped. The potential biochemical transformations were further calculated using the data generated by FT-ICR MS. Under severe drought stress, the highest number of potential biochemical transformations, including methylation, ethyl addition, and oxidation/hydroxylation, were identified, many of which are known reactions in some of the mapped pathways. With the application of FT-ICR MS, we revealed the dynamics of drought-induced secondary metabolites in root exudates in response to drought, providing valuable information for drought-tolerance strategies in cotton.
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Affiliation(s)
- Heng-An Lin
- Department of Soil and Crop Sciences, Texas A&M University and Texas A&M AgriLife Research, College Station, TX, United States
| | - Harrison R. Coker
- Department of Soil and Crop Sciences, Texas A&M University and Texas A&M AgriLife Research, College Station, TX, United States
| | - Julie A. Howe
- Department of Soil and Crop Sciences, Texas A&M University and Texas A&M AgriLife Research, College Station, TX, United States
| | - Malak M. Tfaily
- Department of Environmental Science, University of Arizona, Tucson, AZ, United States
| | - Elek M. Nagy
- Department of Plant Pathology and Microbiology, Texas A&M University and Texas A&M AgriLife Research, College Station, TX, United States
| | - Sanjay Antony-Babu
- Department of Plant Pathology and Microbiology, Texas A&M University and Texas A&M AgriLife Research, College Station, TX, United States
| | - Steve Hague
- Department of Soil and Crop Sciences, Texas A&M University and Texas A&M AgriLife Research, College Station, TX, United States
| | - A. Peyton Smith
- Department of Soil and Crop Sciences, Texas A&M University and Texas A&M AgriLife Research, College Station, TX, United States
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26
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Paweletz LC, Holtbrügge SL, Löb M, De Vecchis D, Schäfer LV, Günther Pomorski T, Justesen BH. Anionic Phospholipids Stimulate the Proton Pumping Activity of the Plant Plasma Membrane P-Type H +-ATPase. Int J Mol Sci 2023; 24:13106. [PMID: 37685912 PMCID: PMC10488199 DOI: 10.3390/ijms241713106] [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: 08/03/2023] [Revised: 08/16/2023] [Accepted: 08/18/2023] [Indexed: 09/10/2023] Open
Abstract
The activity of membrane proteins depends strongly on the surrounding lipid environment. Here, we characterize the lipid stimulation of the plant plasma membrane H+-ATPase Arabidopsis thaliana H+-ATPase isoform 2 (AHA2) upon purification and reconstitution into liposomes of defined lipid compositions. We show that the proton pumping activity of AHA2 is stimulated by anionic phospholipids, especially by phosphatidylserine. This activation was independent of the cytoplasmic C-terminal regulatory domain of the pump. Molecular dynamics simulations revealed several preferential contact sites for anionic phospholipids in the transmembrane domain of AHA2. These contact sites are partially conserved in functionally different P-type ATPases from different organisms, suggesting a general regulation mechanism by the membrane lipid environment. Our findings highlight the fact that anionic lipids play an important role in the control of H+-ATPase activity.
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Affiliation(s)
- Laura C. Paweletz
- Department of Molecular Biochemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, 44780 Bochum, Germany; (L.C.P.); (M.L.); (T.G.P.)
| | - Simon L. Holtbrügge
- Center for Theoretical Chemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, 44780 Bochum, Germany; (S.L.H.); (D.D.V.)
| | - Malina Löb
- Department of Molecular Biochemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, 44780 Bochum, Germany; (L.C.P.); (M.L.); (T.G.P.)
| | - Dario De Vecchis
- Center for Theoretical Chemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, 44780 Bochum, Germany; (S.L.H.); (D.D.V.)
| | - Lars V. Schäfer
- Center for Theoretical Chemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, 44780 Bochum, Germany; (S.L.H.); (D.D.V.)
| | - Thomas Günther Pomorski
- Department of Molecular Biochemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, 44780 Bochum, Germany; (L.C.P.); (M.L.); (T.G.P.)
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark
| | - Bo Højen Justesen
- Department of Molecular Biochemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, 44780 Bochum, Germany; (L.C.P.); (M.L.); (T.G.P.)
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27
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Rani R, Raza G, Ashfaq H, Rizwan M, Razzaq MK, Waheed MQ, Shimelis H, Babar AD, Arif M. Genome-wide association study of soybean ( Glycine max [L.] Merr.) germplasm for dissecting the quantitative trait nucleotides and candidate genes underlying yield-related traits. FRONTIERS IN PLANT SCIENCE 2023; 14:1229495. [PMID: 37636105 PMCID: PMC10450938 DOI: 10.3389/fpls.2023.1229495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 07/25/2023] [Indexed: 08/29/2023]
Abstract
Soybean (Glycine max [L.] Merr.) is one of the most significant crops in the world in terms of oil and protein. Owing to the rising demand for soybean products, there is an increasing need for improved varieties for more productive farming. However, complex correlation patterns among quantitative traits along with genetic interactions pose a challenge for soybean breeding. Association studies play an important role in the identification of accession with useful alleles by locating genomic sites associated with the phenotype in germplasm collections. In the present study, a genome-wide association study was carried out for seven agronomic and yield-related traits. A field experiment was conducted in 2015/2016 at two locations that include 155 diverse soybean germplasm. These germplasms were genotyped using SoySNP50K Illumina Infinium Bead-Chip. A total of 51 markers were identified for node number, plant height, pods per plant, seeds per plant, seed weight per plant, hundred-grain weight, and total yield using a multi-locus linear mixed model (MLMM) in FarmCPU. Among these significant SNPs, 18 were putative novel QTNs, while 33 co-localized with previously reported QTLs. A total of 2,356 genes were found in 250 kb upstream and downstream of significant SNPs, of which 17 genes were functional and the rest were hypothetical proteins. These 17 candidate genes were located in the region of 14 QTNs, of which ss715580365, ss715608427, ss715632502, and ss715620131 are novel QTNs for PH, PPP, SDPP, and TY respectively. Four candidate genes, Glyma.01g199200, Glyma.10g065700, Glyma.18g297900, and Glyma.14g009900, were identified in the vicinity of these novel QTNs, which encode lsd one like 1, Ergosterol biosynthesis ERG4/ERG24 family, HEAT repeat-containing protein, and RbcX2, respectively. Although further experimental validation of these candidate genes is required, several appear to be involved in growth and developmental processes related to the respective agronomic traits when compared with their homologs in Arabidopsis thaliana. This study supports the usefulness of association studies and provides valuable data for functional markers and investigating candidate genes within a diverse germplasm collection in future breeding programs.
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Affiliation(s)
- Reena Rani
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Ghulam Raza
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Hamza Ashfaq
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Muhammad Rizwan
- Plant Breeding and Genetics Division, Nuclear Institute of Agriculture (NIA), Tando Jam, Pakistan
| | - Muhammad Khuram Razzaq
- Soybean Research Institute, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, China
| | - Muhammad Qandeel Waheed
- Plant Breeding and Genetics Division, Nuclear Institute for Agriculture and Biology (NIAB), Constituent College Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Hussein Shimelis
- School of Agricultural, Earth and Environmental Sciences, African Centre for Crop Improvement, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Allah Ditta Babar
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Muhammad Arif
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
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28
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Naaz S, Ahmad N, Jameel MR, Al-Huqail AA, Khan F, Qureshi MI. Impact of Some Toxic Metals on Important ABC Transporters in Soybean ( Glycine max L.). ACS OMEGA 2023; 8:27597-27611. [PMID: 37546587 PMCID: PMC10399161 DOI: 10.1021/acsomega.3c03325] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 07/05/2023] [Indexed: 08/08/2023]
Abstract
In plants, ATP-binding cassette (ABC) transporters facilitate the movement of substrates across membranes using ATP for growth, development, and defense. Soils contaminated with toxic metals such as cadmium (Cd) and mercury (Hg) might adversely affect the metabolism of plants and humans. In this study, a phylogenetic relationship among soybeans' (Glycine max) ATP binding cassette (GmABCs) and other plant ABCs was analyzed using sequence information, gene structure, chromosomal distribution, and conserved motif-domain. The ontology of GmABCs indicated their active involvement in trans-membrane transport and ATPase activity. Thirty-day-old soybean plants were exposed to 100 μM CdCl2 and 100 μM HgCl2 for 10 days. Physiological and biochemical traits were altered under stress conditions. Compared to Control, GmABC transporter genes were differentially expressed in response to Cd and Hg. The qRT-PCR data showed upregulation of seven ABC transporter genes in response to Cd stress and three were downregulated. On the other hand, Hg stress upregulated four GmABC genes and downregulated six. It could be concluded that most of the ABCB and ABCG subfamily members were actively involved in heavy metal responses. Real-time expression studies suggest the function of specific ABC transporters in Cd and Hg stress response and are helpful in future research to develop stress-tolerant varieties of soybean.
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Affiliation(s)
- Sheeba Naaz
- Department
of Biotechnology, Faculty of Natural Sciences, Jamia Millia Islamia (A Central University), New Delhi 110025, India
- Department
of Biosciences, Faculty of Natural Sciences, Jamia Millia Islamia (A Central University), New Delhi 110025, India
| | - Nadeem Ahmad
- Department
of Biosciences, Faculty of Natural Sciences, Jamia Millia Islamia (A Central University), New Delhi 110025, India
| | - M. Rizwan Jameel
- Centre
for Interdisciplinary Research in Basic Sciences, Faculty of Natural
Sciences, Jamia Millia Islamia (A Central
University), New Delhi 110025, India
| | - Asma A. Al-Huqail
- Chair
of Climate Change, Environmental Development and Vegetation Cover,
Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Faheema Khan
- Chair
of Climate Change, Environmental Development and Vegetation Cover,
Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - M. Irfan Qureshi
- Department
of Biotechnology, Faculty of Natural Sciences, Jamia Millia Islamia (A Central University), New Delhi 110025, India
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Lai YH, Peng MY, Rao RY, Chen WS, Huang WT, Ye X, Yang LT, Chen LS. An Integrated Analysis of Metabolome, Transcriptome, and Physiology Revealed the Molecular and Physiological Response of Citrus sinensis Roots to Prolonged Nitrogen Deficiency. PLANTS (BASEL, SWITZERLAND) 2023; 12:2680. [PMID: 37514294 PMCID: PMC10383776 DOI: 10.3390/plants12142680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 07/08/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023]
Abstract
Citrus sinensis seedlings were supplied with a nutrient solution containing 15 (control) or 0 (nitrogen (N) deficiency) mM N for 10 weeks. Extensive metabolic and gene reprogramming occurred in 0 mM N-treated roots (RN0) to cope with N deficiency, including: (a) enhancing the ability to keep phosphate homeostasis by elevating the abundances of metabolites containing phosphorus and the compartmentation of phosphate in plastids, and/or downregulating low-phosphate-inducible genes; (b) improving the ability to keep N homeostasis by lowering the levels of metabolites containing N but not phosphorus, upregulating N compound degradation, the root/shoot ratio, and the expression of genes involved in N uptake, and resulting in transitions from N-rich alkaloids to carbon (C)-rich phenylpropanoids and phenolic compounds (excluding indole alkaloids) and from N-rich amino acids to C-rich carbohydrates and organic acids; (c) upregulating the ability to maintain energy homeostasis by increasing energy production (tricarboxylic acid cycle, glycolysis/gluconeogenesis, oxidative phosphorylation, and ATP biosynthetic process) and decreasing energy utilization for amino acid and protein biosynthesis and new root building; (d) elevating the transmembrane transport of metabolites, thus enhancing the remobilization and recycling of useful compounds; and (e) activating protein processing in the endoplasmic reticulum. RN0 had a higher ability to detoxify reactive oxygen species and aldehydes, thus protecting RN0 against oxidative injury and delaying root senescence.
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Affiliation(s)
- Yin-Hua Lai
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ming-Yi Peng
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Rong-Yu Rao
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wen-Shu Chen
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wei-Tao Huang
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xin Ye
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lin-Tong Yang
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Li-Song Chen
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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30
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Živanović BD, Ullrich K, Spasić SZ, Galland P. Auxin- and pH-induced guttation in Phycomyces sporangiophores: relation between guttation and diminished elongation growth. PROTOPLASMA 2023; 260:1109-1133. [PMID: 36622433 DOI: 10.1007/s00709-022-01833-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 12/22/2022] [Indexed: 06/07/2023]
Abstract
Guttation, the formation of exudation water, is widespread among plants and fungi, yet the underlying mechanisms remain largely unknown. We describe the conditions for inducing guttation in sporangiophores of the mucoracean fungus, Phycomyces blakesleeanus. Cultivation on peptone-enriched potato dextrose agar elicits vigorous guttation mainly below the apical growing zone, while sporangiophores raised on a glucose-mineral medium manifest only moderate guttation. Mycelia do not guttate irrespective of the employed media. The topology of guttation droplets allows identifying the non-growing part of the sporangiophore as a guttation zone, which responds to humidity and medium composition in ways that become relevant for turgor homeostasis and thus the sensor physiology of the growing zone. Apparently, the entire sporangiophore, rather than exclusively the growing zone, participates in signal reception and integration to generate a common growth output. Exogenous auxin applied to the growing zones elicits two correlated responses: (i) formation of guttation droplets in the growing and transition zones below the sporangium and (ii) a diminution of the growth rate. In sporangiophore populations, guttation-induction by exogenous control buffer occurs at low frequencies; the bias for guttation increases with increasing auxin concentration. Synthetic auxins and the transport inhibitor NPA suppress guttation completely, but leave growth rates largely unaffected. Mutants C2 carA and C148 carA madC display higher sensitivities for auxin-induced guttation compared to wild type. A working model for guttation includes aquaporins and mechanosensitive ion channels that we identified in Phycomyces by sequence domain searches.
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Affiliation(s)
- Branka D Živanović
- Institute for Multidisciplinary Research, University of Belgrade, Kneza Višeslava 1, 11030, Belgrade, Serbia.
| | - Kristian Ullrich
- Max Planck Institute for Evolutionary Biology, Department of Evolutionary Biology, August Thienemann Str. 2, 24306, Plön, Germany
| | - Sladjana Z Spasić
- Institute for Multidisciplinary Research, University of Belgrade, Kneza Višeslava 1, 11030, Belgrade, Serbia
- Singidunum University, Danijelova 32, 11010, Belgrade, Serbia
| | - Paul Galland
- Faculty of Biology, Philipps-University Marburg, Karl-Von-Frisch Str. 8, 35032, Marburg, Germany
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31
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Popova LG, Khramov DE, Nedelyaeva OI, Volkov VS. Yeast Heterologous Expression Systems for the Study of Plant Membrane Proteins. Int J Mol Sci 2023; 24:10768. [PMID: 37445944 DOI: 10.3390/ijms241310768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/23/2023] [Accepted: 06/26/2023] [Indexed: 07/15/2023] Open
Abstract
Researchers are often interested in proteins that are present in cells in small ratios compared to the total amount of proteins. These proteins include transcription factors, hormones and specific membrane proteins. However, sufficient amounts of well-purified protein preparations are required for functional and structural studies of these proteins, including the creation of artificial proteoliposomes and the growth of protein 2D and 3D crystals. This aim can be achieved by the expression of the target protein in a heterologous system. This review describes the applications of yeast heterologous expression systems in studies of plant membrane proteins. An initial brief description introduces the widely used heterologous expression systems of the baker's yeast Saccharomyces cerevisiae and the methylotrophic yeast Pichia pastoris. S. cerevisiae is further considered a convenient model system for functional studies of heterologously expressed proteins, while P. pastoris has the advantage of using these yeast cells as factories for producing large quantities of proteins of interest. The application of both expression systems is described for functional and structural studies of membrane proteins from plants, namely, K+- and Na+-transporters, various ATPases and anion transporters, and other transport proteins.
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Affiliation(s)
- Larissa G Popova
- K.A. Timiryazev Institute of Plant Physiology RAS, 127276 Moscow, Russia
| | - Dmitrii E Khramov
- K.A. Timiryazev Institute of Plant Physiology RAS, 127276 Moscow, Russia
| | - Olga I Nedelyaeva
- K.A. Timiryazev Institute of Plant Physiology RAS, 127276 Moscow, Russia
| | - Vadim S Volkov
- K.A. Timiryazev Institute of Plant Physiology RAS, 127276 Moscow, Russia
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32
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Chambard M, Albert B, Cadiou M, Auby S, Profizi C, Boulogne I. Living yeast-based biostimulants: different genes for the same results? FRONTIERS IN PLANT SCIENCE 2023; 14:1171564. [PMID: 37404542 PMCID: PMC10315835 DOI: 10.3389/fpls.2023.1171564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 05/31/2023] [Indexed: 07/06/2023]
Abstract
Nowadays, many products are available in the plant biostimulants market. Among them, living yeast-based biostimulants are also commercialized. Given the living aspect of these last products, the reproducibility of their effects should be investigated to ensure end-users' confidence. Therefore, this study aimed to compare the effects of a living yeast-based biostimulant between two different soybean cultures. These two cultures named C1 and C2 were conducted on the same variety and soil but in different locations and dates until the VC developmental stage (unifoliate leaves unrolled), with Bradyrhizobium japonicum (control and Bs condition) and with and without biostimulant coating seed treatment. The foliar transcriptomic analysis done first showed a high gene expression difference between the two cultures. Despite this first result, a secondary analysis seemed to show that this biostimulant led to a similar pathway enhancement in plants and with common genes even if the expressed genes were different between the two cultures. The pathways which seem to be reproducibly impacted by this living yeast-based biostimulant are abiotic stress tolerance and cell wall/carbohydrate synthesis. Impacting these pathways may protect the plant from abiotic stresses and maintain a higher level of sugars in plant.
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Affiliation(s)
- Marie Chambard
- Univ Rouen Normandie, GLYCOMEV UR 4358, SFR Normandie Végétal FED 4277, Innovation Chimie Carnot, IRIB, Rouen, France
| | | | | | - Sarah Auby
- Agrauxine by Lesaffre, Beaucouzé, France
| | | | - Isabelle Boulogne
- Univ Rouen Normandie, GLYCOMEV UR 4358, SFR Normandie Végétal FED 4277, Innovation Chimie Carnot, IRIB, Rouen, France
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33
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Mi Y, Cao X, Zhu X, Chen W, Meng X, Wan H, Sun W, Wang S, Chen S. Characterization and co-expression analysis of ATP-binding cassette transporters provide insight into genes related to cannabinoid transport in Cannabis sativa L. Int J Biol Macromol 2023:124934. [PMID: 37224907 DOI: 10.1016/j.ijbiomac.2023.124934] [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: 12/22/2022] [Revised: 05/06/2023] [Accepted: 05/09/2023] [Indexed: 05/26/2023]
Abstract
Plant ATP-binding cassette (ABC) transporters contribute the transport of diverse secondary metabolites. However, their roles in cannabinoid trafficking are still unsolved in Cannabis sativa. In this study, 113 ABC transporters were identified and characterized in C. sativa from their physicochemical properties, gene structure, and phylogenic relationship, as well as spatial gene expression patterns. Eventually, seven core transporters were proposed including one member in ABC subfamily B (CsABCB8) and six ABCG members (CsABCG4, CsABCG10, CsABCG11, CsABCG32, CsABCG37, and CsABCG41), harboring potential in participating cannabinoid transport, by combining phylogenetic and co-expression analysis from the gene and metabolite level. The candidate genes exhibited a high correlation with cannabinoid biosynthetic pathway genes and the cannabinoid content, and they were highly expressed where cannabinoids appropriately biosynthesized and accumulated. The findings underpin further research on the function of ABC transporters in C. sativa, especially in unveiling the mechanisms of cannabinoid transport to boost systematic and targeted metabolic engineering.
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Affiliation(s)
- Yaolei Mi
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100070, China
| | - Xue Cao
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100070, China
| | - Xuewen Zhu
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100070, China
| | - Weiqiang Chen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100070, China
| | - Xiangxiao Meng
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100070, China
| | - Huihua Wan
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100070, China
| | - Wei Sun
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100070, China
| | - Sifan Wang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100070, China.
| | - Shilin Chen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100070, China; Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China.
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34
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Chen J, Hu Y, Hao P, Tsering T, Xia J, Zhang Y, Roth O, Njo MF, Sterck L, Hu Y, Zhao Y, Geelen D, Geisler M, Shani E, Beeckman T, Vanneste S. ABCB-mediated shootward auxin transport feeds into the root clock. EMBO Rep 2023; 24:e56271. [PMID: 36718777 PMCID: PMC10074126 DOI: 10.15252/embr.202256271] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/29/2022] [Accepted: 01/10/2023] [Indexed: 02/01/2023] Open
Abstract
Although strongly influenced by environmental conditions, lateral root (LR) positioning along the primary root appears to follow obediently an internal spacing mechanism dictated by auxin oscillations that prepattern the primary root, referred to as the root clock. Surprisingly, none of the hitherto characterized PIN- and ABCB-type auxin transporters seem to be involved in this LR prepatterning mechanism. Here, we characterize ABCB15, 16, 17, 18, and 22 (ABCB15-22) as novel auxin-transporting ABCBs. Knock-down and genome editing of this genetically linked group of ABCBs caused strongly reduced LR densities. These phenotypes were correlated with reduced amplitude, but not reduced frequency of the root clock oscillation. High-resolution auxin transport assays and tissue-specific silencing revealed contributions of ABCB15-22 to shootward auxin transport in the lateral root cap (LRC) and epidermis, thereby explaining the reduced auxin oscillation. Jointly, these data support a model in which LRC-derived auxin contributes to the root clock amplitude.
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Affiliation(s)
- Jian Chen
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- Center for Plant Systems Biology, VIBGhentBelgium
| | - Yangjie Hu
- School of Plant Sciences and Food SecurityTel‐Aviv UniversityTel‐AvivIsrael
| | - Pengchao Hao
- Department of BiologyUniversity of FribourgFribourgSwitzerland
| | - Tashi Tsering
- Department of BiologyUniversity of FribourgFribourgSwitzerland
| | - Jian Xia
- Department of BiologyUniversity of FribourgFribourgSwitzerland
| | - Yuqin Zhang
- School of Plant Sciences and Food SecurityTel‐Aviv UniversityTel‐AvivIsrael
| | - Ohad Roth
- School of Plant Sciences and Food SecurityTel‐Aviv UniversityTel‐AvivIsrael
| | - Maria F Njo
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- Center for Plant Systems Biology, VIBGhentBelgium
| | - Lieven Sterck
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- Center for Plant Systems Biology, VIBGhentBelgium
| | - Yun Hu
- Section of Cell and Developmental BiologyUniversity of California San DiegoLa JollaCAUSA
| | - Yunde Zhao
- Section of Cell and Developmental BiologyUniversity of California San DiegoLa JollaCAUSA
| | - Danny Geelen
- Department of Plants and CropsGhent UniversityGhentBelgium
| | - Markus Geisler
- Department of BiologyUniversity of FribourgFribourgSwitzerland
| | - Eilon Shani
- School of Plant Sciences and Food SecurityTel‐Aviv UniversityTel‐AvivIsrael
| | - Tom Beeckman
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- Center for Plant Systems Biology, VIBGhentBelgium
| | - Steffen Vanneste
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- Center for Plant Systems Biology, VIBGhentBelgium
- Department of Plants and CropsGhent UniversityGhentBelgium
- Lab of Plant Growth AnalysisGhent University Global CampusIncheonRepublic of Korea
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35
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Hu Y, Patra P, Pisanty O, Shafir A, Belew ZM, Binenbaum J, Ben Yaakov S, Shi B, Charrier L, Hyams G, Zhang Y, Trabulsky M, Caldararu O, Weiss D, Crocoll C, Avni A, Vernoux T, Geisler M, Nour-Eldin HH, Mayrose I, Shani E. Multi-Knock-a multi-targeted genome-scale CRISPR toolbox to overcome functional redundancy in plants. NATURE PLANTS 2023; 9:572-587. [PMID: 36973414 PMCID: PMC7615256 DOI: 10.1038/s41477-023-01374-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 02/15/2023] [Indexed: 06/18/2023]
Abstract
Plant genomes are characterized by large and complex gene families that often result in similar and partially overlapping functions. This genetic redundancy severely hampers current efforts to uncover novel phenotypes, delaying basic genetic research and breeding programmes. Here we describe the development and validation of Multi-Knock, a genome-scale clustered regularly interspaced short palindromic repeat toolbox that overcomes functional redundancy in Arabidopsis by simultaneously targeting multiple gene-family members, thus identifying genetically hidden components. We computationally designed 59,129 optimal single-guide RNAs that each target two to ten genes within a family at once. Furthermore, partitioning the library into ten sublibraries directed towards a different functional group allows flexible and targeted genetic screens. From the 5,635 single-guide RNAs targeting the plant transportome, we generated over 3,500 independent Arabidopsis lines that allowed us to identify and characterize the first known cytokinin tonoplast-localized transporters in plants. With the ability to overcome functional redundancy in plants at the genome-scale level, the developed strategy can be readily deployed by scientists and breeders for basic research and to expedite breeding efforts.
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Affiliation(s)
- Yangjie Hu
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Priyanka Patra
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, CNRS, INRAE, Lyon, France
| | - Odelia Pisanty
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Anat Shafir
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Zeinu Mussa Belew
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Jenia Binenbaum
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Shir Ben Yaakov
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Bihai Shi
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, CNRS, INRAE, Lyon, France
| | - Laurence Charrier
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Gal Hyams
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Yuqin Zhang
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Maor Trabulsky
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Omer Caldararu
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Daniela Weiss
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Christoph Crocoll
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Adi Avni
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Teva Vernoux
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, CNRS, INRAE, Lyon, France
| | - Markus Geisler
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Hussam Hassan Nour-Eldin
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Itay Mayrose
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel.
| | - Eilon Shani
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel.
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36
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Cloutier S, Reimer E, Khadka B, McCallum BD. Variations in exons 11 and 12 of the multi-pest resistance wheat gene Lr34 are independently additive for leaf rust resistance. FRONTIERS IN PLANT SCIENCE 2023; 13:1061490. [PMID: 36910459 PMCID: PMC9995823 DOI: 10.3389/fpls.2022.1061490] [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: 10/04/2022] [Accepted: 12/22/2022] [Indexed: 06/18/2023]
Abstract
INTRODUCTION Characterization of germplasm collections for the wheat leaf rust gene Lr34 previously defined five haplotypes in spring wheat. All resistant lines had a 3-bp TTC deletion (null) in exon 11, resulting in the absence of a phenylalanine residue in the ABC transporter, as well as a single nucleotide C (Tyrosine in Lr34+) to T (Histidine in Lr34-) transition in exon 12. A rare haplotype present in Odesskaja 13 and Koktunkulskaja 332, both of intermediate rust resistance, had the 3-bp deletion typical of Lr34+ in exon 11 but the T nucleotide of Lr34- in exon 12. METHODS To quantify the role of each mutation in leaf rust resistance, Odesskaja 13 and Koktunkulskaja 332 were crossed to Thatcher and its near-isogenic line Thatcher-Lr34 (RL6058). Single seed descent populations were generated and evaluated for rust resistance in six different rust nurseries. RESULTS The Odesskaja 13 progeny with the TTC/T haplotype were susceptible with an average severity rating of 62.3%, the null/T haplotype progeny averaged 39.7% and the null/C haplotype was highly resistant, averaging 13.3% severity. The numbers for the Koktunkulskaja 332 crosses were similar with 63.5%, 43.5% and 23.7% severity ratings, respectively. Differences between all classes in all crosses were statistically significant, indicating that both mutations are independently additive for leaf rust resistance. The three-dimensional structural models of LR34 were used to analyze the locations and putative interference of both amino acids with the transport channel. Koktunkulskaja 332 also segregated for marker csLV46 which is linked to Lr46. Rust severity in lines with Lr34+ and csLV46+ had significantly lower rust severity ratings than those without, indicating the additivity of the two loci. DISCUSSION This has implications for the deployment of Lr34 in wheat cultivars and for the basic understanding of this important wheat multi-pest durable resistance gene.
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Affiliation(s)
- Sylvie Cloutier
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Elsa Reimer
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, Canada
| | - Bijendra Khadka
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Brent D. McCallum
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, Canada
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37
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Kaur S, Gill HS, Breiland M, Kolmer JA, Gupta R, Sehgal SK, Gill U. Identification of leaf rust resistance loci in a geographically diverse panel of wheat using genome-wide association analysis. FRONTIERS IN PLANT SCIENCE 2023; 14:1090163. [PMID: 36818858 PMCID: PMC9929074 DOI: 10.3389/fpls.2023.1090163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
Leaf rust, caused by Puccinia triticina (Pt) is among the most devastating diseases posing a significant threat to global wheat production. The continuously evolving virulent Pt races in North America calls for exploring new sources of leaf rust resistance. A diversity panel of 365 bread wheat accessions selected from a worldwide population of landraces and cultivars was evaluated at the seedling stage against four Pt races (TDBJQ, TBBGS, MNPSD and, TNBJS). A wide distribution of seedling responses against the four Pt races was observed. Majority of the genotypes displayed a susceptible response with only 28 (9.8%), 59 (13.5%), 45 (12.5%), and 29 (8.1%) wheat accessions exhibiting a highly resistant response to TDBJQ, TBBGS, MNPSD and, TNBJS, respectively. Further, we conducted a high-resolution multi-locus genome-wide association study (GWAS) using a set of 302,524 high-quality single nucleotide polymorphisms (SNPs). The GWAS analysis identified 27 marker-trait associations (MTAs) for leaf rust resistance on different wheat chromosomes of which 20 MTAs were found in the vicinity of known Lr genes, MTAs, or quantitative traits loci (QTLs) identified in previous studies. The remaining seven significant MTAs identified represent genomic regions that harbor potentially novel genes for leaf rust resistance. Furthermore, the candidate gene analysis for the significant MTAs identified various genes of interest that may be involved in disease resistance. The identified resistant lines and SNPs linked to the QTLs in this study will serve as valuable resources in wheat rust resistance breeding programs.
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Affiliation(s)
- Shivreet Kaur
- Department of Plant Pathology, North Dakota State University, Fargo, ND, United States
| | - Harsimardeep S. Gill
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, United States
| | - Matthew Breiland
- Department of Plant Pathology, North Dakota State University, Fargo, ND, United States
| | - James A. Kolmer
- Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), St. Paul, MN, United States
| | - Rajeev Gupta
- Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Fargo, ND, United States
| | - Sunish K. Sehgal
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, United States
| | - Upinder Gill
- Department of Plant Pathology, North Dakota State University, Fargo, ND, United States
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Huo X, Pan A, Lei M, Song Z, Chen Y, Wang X, Gao Y, Zhang J, Wang S, Zhao Y, Wang F, Zhang J. Genome-Wide Characterization and Functional Analysis of ABCG Subfamily Reveal Its Role in Cutin Formation in Cotton. Int J Mol Sci 2023; 24:ijms24032379. [PMID: 36768702 PMCID: PMC9916852 DOI: 10.3390/ijms24032379] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/11/2023] [Accepted: 01/20/2023] [Indexed: 01/27/2023] Open
Abstract
ATP-binding cassette transporter G (ABCG) has been shown to be engaged in export of broad-spectrum compounds with structural differences, but little is known concerning its role in cutin formation of cotton (Gossypium spp.). In this study, we conduct a genome-wide survey and detected 69, 71, 124 and 131 ABCG genes within G. arboretum, G. raimondii, G. hirsutum and G. barbadense, separately. The above ABCGs could be divided into four groups (Ia, Ib, Ic, II). Some ABCG genes such as GhABCG15, whose homologous gene transports cuticular lipid in Arabidopsis, was preferentially expressed in the development of fiber. A weighted gene co-expression network analysis (WGCNA) demonstrated that GhABCG expression was significantly associated with the amount of 16-Hydroxypalmitate (a main component of cutin precursor) in cotton fibers. Further, silencing of GhABCG15 by virus-induced gene silencing (VIGS) in cotton generated brightened and crinkled leaves as well as reduced thickness of cuticle and increased permeability. Chemical composition analysis showed the cutin content in GhABCG15-silenced leaves had decreased while the wax content had increased. Our results provide an insight for better understanding of the role of the Gossypium ABCG family and revealed the essential role of GhABCGs in cotton cutin formation.
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Affiliation(s)
- Xuehan Huo
- Life Science College, Shandong Normal University, Jinan 250358, China
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs, Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Ao Pan
- College of Bioscience & Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Mingyang Lei
- Life Science College, Shandong Normal University, Jinan 250358, China
| | - Zhangqiang Song
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs, Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Yu Chen
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs, Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Xin Wang
- Life Science College, Shandong Normal University, Jinan 250358, China
| | - Yang Gao
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs, Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Jingxia Zhang
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs, Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Shengli Wang
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs, Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Yanxiu Zhao
- Life Science College, Shandong Normal University, Jinan 250358, China
- Correspondence: (Y.Z.); (J.Z.)
| | - Furong Wang
- Life Science College, Shandong Normal University, Jinan 250358, China
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs, Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Jun Zhang
- Life Science College, Shandong Normal University, Jinan 250358, China
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs, Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan 250100, China
- Correspondence: (Y.Z.); (J.Z.)
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Mikołajczak K, Kuczyńska A, Krajewski P, Kempa M, Nuc M. Transcriptome profiling disclosed the effect of single and combined drought and heat stress on reprogramming of genes expression in barley flag leaf. FRONTIERS IN PLANT SCIENCE 2023; 13:1096685. [PMID: 36726667 PMCID: PMC9885109 DOI: 10.3389/fpls.2022.1096685] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 12/14/2022] [Indexed: 06/18/2023]
Abstract
Despite numerous studies aimed at unraveling the genetic background of barley's response to abiotic stress, the modulation of the transcriptome induced by combinatorial drought and increased temperature remains largely unrecognized. Very limited studies were done, especially on the flag leaf, which plays an important role in grain filling in cereals. In the present study, transcriptome profiles, along with chlorophyll fluorescence parameters and yield components, were compared between barley genotypes with different flag leaf sizes under single and combined drought and heat stress. High-throughput mRNA sequencing revealed 2,457 differentially expressed genes, which were functionally interpreted using Gene Ontology term enrichment analysis. The transcriptomic signature under double stress was more similar to effects caused by drought than by elevated temperature; it was also manifested at phenotypic and chlorophyll fluorescence levels. Both common and stress-specific changes in transcript abundance were identified. Genes regulated commonly across stress treatments, determining universal stress responses, were associated, among others, with responses to drought, heat, and oxidative stress. In addition, changes specific to the size of the flag leaf blade were found. Our study allowed us to identify sets of genes assigned to various processes underlying the response to drought and heat, including photosynthesis, the abscisic acid pathway, and lipid transport. Genes encoding LEA proteins, including dehydrins and heat shock proteins, were especially induced by stress treatments. Some association between genetic composition and flag leaf size was confirmed. However, there was no general coincidence between SNP polymorphism of genotypes and differential expression of genes induced by stress factors. This research provided novel insight into the molecular mechanisms of barley flag leaf that determine drought and heat response, as well as their co-occurrence.
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Wang ZF, Rouard M, Droc G, Heslop-Harrison P(JS, Ge XJ. Genome assembly of Musa beccarii shows extensive chromosomal rearrangements and genome expansion during evolution of Musaceae genomes. Gigascience 2022; 12:giad005. [PMID: 36807539 PMCID: PMC9941839 DOI: 10.1093/gigascience/giad005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 11/24/2022] [Accepted: 01/27/2023] [Indexed: 02/23/2023] Open
Abstract
BACKGROUND Musa beccarii (Musaceae) is a banana species native to Borneo, sometimes grown as an ornamental plant. The basic chromosome number of Musa species is x = 7, 10, or 11; however, M. beccarii has a basic chromosome number of x = 9 (2n = 2x = 18), which is the same basic chromosome number of species in the sister genera Ensete and Musella. Musa beccarii is in the section Callimusa, which is sister to the section Musa. We generated a high-quality chromosome-scale genome assembly of M. beccarii to better understand the evolution and diversity of genomes within the family Musaceae. FINDINGS The M. beccarii genome was assembled by long-read and Hi-C sequencing, and genes were annotated using both long Iso-seq and short RNA-seq reads. The size of M. beccarii was the largest among all known Musaceae assemblies (∼570 Mbp) due to the expansion of transposable elements and increased 45S ribosomal DNA sites. By synteny analysis, we detected extensive genome-wide chromosome fusions and fissions between M. beccarii and the other Musa and Ensete species, far beyond those expected from differences in chromosome number. Within Musaceae, M. beccarii showed a reduced number of terpenoid synthase genes, which are related to chemical defense, and enrichment in lipid metabolism genes linked to the physical defense of the cell wall. Furthermore, type III polyketide synthase was the most abundant biosynthetic gene cluster (BGC) in M. beccarii. BGCs were not conserved in Musaceae genomes. CONCLUSIONS The genome assembly of M. beccarii is the first chromosome-scale genome assembly in the Callimusa section in Musa, which provides an important genetic resource that aids our understanding of the evolution of Musaceae genomes and enhances our knowledge of the pangenome.
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Affiliation(s)
- Zheng-Feng Wang
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, Key Laboratory of Carbon Sequestration in Terrestrial Ecosystem, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Mathieu Rouard
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier, France
| | - Gaetan Droc
- CIRAD, UMR AGAP Institut, F-34398 Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Pat (J S) Heslop-Harrison
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Xue-Jun Ge
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
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Melnikova DN, Finkina EI, Bogdanov IV, Tagaev AA, Ovchinnikova TV. Features and Possible Applications of Plant Lipid-Binding and Transfer Proteins. MEMBRANES 2022; 13:2. [PMID: 36676809 PMCID: PMC9866449 DOI: 10.3390/membranes13010002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/09/2022] [Accepted: 12/14/2022] [Indexed: 06/17/2023]
Abstract
In plants, lipid trafficking within and inside the cell is carried out by lipid-binding and transfer proteins. Ligands for these proteins are building and signaling lipid molecules, secondary metabolites with different biological activities due to which they perform diverse functions in plants. Many different classes of such lipid-binding and transfer proteins have been found, but the most common and represented in plants are lipid transfer proteins (LTPs), pathogenesis-related class 10 (PR-10) proteins, acyl-CoA-binding proteins (ACBPs), and puroindolines (PINs). A low degree of amino acid sequence homology but similar spatial structures containing an internal hydrophobic cavity are common features of these classes of proteins. In this review, we summarize the latest known data on the features of these protein classes with particular focus on their ability to bind and transfer lipid ligands. We analyzed the structural features of these proteins, the diversity of their possible ligands, the key amino acids participating in ligand binding, the currently known mechanisms of ligand binding and transferring, as well as prospects for possible application.
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Affiliation(s)
- Daria N. Melnikova
- M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, the Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology (State University), 141701 Dolgoprudny, Russia
| | - Ekaterina I. Finkina
- M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, the Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia
| | - Ivan V. Bogdanov
- M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, the Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia
| | - Andrey A. Tagaev
- M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, the Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia
| | - Tatiana V. Ovchinnikova
- M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, the Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology (State University), 141701 Dolgoprudny, Russia
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Pereira Neto LG, Rossini BC, Marino CL, Toorop PE, Silva EAA. Comparative Seeds Storage Transcriptome Analysis of Astronium fraxinifolium Schott, a Threatened Tree Species from Brazil. Int J Mol Sci 2022; 23:ijms232213852. [PMID: 36430327 PMCID: PMC9696909 DOI: 10.3390/ijms232213852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/27/2022] [Accepted: 10/28/2022] [Indexed: 11/12/2022] Open
Abstract
Astronium fraxinifolium Schott (Anacardiaceae), also known as a 'gonçalo-alves', is a tree of the American tropics, with distribution in Mexico, part of Central America, Argentina, Bolivia, Brazil and Paraguay. In Brazil it is an endangered species that occurs in the Cerrado, Caatinga and in the Amazon biomes. In support of ex situ conservation, this work aimed to study two accessions with different longevity (p50) of A. fraxinifolium collected from two different geographic regions, and to evaluate the transcriptome during aging of the seeds in order to identify genes related to seed longevity. Artificial ageing was performed at a constant temperature of 45 °C and 60% relative humidity. RNA was extracted from 100 embryonic axes exposed to control and aging conditions for 21 days. The transcriptome analysis revealed differentially expressed genes such as Late Embryogenesis Abundant (LEA) genes, genes involved in the photosystem, glycine rich protein (GRP) genes, and several transcription factors associated with embryo development and ubiquitin-conjugating enzymes. Thus, these results contribute to understanding which genes play a role in seed ageing, and may serve as a basis for future functional characterization of the seed aging process in A. fraxinifolium.
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Affiliation(s)
| | - Bruno Cesar Rossini
- Biotechnology Institute, São Paulo State University “Júlio de Mesquita Filho”, Botucatu 18607-440, Brazil
- Correspondence:
| | - Celso Luis Marino
- Biotechnology Institute, São Paulo State University “Júlio de Mesquita Filho”, Botucatu 18607-440, Brazil
- Departament of Biological and Chemical Sciences, Biosciences Institute, São Paulo State University “Júlio de Mesquita Filho”, Botucatu 18618-689, Brazil
| | - Peter E. Toorop
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Wakehurst Place, Ardingly, West Sussex RH17 6TN, UK
| | - Edvaldo Aparecido Amaral Silva
- Departamento de Produção Vegetal, Faculdade de Ciências Agronômicas, Universidade Estadual Paulista, Botucatu 18610-034, Brazil
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Proteomic Analysis of Roots Response to Potassium Deficiency and the Effect of TaHAK1-4A on K+ Uptake in Wheat. Int J Mol Sci 2022; 23:ijms232113504. [PMID: 36362290 PMCID: PMC9659051 DOI: 10.3390/ijms232113504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/17/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022] Open
Abstract
Potassium (K+) is essential for plant growth and stress responses. A deficiency in soil K+ contents can result in decreased wheat quality and productivity. Thus, clarifying the molecular mechanism underlying wheat responses to low-K+ (LK) stress is critical. In this study, a tandem mass tag (TMT)-based quantitative proteomic analysis was performed to investigate the differentially abundant proteins (DAPs) in roots of the LK-tolerant wheat cultivar “KN9204” at the seedling stage after exposure to LK stress. A total of 104 DAPs were identified in the LK-treated roots. The DAPs related to carbohydrate and energy metabolism, transport, stress responses and defense, and post-translational modifications under LK conditions were highlighted. We identified a high-affinity potassium transporter (TaHAK1-4A) that was significantly up-regulated after the LK treatment. Additionally, TaHAK1-4A was mainly expressed in roots, and the encoded protein was localized in the plasma membrane. The complementation assay in yeast suggested that TaHAK1-4A mediates K+ uptake under extreme LK conditions. The overexpression of TaHAK1-4A increased the fresh weight and root length of Arabidopsis under LK conditions and improved the growth of Arabidopsis athak5 mutant seedlings, which grow poorly under LK conditions. Moreover, silencing of TaHAK1-4A in wheat roots treated with LK stress decreased the root length, dry weight, K+ concentration, and K+ influx. Accordingly, TaHAK1-4A is important for the uptake of K+ by roots exposed to LK stress. Our results reveal the protein metabolic changes in wheat induced by LK stress. Furthermore, we identified a candidate gene potentially relevant for developing wheat lines with increased K+ use efficiency.
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Pongprayoon W, Panya A, Jaresitthikunchai J, Phaonakrop N, Roytrakul S. Phosphoprotein Profile of Rice ( Oryza sativa L.) Seedlings under Osmotic Stress after Pretreatment with Chitosan. PLANTS (BASEL, SWITZERLAND) 2022; 11:2729. [PMID: 36297750 PMCID: PMC9611960 DOI: 10.3390/plants11202729] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/06/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
This study aims to identify novel chitosan (CTS)-responsive phosphoproteins in Leung Pratew 123 (LPT123) and Khao Dawk Mali 105 (KDML105) as drought-sensitive rice cultivars and differences in the CTS response. Rice seeds were soaked in CTS solution before germination, and 2- and 4-week-old rice seedlings sprayed with CTS before osmotic stress comprised the following four groups: (1) seedlings treated with distilled water; (2) seedlings treated with CTS; (3) seedlings pretreated with distilled water and subjected to osmotic stress; and (4) seedlings pretreated with CTS and subjected to osmotic stress. Phosphoproteins of leaf tissues were enriched using immobilized metal affinity chromatography (IMAC) before tryptic digestion and analysis via LC-MS. Phosphoprotein profiling analyses led to the identification of 4721 phosphoproteins representing 1052 and 1040 unique phosphoproteins in the LPT123 and KDML105 seedlings, respectively. In response to CTS pretreatment before osmotic stress, 22 differently expressed proteins were discovered, of which 10 and 12 were identified in the LPT123 and KDML105, respectively. These proteins are typically involved in signaling, transport, protein folding, protein degradation, and metabolism. This study provides fruitful data to understand the signal transduction mechanisms of rice seedlings pretreated with CTS before exposure to osmotic stress.
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Affiliation(s)
- Wasinee Pongprayoon
- Department of Biology, Faculty of Science, Burapha University, 169 Longhaad Bangsaen Rd, Saensook, Mueang, Chonburi 20131, Thailand
| | - Atikorn Panya
- Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phaholyothin Rd., Klong Luang, Pathum Thani 12120, Thailand
| | - Janthima Jaresitthikunchai
- Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phaholyothin Rd., Klong Luang, Pathum Thani 12120, Thailand
| | - Narumon Phaonakrop
- Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phaholyothin Rd., Klong Luang, Pathum Thani 12120, Thailand
| | - Sittiruk Roytrakul
- Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phaholyothin Rd., Klong Luang, Pathum Thani 12120, Thailand
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Mapuranga J, Zhang N, Zhang L, Liu W, Chang J, Yang W. Harnessing genetic resistance to rusts in wheat and integrated rust management methods to develop more durable resistant cultivars. FRONTIERS IN PLANT SCIENCE 2022; 13:951095. [PMID: 36311120 PMCID: PMC9614308 DOI: 10.3389/fpls.2022.951095] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
Wheat is one of the most important staple foods on earth. Leaf rust, stem rust and stripe rust, caused by Puccini triticina, Puccinia f. sp. graminis and Puccinia f. sp. striiformis, respectively, continue to threaten wheat production worldwide. Utilization of resistant cultivars is the most effective and chemical-free strategy to control rust diseases. Convectional and molecular biology techniques identified more than 200 resistance genes and their associated markers from common wheat and wheat wild relatives, which can be used by breeders in resistance breeding programmes. However, there is continuous emergence of new races of rust pathogens with novel degrees of virulence, thus rendering wheat resistance genes ineffective. An integration of genomic selection, genome editing, molecular breeding and marker-assisted selection, and phenotypic evaluations is required in developing high quality wheat varieties with resistance to multiple pathogens. Although host genotype resistance and application of fungicides are the most generally utilized approaches for controlling wheat rusts, effective agronomic methods are required to reduce disease management costs and increase wheat production sustainability. This review gives a critical overview of the current knowledge of rust resistance, particularly race-specific and non-race specific resistance, the role of pathogenesis-related proteins, non-coding RNAs, and transcription factors in rust resistance, and the molecular basis of interactions between wheat and rust pathogens. It will also discuss the new advances on how integrated rust management methods can assist in developing more durable resistant cultivars in these pathosystems.
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Affiliation(s)
| | | | | | | | | | - Wenxiang Yang
- College of Plant Protection, Technological Innovation Center for Biological Control of Plant Diseases and Insect Pests of Hebei Province, Hebei Agricultural University, Baoding, China
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Duan Y, Liu X, Wu J, You J, Wang F, Guo X, Tang T, Liao M, Guo J. Transcriptomic and metabolic analyses reveal the potential mechanism of increasing steroidal alkaloids in Fritillaria hupehensis through intercropping with Magnolia officinalis. FRONTIERS IN PLANT SCIENCE 2022; 13:997868. [PMID: 36275508 PMCID: PMC9585282 DOI: 10.3389/fpls.2022.997868] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
Fritillaria hupehensis, a well-known medicinal perennial herb, is used as an antitussive and an expectorant. Continuous cropping and monoculture cultivation usually negativly affect the growth of F. hupehensis. Compared with the monoculture system, the F. hupehensis-Magnolia officinalis intercropping system significantly increases the yield of F. hupehensis. However, changes in steroidal alkaloid metabolites (the most important bioactive components) and their molecular regulatory mechanisms in F. hupehensis intercropping system remain unclear. We performed comparative transcriptomic and metabolomic analyses of F. hupehensis bulbs grown in monocropping and intercropping systems. A total of 40 alkaloids were identified, including 26 steroidal alkaloids, 4 plumeranes, 3 phenolamines, 1 pyridine alkaloid, and 6 other alkaloids. The results showed that intercropping significantly increased the levels of peimine, peiminine, hupehenine, korseveridine, verticinone N-oxide, delafrine, tortifoline, pingbeinone, puqienine B, puqienine E, jervine, ussuriedine, hydroxymandelonitrile, N-feruloylputrescine, and N-benzylmethylene isomethylamine in F. hupehensis, but decreased the levels of indole, p-coumaroylputrescine, and N-benzylformamide. Transcriptome sequencing identified 11,466 differentially expressed unigenes in F. hupehensis under the intercropping system, of which 5,656 genes were up-regulated and 5,810 genes were down-regulated. We proposed a possible steroidal alkaloid biosynthesis pathway, in which 12 differentially expressed genes were identified. The higher expressions of these genes in the intercropping system positively correlated with the high accumulation of peimine, peiminine, and hupehenine, further validating our proposal. Moreover, the biological processes of oxidative phosphorylation and plant hormone signal transduction, cytochrome P450 enzymes, ATP-binding cassette transporters, and transcription factors may play pivotal roles in the regulation of steroidal alkaloid biosynthesis. This study revealed the underlying molecular mechanisms of intercropping in improving steroidal alkaloids in F. hupehensis at the transcriptome and metabolome levels. These findings provided a theoretical foundation for sustainable development of this ecological planting method.
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Affiliation(s)
- Yuanyuan Duan
- Key Laboratory of Biology and Cultivation of Chinese Herbal Medicines, Ministry of Agriculture and Rural Affairs, Institute of Chinese Herbel Medicines, Hubei Academy of Agricultural Sciences, Enshi, China
- Hubei Engineering Research Center of Under-forest Economy, Hubei Academy of Agricultural Sciences, Wuhan, China
- Hubei Engineering Research Center of Good Agricultural Practices (GAP) Production for Chinese Herbal Medicines, Institute of Chinese Herbel Medicines, Hubei Academy of Agricultural Sciences, Enshi, China
| | - Xiaohong Liu
- Hubei Engineering Research Center of Under-forest Economy, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Jiaqi Wu
- Key Laboratory of Biology and Cultivation of Chinese Herbal Medicines, Ministry of Agriculture and Rural Affairs, Institute of Chinese Herbel Medicines, Hubei Academy of Agricultural Sciences, Enshi, China
| | - Jingmao You
- Key Laboratory of Biology and Cultivation of Chinese Herbal Medicines, Ministry of Agriculture and Rural Affairs, Institute of Chinese Herbel Medicines, Hubei Academy of Agricultural Sciences, Enshi, China
- Hubei Engineering Research Center of Good Agricultural Practices (GAP) Production for Chinese Herbal Medicines, Institute of Chinese Herbel Medicines, Hubei Academy of Agricultural Sciences, Enshi, China
| | - Fanfan Wang
- Key Laboratory of Biology and Cultivation of Chinese Herbal Medicines, Ministry of Agriculture and Rural Affairs, Institute of Chinese Herbel Medicines, Hubei Academy of Agricultural Sciences, Enshi, China
- Hubei Engineering Research Center of Good Agricultural Practices (GAP) Production for Chinese Herbal Medicines, Institute of Chinese Herbel Medicines, Hubei Academy of Agricultural Sciences, Enshi, China
| | - Xiaoliang Guo
- Key Laboratory of Biology and Cultivation of Chinese Herbal Medicines, Ministry of Agriculture and Rural Affairs, Institute of Chinese Herbel Medicines, Hubei Academy of Agricultural Sciences, Enshi, China
- Hubei Engineering Research Center of Under-forest Economy, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Tao Tang
- Key Laboratory of Biology and Cultivation of Chinese Herbal Medicines, Ministry of Agriculture and Rural Affairs, Institute of Chinese Herbel Medicines, Hubei Academy of Agricultural Sciences, Enshi, China
- Hubei Engineering Research Center of Good Agricultural Practices (GAP) Production for Chinese Herbal Medicines, Institute of Chinese Herbel Medicines, Hubei Academy of Agricultural Sciences, Enshi, China
| | - Mingyan Liao
- Productivity Promotion Center of Enshi Tujia and Miao Autonomous Prefecture, Bureau of Science and Technology of Enshi Tujia and Miao Autonomous Prefecture, Enshi, China
| | - Jie Guo
- Key Laboratory of Biology and Cultivation of Chinese Herbal Medicines, Ministry of Agriculture and Rural Affairs, Institute of Chinese Herbel Medicines, Hubei Academy of Agricultural Sciences, Enshi, China
- Hubei Engineering Research Center of Under-forest Economy, Hubei Academy of Agricultural Sciences, Wuhan, China
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Ma W, Tang S, Dengzeng Z, Zhang D, Zhang T, Ma X. Root exudates contribute to belowground ecosystem hotspots: A review. Front Microbiol 2022; 13:937940. [PMID: 36274740 PMCID: PMC9581264 DOI: 10.3389/fmicb.2022.937940] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 08/30/2022] [Indexed: 09/19/2023] Open
Abstract
Root exudates are an essential carrier for material cycling, energy exchange, and information transfer between the belowground parts of plants and the soil. We synthesize current properties and regulators of root exudates and their role in the belowground ecosystem as substances cycle and signal regulation. We discussed the composition and amount of root exudates and their production mechanism, indicating that plant species, growth stage, environmental factors, and microorganisms are primary influence factors. The specific mechanisms by which root secretions mobilize the soil nutrients were summarized. First, plants improve the nutrient status of the soil by releasing organic acids for acidification and chelation. Then, root exudates accelerated the SOC turnover due to their dual impacts, forming and destabilizing aggregates and MASOC. Eventually, root exudates mediate the plant-plant interaction and plant-microbe interaction. Additionally, a summary of the current collection methods of root exudates is presented.
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Affiliation(s)
- Wenming Ma
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, China
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Nazareno ES, Fiedler J, Miller ME, Figueroa M, Kianian SF. A reference-anchored oat linkage map reveals quantitative trait loci conferring adult plant resistance to crown rust (Puccinia coronata f. sp. avenae). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:3307-3321. [PMID: 36029319 DOI: 10.1007/s00122-022-04128-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 05/13/2022] [Indexed: 06/15/2023]
Abstract
We mapped three adult plant resistance (APR) loci on oat chromosomes 4D and 6C and developed flanking KASP/PACE markers for marker-assisted selection and gene pyramiding. Using sequence orthology search and the available oat genomic and transcriptomic data, we surveyed these genomic regions for genes that may control disease resistance. Sources of durable disease resistance are needed to minimize yield losses in cultivated oat caused by crown rust (Puccinia coronata f. sp. avenae). In this study, we developed five oat recombinant inbred line mapping populations to identify sources of adult plant resistance from crosses between five APR donors and Otana, a susceptible variety. The preliminary bulk segregant mapping based on allele frequencies showed two regions in linkage group Mrg21 (Chr4D) that are associated with the APR phenotype in all five populations. Six markers from these regions in Chr4D were converted to high-throughput allele specific PCR assays and were used to genotype all individuals in each population. Simple interval mapping showed two peaks in Chr4D, named QPc.APR-4D.1 and QPc.APR-4D.2, which were detected in the OtanaA/CI4706-2 and OtanaA/CI9416-2 and in the Otana/PI189733, OtanaD/PI260616, and OtanaA/CI8000-4 populations, respectively. These results were validated by mapping two entire populations, Otana/PI189733 and OtanaA/CI9416, genotyped using Illumina HiSeq, in which polymorphisms were called against the OT3098 oat reference genome. Composite interval mapping results confirmed the presence of the two quantitative trait loci (QTL) located on oat chromosome 4D and an additional QTL with a smaller effect located on chromosome 6C. This mapping approach also narrowed down the physical intervals to between 5 and 19 Mb, and indicated that QPc.APR-4D.1, QPc.APR-4D.2, and QPc.APR-6C explained 43.4%, 38.5%, and 21.5% of the phenotypic variation, respectively. In a survey of the gene content of each QTL, several clusters of disease resistance genes that may contribute to APR were found. The allele specific PCR markers developed for these QTL regions would be beneficial for marker-assisted breeding, gene pyramiding, and future cloning of resistance genes from oat.
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Affiliation(s)
- Eric S Nazareno
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA
| | - Jason Fiedler
- US Department of Agriculture-Agricultural Research Service, Cereal Crops Research Unit, Fargo, ND, USA
| | - Marisa E Miller
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA
- Pairwise Plants, LLC. 807 East Main Street, Suite 4-100, Durham, NC, USA
| | - Melania Figueroa
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia
| | - Shahryar F Kianian
- US Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory, St. Paul, MN, USA.
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Knoch E, Kovács J, Deiber S, Tomita K, Shanmuganathan R, Serra Serra N, Okada K, Becker C, Schandry N. Transcriptional response of a target plant to benzoxazinoid and diterpene allelochemicals highlights commonalities in detoxification. BMC PLANT BIOLOGY 2022; 22:402. [PMID: 35974304 PMCID: PMC9382751 DOI: 10.1186/s12870-022-03780-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 07/28/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Plants growing in proximity to other plants are exposed to a variety of metabolites that these neighbors release into the environment. Some species produce allelochemicals to inhibit growth of neighboring plants, which in turn have evolved ways to detoxify these compounds. RESULTS In order to understand how the allelochemical-receiving target plants respond to chemically diverse compounds, we performed whole-genome transcriptome analysis of Arabidopsis thaliana exposed to either the benzoxazinoid derivative 2-amino- 3H-phenoxazin-3-one (APO) or momilactone B. These two allelochemicals belong to two very different compound classes, benzoxazinoids and diterpenes, respectively, produced by different Poaceae crop species. CONCLUSIONS Despite their distinct chemical nature, we observed similar molecular responses of A. thaliana to these allelochemicals. In particular, many of the same or closely related genes belonging to the three-phase detoxification pathway were upregulated in both treatments. Further, we observed an overlap between genes upregulated by allelochemicals and those involved in herbicide detoxification. Our findings highlight the overlap in the transcriptional response of a target plant to natural and synthetic phytotoxic compounds and illustrate how herbicide resistance could arise via pathways involved in plant-plant interaction.
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Affiliation(s)
- Eva Knoch
- LMU Biocenter, Faculty of Biology, Ludwig-Maximilians-University Munich, 82152, Martinsried, Germany
- Gregor Mendel Institute of Molecular Plant Biology GmbH, Austrian Academy of Sciences, Vienna BioCenter (VBC), 1030, Vienna, Austria
| | - Judit Kovács
- Gregor Mendel Institute of Molecular Plant Biology GmbH, Austrian Academy of Sciences, Vienna BioCenter (VBC), 1030, Vienna, Austria
| | - Sebastian Deiber
- Gregor Mendel Institute of Molecular Plant Biology GmbH, Austrian Academy of Sciences, Vienna BioCenter (VBC), 1030, Vienna, Austria
| | - Keisuke Tomita
- Agro-Biotechnology Research Center (AgTECH), Graduate School of Agricultural and Life Sciences (GSALS), The University of Tokyo, Tokyo, 113-8657, Japan
| | - Reshi Shanmuganathan
- LMU Biocenter, Faculty of Biology, Ludwig-Maximilians-University Munich, 82152, Martinsried, Germany
- Gregor Mendel Institute of Molecular Plant Biology GmbH, Austrian Academy of Sciences, Vienna BioCenter (VBC), 1030, Vienna, Austria
| | - Núria Serra Serra
- Gregor Mendel Institute of Molecular Plant Biology GmbH, Austrian Academy of Sciences, Vienna BioCenter (VBC), 1030, Vienna, Austria
| | - Kazunori Okada
- Agro-Biotechnology Research Center (AgTECH), Graduate School of Agricultural and Life Sciences (GSALS), The University of Tokyo, Tokyo, 113-8657, Japan
| | - Claude Becker
- LMU Biocenter, Faculty of Biology, Ludwig-Maximilians-University Munich, 82152, Martinsried, Germany.
- Gregor Mendel Institute of Molecular Plant Biology GmbH, Austrian Academy of Sciences, Vienna BioCenter (VBC), 1030, Vienna, Austria.
| | - Niklas Schandry
- LMU Biocenter, Faculty of Biology, Ludwig-Maximilians-University Munich, 82152, Martinsried, Germany.
- Gregor Mendel Institute of Molecular Plant Biology GmbH, Austrian Academy of Sciences, Vienna BioCenter (VBC), 1030, Vienna, Austria.
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50
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Luo B, Guang M, Yun W, Ding S, Ren S, Gao H. Camellia sinensis Chloroplast Fluoride Efflux Gene CsABCB9 Is Involved in the Fluoride Tolerance Mechanism. Int J Mol Sci 2022; 23:ijms23147756. [PMID: 35887104 PMCID: PMC9317437 DOI: 10.3390/ijms23147756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/08/2022] [Accepted: 07/12/2022] [Indexed: 12/10/2022] Open
Abstract
Soil is a main source of fluoride for plants. The tea plants (Camellia sinensis) accumulate excessive amounts of fluoride in their leaves compared to other plants, but their fluoride tolerance mechanism is poorly understood. A chloroplast fluoride efflux gene (CsABCB9) was newly discovered by using transcriptome analysis, cloned from Camellia sinensis, and its function was demonstrated in the fluoride detoxication mechanism in Escherichia coli/Xenopus laevis oocytes and Arabidopsis thaliana. CsABCB9 is expressed in tea leaves upon F− treatment. The growth of tea, E. coli, and Arabidopsis were inhibited by F− treatment. However, growth of CsABCB9-overexpression in E. coli was shown to increase with lower fluoride content under F− treatment compared to the control. Furthermore, chlorophyll, xanthophyll and soluble sugar contents of CsABCB9-overexpression in Arabidopsis were improved under F− treatment compared to the wild type. CsABCB9 functions in fluoride transport, and the mechanism by which CsABCB9 improves fluoride resistance in tea is mainly chloroplast protection through fluoride efflux.
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Affiliation(s)
- Bingbing Luo
- Anhui Province Key Lab of Farmland Ecological Conservation and Pollution Prevention, Engineering and Technology Research Center of Intelligent Manufacture and Efficient Utilization of Green Phosphorus Fertilizer of Anhui Province, College of Resources and Environment, Anhui Agricultural University, Hefei 230036, China; (M.G.); (W.Y.); (S.D.); (S.R.)
- Key Laboratory of JiangHuai Arable Land Resources Protection and Eco-Restoration, Ministry of Natural Resources, College of Resources and Environment, Anhui Agricultural University, Hefei 230036, China
- Correspondence: (B.L.); (H.G.); Tel./Fax: +86-0551-65786447 (H.G.)
| | - Min Guang
- Anhui Province Key Lab of Farmland Ecological Conservation and Pollution Prevention, Engineering and Technology Research Center of Intelligent Manufacture and Efficient Utilization of Green Phosphorus Fertilizer of Anhui Province, College of Resources and Environment, Anhui Agricultural University, Hefei 230036, China; (M.G.); (W.Y.); (S.D.); (S.R.)
- Key Laboratory of JiangHuai Arable Land Resources Protection and Eco-Restoration, Ministry of Natural Resources, College of Resources and Environment, Anhui Agricultural University, Hefei 230036, China
| | - Wenjing Yun
- Anhui Province Key Lab of Farmland Ecological Conservation and Pollution Prevention, Engineering and Technology Research Center of Intelligent Manufacture and Efficient Utilization of Green Phosphorus Fertilizer of Anhui Province, College of Resources and Environment, Anhui Agricultural University, Hefei 230036, China; (M.G.); (W.Y.); (S.D.); (S.R.)
- Key Laboratory of JiangHuai Arable Land Resources Protection and Eco-Restoration, Ministry of Natural Resources, College of Resources and Environment, Anhui Agricultural University, Hefei 230036, China
| | - Shitao Ding
- Anhui Province Key Lab of Farmland Ecological Conservation and Pollution Prevention, Engineering and Technology Research Center of Intelligent Manufacture and Efficient Utilization of Green Phosphorus Fertilizer of Anhui Province, College of Resources and Environment, Anhui Agricultural University, Hefei 230036, China; (M.G.); (W.Y.); (S.D.); (S.R.)
- Key Laboratory of JiangHuai Arable Land Resources Protection and Eco-Restoration, Ministry of Natural Resources, College of Resources and Environment, Anhui Agricultural University, Hefei 230036, China
| | - Suna Ren
- Anhui Province Key Lab of Farmland Ecological Conservation and Pollution Prevention, Engineering and Technology Research Center of Intelligent Manufacture and Efficient Utilization of Green Phosphorus Fertilizer of Anhui Province, College of Resources and Environment, Anhui Agricultural University, Hefei 230036, China; (M.G.); (W.Y.); (S.D.); (S.R.)
- Key Laboratory of JiangHuai Arable Land Resources Protection and Eco-Restoration, Ministry of Natural Resources, College of Resources and Environment, Anhui Agricultural University, Hefei 230036, China
| | - Hongjian Gao
- Anhui Province Key Lab of Farmland Ecological Conservation and Pollution Prevention, Engineering and Technology Research Center of Intelligent Manufacture and Efficient Utilization of Green Phosphorus Fertilizer of Anhui Province, College of Resources and Environment, Anhui Agricultural University, Hefei 230036, China; (M.G.); (W.Y.); (S.D.); (S.R.)
- Key Laboratory of JiangHuai Arable Land Resources Protection and Eco-Restoration, Ministry of Natural Resources, College of Resources and Environment, Anhui Agricultural University, Hefei 230036, China
- Correspondence: (B.L.); (H.G.); Tel./Fax: +86-0551-65786447 (H.G.)
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