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Khan NM, Ali A, Wan Y, Zhou G. Genome-wide identification of heavy-metal ATPases genes in Areca catechu: investigating their functionality under heavy metal exposure. BMC PLANT BIOLOGY 2024; 24:484. [PMID: 38822228 PMCID: PMC11141028 DOI: 10.1186/s12870-024-05201-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 05/26/2024] [Indexed: 06/02/2024]
Abstract
Heavy-metal ATPases (HMAs) play a vital role in plants, helping to transport heavy metal ions across cell membranes.However, insufficient data exists concerning HMAs genes within the Arecaceae family.In this study, 12 AcHMA genes were identified within the genome of Areca catechu, grouped into two main clusters based on their phylogenetic relationships.Genomic distribution analysis reveals that the AcHMA genes were unevenly distributed across six chromosomes. We further analyzed their physicochemical properties, collinearity, and gene structure.Furthermore, RNA-seq data analysis exhibited varied expressions in different tissues of A. catechu and found that AcHMA1, AcHMA2, and AcHMA7 were highly expressed in roots, leaves, pericarp, and male/female flowers. A total of six AcHMA candidate genes were selected based on gene expression patterns, and their expression in the roots and leaves was determined using RT-qPCR under heavy metal stress. Results showed that the expression levels of AcHMA1 and AcHMA3 genes were significantly up-regulated under Cd2 + and Zn2 + stress. Similarly, in response to Cu2+, the AcHMA5 and AcHMA8 revealed the highest expression in roots and leaves, respectively. In conclusion, this study will offer a foundation for exploring the role of the HMAs gene family in dealing with heavy metal stress conditions in A. catechu.
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Affiliation(s)
- Noor Muhammad Khan
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, School of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Akhtar Ali
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, School of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Yinglang Wan
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, Hainan, China
| | - Guangzhen Zhou
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, Hainan, China.
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Shomali A, Das S, Sarraf M, Johnson R, Janeeshma E, Kumar V, Aliniaeifard S, Puthur JT, Hasanuzzaman M. Modulation of plant photosynthetic processes during metal and metalloid stress, and strategies for manipulating photosynthesis-related traits. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 206:108211. [PMID: 38029618 DOI: 10.1016/j.plaphy.2023.108211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 11/02/2023] [Accepted: 11/19/2023] [Indexed: 12/01/2023]
Abstract
Metals constitute vital elements for plant metabolism and survival, acting as essential co-factors in cellular processes which are indispensable for plant growth and survival. Excess or deficient provision of metal/metalloids puts plant's life and survival at risk, thus considered a potent stress for plants. Chloroplasts as an organelle with a high metal demand form a pivotal site within the metal homeostasis network. Therefore, the metal-mediated electron transport chain (ETC) in chloroplasts is a primary target site of metal/metalloid-induced stresses. Both excess and deficient availability of metal/metalloids threatens plant's photosynthesis in several ways. Energy demands from the photosynthetic carbon reactions should be in balance with energy output of ETC. Malfunctioning of ETC components as a result of metal/metalloid stress initiates photoinhiition. A feedback inhibition from carbon fixation process also impedes the ETC. Metal stress impairs antioxidant enzyme activity, pigment biosynthesis, and stomatal function. However, genetic manipulations, nutrient management, keeping photostasis, and application of phytohormones are among strategies for coping with metal stress. Consequently, a comprehensive understanding of the underlying mechanisms of metal/metalloid stress, as well as the exploration of potential strategies to mitigate its impact on plants are imperative. This review offers a mechanistic insight into the disruption of photosynthesis regulation by metal/metalloids and highlights adaptive approaches to ameliorate their effects on plants. Focus was made on photostasis, nutrient interactions, phytohormones, and genetic interventions for mitigating metal/metalloid stresses.
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Affiliation(s)
- Aida Shomali
- Photosynthesis Laboratory, Department of Horticulture, College of Agricultural Technology (Aburaihan), University of Tehran, Tehran, Iran; Controlled Environment Agriculture Center, College of Agricultural and Natural Sciences, University of Tehran, Iran
| | - Susmita Das
- Agricultural and Ecological Research Unit, Indian Statistical Institute, Kolkata 700108, India
| | - Mohammad Sarraf
- Department of Horticultural Science, Faculty of Agriculture, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Riya Johnson
- Plant Physiology and Biochemistry Division, Department of Botany, University of Calicut, C.U. Campus P.O, Kerala 673635, India
| | - Edappayil Janeeshma
- Department of Botany, MES KEVEEYAM College, Valanchery, Malappuram, Kerala, India
| | - Vinod Kumar
- Department of Botany, Government College for Women Gandhi Nagar, Jammu 180004, Jammu and Kashmir, India
| | - Sasan Aliniaeifard
- Photosynthesis Laboratory, Department of Horticulture, College of Agricultural Technology (Aburaihan), University of Tehran, Tehran, Iran.
| | - Jos T Puthur
- Plant Physiology and Biochemistry Division, Department of Botany, University of Calicut, C.U. Campus P.O, Kerala 673635, India
| | - Mirza Hasanuzzaman
- Department of Agronomy, Faculty of Agriculture, Sher-e-Bangla Agricultural University, Dhaka 1207, Bangladesh; Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul 02447, Republic of Korea.
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Mushtaq NU, Alghamdi KM, Saleem S, Tahir I, Bahieldin A, Henrissat B, Alghamdi MK, Rehman RU, Hakeem KR. Exogenous zinc mitigates salinity stress by stimulating proline metabolism in proso millet ( Panicum miliaceum L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1053869. [PMID: 36968428 PMCID: PMC10036794 DOI: 10.3389/fpls.2023.1053869] [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: 09/26/2022] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
Salinity is one of the most concerning ecological restrictions influencing plant growth, which poses a devastating threat to global agriculture. Surplus quantities of ROS generated under stress conditions have negative effects on plants' growth and survival by damaging cellular components, including nucleic acids, lipids, proteins and carbohydrates. However, low levels of ROS are also necessary because of their role as signalling molecules in various development-related pathways. Plants possess sophisticated antioxidant systems for scavenging as well as regulating ROS levels to protect cells from damage. Proline is one such crucial non-enzymatic osmolyte of antioxidant machinery that functions in the reduction of stress. There has been extensive research on improving the tolerance, effectiveness, and protection of plants against stress, and to date, various substances have been used to mitigate the adverse effects of salt. In the present study Zinc (Zn) was applied to elucidate its effect on proline metabolism and stress-responsive mechanisms in proso millet. The results of our study indicate the negative impact on growth and development with increasing treatments of NaCl. However, the low doses of exogenous Zn proved beneficial in mitigating the effects of NaCl by improving morphological and biochemical features. In salt-treated plants, the low doses of Zn (1 mg/L, 2 mg/L) rescued the negative impact of salt (150mM) as evidenced by increase in shoot length (SL) by 7.26% and 25.5%, root length (RL) by 21.84% and 39.07% and membrane stability index (MSI) by 132.57% and 151.58% respectively.The proline content improved at all concentrations with maximum increase of 66.65% at 2 mg/L Zn. Similarly, the low doses of Zn also rescued the salt induced stress at 200mM NaCl. The enzymes related to proline biosynthesis were also improved at lower doses of Zn. In salt treated plants (150mM), Zn (1 mg/L, 2 mg/L) increased the activity of P5CS by 19.344% and 21%. The P5CR and OAT activities were also improved with maximum increase of 21.66% and 21.84% at 2 mg/L Zn respectively. Similarly, the low doses of Zn also increased the activities of P5CS, P5CR and OAT at 200mM NaCl. Whereas P5CDH enzyme activity showed a decrease of 82.5% at 2mg/L Zn+150mM NaCl and 56.7% at 2mg/L Zn+200 mM NaCl. These results strongly imply the modulatory role of Zn in maintaining of proline pool during NaCl stress.
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Affiliation(s)
- Naveed Ul Mushtaq
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar, India
| | - Khalid M. Alghamdi
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Seerat Saleem
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar, India
| | - Inayatullah Tahir
- Department of Botany, School of Biological Sciences, University of Kashmir, Srinagar, India
| | - Ahmad Bahieldin
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Mohammed Khalid Alghamdi
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Reiaz Ul Rehman
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar, India
| | - Khalid Rehman Hakeem
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Princess Dr. Najla Bint Saud Al-Saud Center for Excellence Research in Biotechnology, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Public Health, Daffodil International University, Dhaka, Bangladesh
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Sayyadi G, Niknezhad Y, Fallah H. Sodium nitroprusside ameliorates lead toxicity in rice (Oryza sativa L.) by modulating the antioxidant scavenging system, nitrogen metabolism, lead sequestration mechanism, and proline metabolism. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:24408-24423. [PMID: 36342601 DOI: 10.1007/s11356-022-23913-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 10/26/2022] [Indexed: 06/16/2023]
Abstract
As a toxic anthropogenic pollutant, lead (Pb) can be harmful to both plants and animals. Here, the effects of the application of nitric oxide (NO) donor, sodium nitroprusside (SNP, 0, 50, and 100 μM), on the morphological, biochemical, and molecular responses of rice plants under Pb (0, 150, and 300 μM) toxicity in hydroponic conditions were investigated. Pb stress decreased biomass, photosynthetic pigments, Fv/Fm value, and nitrogen (N) and increased the accumulation of hydrogen peroxide (H2O2), methylglyoxal (MG), malondialdehyde (MDA), and electrolyte leakage (EL) in rice seedlings. However, by improving the metabolism of chlorophyll and proline, SNP increased the content of chlorophyll and proline, restored the performance of the photosynthetic apparatus, and stimulated the growth of Pb-stressed rice seedlings. SNP by reducing the expression of HMA2 and increasing the expression of HMA3 and HMA4 caused the immobilization of Pb in the roots and reduced its transfer to the leaves. Adding SNP increased the activity of antioxidant enzymes and glyoxalase cycle and decreased H2O2, MG, MDA, and EL in the leaves of Pb-stressed rice seedlings. By upregulating the expression of genes GSH1, PCS, and ABCC1, SNP increased the accumulation of GSH and PCs in the roots and leaves and increased the plant's tolerance to Pb stress. By modulating the activity of enzymes involved in N metabolism, SNP increased the concentration of N and nitrate and decreased the concentration of ammonium in the leaves of Pb-stressed seedlings. Our study provides evidence that NO may become a promising tool for increasing the tolerance of rice plants to Pb toxicity.
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Affiliation(s)
- Gholamreza Sayyadi
- Department of Agronomy, Islamic Azad University of Ayatollah Amoli Branch, Islamic Azad University, Amol, Iran
| | - Yosoof Niknezhad
- Department of Agronomy, Islamic Azad University of Ayatollah Amoli Branch, Islamic Azad University, Amol, Iran.
- Department of Agronomy, Faculty of Agricultural Sciences, Medicinal Plants Research Center, Ayatollah Amoli Branch, Islamic Azad University, Amol, Iran.
| | - Hormoz Fallah
- Department of Agronomy, Islamic Azad University of Ayatollah Amoli Branch, Islamic Azad University, Amol, Iran
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Tian P, Feng YX, Li CZ, Zhang P, Yu XZ. Transcriptional analysis of heavy metal P 1B-ATPases (HMAs) elucidates competitive interaction in metal transport between cadmium and mineral elements in rice plants. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:287-297. [PMID: 35900629 DOI: 10.1007/s11356-022-22243-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 07/21/2022] [Indexed: 06/15/2023]
Abstract
Cadmium (Cd) pollution has become a major threat to crop production and quality globally. The heavy metal P1B-ATPases (HMAs) play a crucial role in metal transport in plants. In the present study, we investigated the interaction in metal transport by HMAs between Cd and mineral elements in rice plants. Rice seedlings were treated with cadmium nitrate either in the nutrient solution ("Cd+M") or in the ultrapure water ("Cd-M"). Result showed that phytotoxicity of Cd to rice seedlings was evident from both Cd treatments, judged by relative growth rate (RGR), where more severe repression (p < 0.05) of RGR was observed in the "Cd-M" treatments than the "Cd+M" treatments. More Cd (p < 0.05) was accumulated in rice tissues from the "Cd-M" treatments than the "Cd+M" treatments, while there is a significant difference (p < 0.05) in distribution and translocation of mineral elements in rice tissues between the "Cd+M" and the "Cd-M" treatments. RT-qPCR analysis displayed that the expression patterns of HMAs related genes were quite different between "Cd+M" and "Cd-M" treatments, suggesting their different regulatory effects during the transport of Cd and mineral elements within rice plants. The competition in metal transport by HMAs mainly occurs between Cd and micro-elements of Zn and Cu in rice tissues during Cd exposure. Overall, this study provides new evidence to clarify the different translocation mechanisms of HMAs in metal transport between Cd and mineral elements in rice seedlings during Cd exposure.
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Affiliation(s)
- Peng Tian
- College of Environmental Science & Engineering, Guilin University of Technology, Guilin, 541004, People's Republic of China
| | - Yu-Xi Feng
- College of Environmental Science & Engineering, Guilin University of Technology, Guilin, 541004, People's Republic of China
| | - Cheng-Zhi Li
- College of Environmental Science & Engineering, Guilin University of Technology, Guilin, 541004, People's Republic of China
| | - Ping Zhang
- College of Environmental Science & Engineering, Guilin University of Technology, Guilin, 541004, People's Republic of China
| | - Xiao-Zhang Yu
- College of Environmental Science & Engineering, Guilin University of Technology, Guilin, 541004, People's Republic of China.
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Noda Y, Furukawa J, Suzui N, Yin YG, Matsuoka K, Kawachi N, Satoh S. Characterization of zinc uptake and translocation visualized with positron-emitting 65Zn tracer and analysis of transport-related gene expression in two Lotus japonicus accessions. ANNALS OF BOTANY 2022; 130:799-810. [PMID: 35948001 PMCID: PMC9758300 DOI: 10.1093/aob/mcac101] [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: 06/13/2022] [Accepted: 08/08/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND AND AIMS Zinc (Zn) is an essential element for humans and plants. However, Zn deficiency is widespread and 25 % of the world's population is at risk of Zn deficiency. To overcome the deficiency of Zn intake, crops with high Zn content are required. However, most crop-producing areas have Zn-deficient soils, therefore crops with excellent Zn uptake/transport characteristics (i.e. high Zn efficiency) are needed. Our objective was to identify the crucial factors responsible for high Zn efficiency in the legume Lotus japonicus. METHODS We evaluated Zn efficiency by static and real-time visualization of radioactive Zn (65Zn) uptake/transport in two L. japonicus accessions, MG-20 and B-129, that differ in Zn efficiency. The combination of visualization methods verified the dynamics of Zn accumulation and transport within the plant. We compared gene expression under a normal Zn concentration (control) and Zn deficiency to evaluate genetic factors that may determine the differential Zn efficiency of the accessions. KEY RESULTS The accession B-129 accumulated almost twice the amount of Zn as MG-20. In the static 65Zn images, 65Zn accumulated in meristematic tissues, such as root tips and the shoot apex, in both accessions. The positron-emitting tracer imaging system (PETIS), which follows the transport process in real time, revealed that 65Zn transport to the shoot was more rapid in B-129 than in MG-20. Many genes associated with Zn uptake and transport were more highly expressed in B-129 than in MG-20 under the control condition. These gene expression patterns under Zn deficiency differed from those under the control Zn condition. CONCLUSIONS PETIS confirmed that the real-time transport of 65Zn to the shoot was faster in B-129 than in MG-20. The high Zn efficiency of B-129 may be due to the elevated expression of a suite of Zn uptake- and transport-related genes.
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Affiliation(s)
- Yusaku Noda
- Takasaki Advanced Radiation Research Institute, National Institutes for Quantum Science and Technology (QST), Gunma, 370-1292Japan
| | - Jun Furukawa
- Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, 305-8572Japan
| | - Nobuo Suzui
- Takasaki Advanced Radiation Research Institute, National Institutes for Quantum Science and Technology (QST), Gunma, 370-1292Japan
| | - Yong-Gen Yin
- Takasaki Advanced Radiation Research Institute, National Institutes for Quantum Science and Technology (QST), Gunma, 370-1292Japan
| | - Keita Matsuoka
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki, 305-8572Japan
| | - Naoki Kawachi
- Takasaki Advanced Radiation Research Institute, National Institutes for Quantum Science and Technology (QST), Gunma, 370-1292Japan
| | - Shinobu Satoh
- Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, 305-8572Japan
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Goud CA, Satturu V, Malipatil R, Viswanath A, Semalaiyappan J, Kudapa H, Rathod S, Rathore A, Govindaraj M, Thirunavukkarasu N. Identification of iron and zinc responsive genes in pearl millet using genome-wide RNA-sequencing approach. Front Nutr 2022; 9:884381. [PMID: 36438771 PMCID: PMC9682069 DOI: 10.3389/fnut.2022.884381] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 10/14/2022] [Indexed: 06/30/2024] Open
Abstract
Pearl millet (Pennisetum glaucum L.), an important source of iron (Fe) and zinc (Zn) for millions of families in dryland tropics, helps in eradicating micronutrient malnutrition. The crop is rich in Fe and Zn, therefore, identification of the key genes operating the mineral pathways is an important step to accelerate the development of biofortified cultivars. In a first-of-its-kind experiment, leaf and root samples of a pearl millet inbred ICMB 1505 were exposed to combinations of Fe and Zn stress conditions using the hydroponics method, and a whole-genome transcriptome assay was carried out to characterize the differentially expressed genes (DEGs) and pathways. A total of 37,093 DEGs under different combinations of stress conditions were identified, of which, 7,023 and 9,996 DEGs were reported in the leaf and root stress treatments, respectively. Among the 10,194 unique DEGs, 8,605 were annotated to cellular, biological, and molecular functions and 458 DEGs were assigned to 39 pathways. The results revealed the expression of major genes related to the mugineic acid pathway, phytohormones, chlorophyll biosynthesis, photosynthesis, and carbohydrate metabolism during Fe and Zn stress. The cross-talks between the Fe and Zn provided information on their dual and opposite regulation of key uptake and transporter genes under Fe and Zn deficiency. SNP haplotypes in rice, maize, sorghum, and foxtail millet as well as in Arabidopsis using pearl millet Fe and Zn responsive genes could be used for designing the markers in staple crops. Our results will assist in developing Fe and Zn-efficient pearl millet varieties in biofortification breeding programs and precision delivery mechanisms to ameliorate malnutrition in South Asia and Sub-Saharan Africa.
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Affiliation(s)
- Chengeshpur Anjali Goud
- Institute of Biotechnology, Professor Jayashankar Telangana State Agricultural University, Hyderabad, India
| | - Vanisri Satturu
- Institute of Biotechnology, Professor Jayashankar Telangana State Agricultural University, Hyderabad, India
| | - Renuka Malipatil
- Genomics and Molecular Breeding Lab, ICAR-Indian Institute of Millets Research, Hyderabad, India
| | - Aswini Viswanath
- Genomics and Molecular Breeding Lab, ICAR-Indian Institute of Millets Research, Hyderabad, India
| | - Janani Semalaiyappan
- Genomics and Molecular Breeding Lab, ICAR-Indian Institute of Millets Research, Hyderabad, India
| | - Himabindu Kudapa
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Santosha Rathod
- Agricultural Statistics, ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - Abhishek Rathore
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Excellence in Breeding Platform, The International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Mahalingam Govindaraj
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- HarvestPlus, Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT), Cali, Colombia
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OsNAC15 Regulates Tolerance to Zinc Deficiency and Cadmium by Binding to OsZIP7 and OsZIP10 in Rice. Int J Mol Sci 2022; 23:ijms231911771. [PMID: 36233067 PMCID: PMC9569620 DOI: 10.3390/ijms231911771] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 09/26/2022] [Accepted: 09/29/2022] [Indexed: 11/16/2022] Open
Abstract
Zinc (Zn) deficiency and cadmium (Cd) stress are severe threats to the growth and development of plants. Increasing Zn content and/or decreasing Cd content in grain are also important objectives of rice breeding. However, the molecular mechanisms of Zn deficiency tolerance (ZDT) and Cd stress tolerance (CDT) are largely unknown in rice. Here, we report that a NAM/CUC2-like transcription factor, OsNAC15, contributes to ZDT and CDT in rice. Knockout of OsNAC15 reduced ZDT and CDT at the vegetative stage. OsNAC15 expresses in all tissues of different developmental stages, and is repressed by Zn deficiency and induced by Cd stress. OsNAC15 is a functional transcription factor with transactivation and DNA binding activities. Expression analysis of rice ZIP family genes suggested that the knockout of OsNAC15 activates or inhibits their transcriptions under Zn deficiency or Cd stress conditions. The yeast one-hybrid assay, transient transcriptional activity assay using the dual-luciferase reporter system and electrophoretic mobility shift assay demonstrated that OsNAC15 directly binds to the zinc deficiency-responsive element motifs in the promoters of OsZIP7 and OsZIP10 to repress their transcriptions. The OsNAC15–OsZIP7/10 module is an essential foundation for further study on the regulatory mechanisms of ZDT and CDT in rice.
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Banerjee A, Roychoudhury A. Dissecting the phytohormonal, genomic and proteomic regulation of micronutrient deficiency during abiotic stresses in plants. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01099-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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10
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Amini S, Arsova B, Hanikenne M. The molecular basis of zinc homeostasis in cereals. PLANT, CELL & ENVIRONMENT 2022; 45:1339-1361. [PMID: 35037265 DOI: 10.1111/pce.14257] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 11/12/2021] [Accepted: 12/16/2021] [Indexed: 06/14/2023]
Abstract
Plants require zinc (Zn) as an essential cofactor for diverse molecular, cellular and physiological functions. Zn is crucial for crop yield, but is one of the most limiting micronutrients in soils. Grasses like rice, wheat, maize and barley are crucial sources of food and nutrients for humans. Zn deficiency in these species therefore not only reduces annual yield but also directly results in Zn malnutrition of more than two billion people in the world. There has been good progress in understanding Zn homeostasis and Zn deficiency mechanisms in plants. However, our current knowledge of monocots, including grasses, remains insufficient. In this review, we provide a summary of our knowledge of molecular Zn homeostasis mechanisms in monocots, with a focus on important cereal crops. We additionally highlight divergences in Zn homeostasis of monocots and the dicot model Arabidopsis thaliana, as well as important gaps in our knowledge that need to be addressed in future research on Zn homeostasis in cereal monocots.
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Affiliation(s)
- Sahand Amini
- InBioS-PhytoSystems, Translational Plant Biology, University of Liège, Liège, Belgium
| | - Borjana Arsova
- Root Dynamics Group, IBG-2 - Plant Sciences, Institut für Bio- und Geowissenschaften (IBG), Forschungszentrum, Jülich, Germany
| | - Marc Hanikenne
- InBioS-PhytoSystems, Translational Plant Biology, University of Liège, Liège, Belgium
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11
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Huang S, Yamaji N, Feng Ma J. Zinc transport in rice: how to balance optimal plant requirements and human nutrition. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:1800-1808. [PMID: 34727182 DOI: 10.1093/jxb/erab478] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 10/27/2021] [Indexed: 05/15/2023]
Abstract
Zinc (Zn) is an essential micronutrient for both plants and animals, while its deficiency in crops and humans is a global problem that affects both crop productivity and human health. Since plants and humans differ in their Zn requirements, it is crucial to balance plant nutrition and human nutrition for Zn. In this review, we focus on the transport system of Zn from soil to grain in rice (Oryza sativa), which is a major dietary source of Zn for people subsiding on rice-based diets. We describe transporters belonging to the different families that are involved in the uptake, vacuolar sequestration, root-to-shoot translocation, and distribution of Zn, and discuss their mechanisms of regulation. We give examples for enhancing Zn accumulation and bioavailability in rice grains through the manipulation of genes that are highly expressed in the nodes, where Zn is deposited at high concentrations. Finally, we provide our perspectives on breeding rice cultivars with both increased tolerance to Zn-deficiency stress and high Zn density in the grains.
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Affiliation(s)
- Sheng Huang
- Institute of Plant Science and Resources, Okayama University, Chuo 2-20-1, Kurashiki, Japan
| | - Naoki Yamaji
- Institute of Plant Science and Resources, Okayama University, Chuo 2-20-1, Kurashiki, Japan
| | - Jian Feng Ma
- Institute of Plant Science and Resources, Okayama University, Chuo 2-20-1, Kurashiki, Japan
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12
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Bashir K, Ishimaru Y. Challenges and opportunities to regulate mineral transport in rice. Biosci Biotechnol Biochem 2021; 86:12-22. [PMID: 34661659 DOI: 10.1093/bbb/zbab180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 10/06/2021] [Indexed: 11/13/2022]
Abstract
Iron (Fe) is an essential mineral for plants, and its deficiency as well as toxicity severely affects plant growth and development. Although Fe is ubiquitous in mineral soils, its acquisition by plants is difficult to regulate particularly in acidic and alkaline soils. Under alkaline conditions, where lime is abundant, Fe and other mineral elements are sparingly soluble. In contrast, under low pH conditions, especially in paddy fields, Fe toxicity could occur. Fe uptake is complicated and could be integrated with copper (Cu), manganese (Mn), zinc (Zn), and cadmium (Cd) uptake. Plants have developed sophisticated mechanisms to regulate the Fe uptake from soil and its transport to root and above-ground parts. Here, we review recent developments in understanding metal transport and discuss strategies to effectively regulate metal transport in plants with a particular focus on rice.
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Affiliation(s)
- Khurram Bashir
- Department of Biology, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, Pakistan
| | - Yasuhiro Ishimaru
- Department of Biomolecular Engineering, Tohoku University, Aoba-ku, Sendai, Japan
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13
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Cheah BH, Chen YL, Lo JC, Tang IC, Yeh KC, Lin YF. Divalent nutrient cations: Friend and foe during zinc stress in rice. PLANT, CELL & ENVIRONMENT 2021; 44:3358-3375. [PMID: 34278584 DOI: 10.1111/pce.14154] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 04/27/2021] [Accepted: 07/10/2021] [Indexed: 06/13/2023]
Abstract
Zn deficiency is the most common micronutrient deficit in rice but Zn is also a widespread industrial pollutant. Zn deficiency responses in rice are well documented, but comparative responses to Zn deficiency and excess have not been reported. Therefore, we compared the physiological, transcriptional and biochemical properties of rice subjected to Zn starvation or excess at early and later treatment stages. Both forms of Zn stress inhibited root and shoot growth. Gene ontology analysis of differentially expressed genes highlighted the overrepresentation of Zn transport and antioxidative defense for both Zn stresses, whereas diterpene biosynthesis was solely induced by excess Zn. Divalent cations (Fe, Cu, Ca, Mn and Mg) accumulated in Zn-deficient shoots but Mg and Mn were depleted in the Zn excess shoots, mirroring the gene expression of non-specific Zn transporters and chelators. Ascorbate peroxidase activity was induced after 14 days of Zn starvation, scavenging H2 O2 more effectively to prevent leaf chlorosis via the Fe-dependent Fenton reaction. Conversely, excess Zn triggered the expression of genes encoding Mg/Mn-binding proteins (OsCPS2/4 and OsKSL4/7) required for antimicrobial diterpenoid biosynthesis. Our study reveals the potential role of divalent cations in the shoot, driving the unique responses of rice to each form of Zn stress.
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Affiliation(s)
- Boon Huat Cheah
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
| | - Yu-Ling Chen
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
| | - Jing-Chi Lo
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
- Department of Horticulture and Biotechnology, Chinese Culture University, Taipei, Taiwan
| | - I-Chien Tang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Kuo-Chen Yeh
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Ya-Fen Lin
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
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14
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Ali S, Tyagi A, Bae H. Ionomic Approaches for Discovery of Novel Stress-Resilient Genes in Plants. Int J Mol Sci 2021; 22:7182. [PMID: 34281232 PMCID: PMC8267685 DOI: 10.3390/ijms22137182] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/25/2021] [Accepted: 06/29/2021] [Indexed: 01/03/2023] Open
Abstract
Plants, being sessile, face an array of biotic and abiotic stresses in their lifespan that endanger their survival. Hence, optimized uptake of mineral nutrients creates potential new routes for enhancing plant health and stress resilience. Recently, minerals (both essential and non-essential) have been identified as key players in plant stress biology, owing to their multifaceted functions. However, a realistic understanding of the relationship between different ions and stresses is lacking. In this context, ionomics will provide new platforms for not only understanding the function of the plant ionome during stresses but also identifying the genes and regulatory pathways related to mineral accumulation, transportation, and involvement in different molecular mechanisms under normal or stress conditions. This article provides a general overview of ionomics and the integration of high-throughput ionomic approaches with other "omics" tools. Integrated omics analysis is highly suitable for identification of the genes for various traits that confer biotic and abiotic stress tolerance. Moreover, ionomics advances being used to identify loci using qualitative trait loci and genome-wide association analysis of element uptake and transport within plant tissues, as well as genetic variation within species, are discussed. Furthermore, recent developments in ionomics for the discovery of stress-tolerant genes in plants have also been addressed; these can be used to produce more robust crops with a high nutritional value for sustainable agriculture.
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Affiliation(s)
- Sajad Ali
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Korea;
| | - Anshika Tyagi
- National Institute for Plant Biotechnology, New Delhi 110012, India;
| | - Hanhong Bae
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Korea;
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15
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Kakei Y, Masuda H, Nishizawa NK, Hattori H, Aung MS. Elucidation of Novel cis-Regulatory Elements and Promoter Structures Involved in Iron Excess Response Mechanisms in Rice Using a Bioinformatics Approach. FRONTIERS IN PLANT SCIENCE 2021; 12:660303. [PMID: 34149757 PMCID: PMC8207140 DOI: 10.3389/fpls.2021.660303] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 04/06/2021] [Indexed: 05/24/2023]
Abstract
Iron (Fe) excess is a major constraint on crop production in flooded acidic soils, particularly in rice cultivation. Under Fe excess, plants activate a complex mechanism and network regulating Fe exclusion by roots and isolation in various tissues. In rice, the transcription factors and cis-regulatory elements (CREs) that regulate Fe excess response mechanisms remain largely elusive. We previously reported comprehensive microarray analyses of several rice tissues in response to various levels of Fe excess stress. In this study, we further explored novel CREs and promoter structures in rice using bioinformatics approaches with this microarray data. We first performed network analyses to predict Fe excess-related CREs through the categorization of the gene expression patterns of Fe excess-responsive transcriptional regulons, and found four major expression clusters: Fe storage type, Fe chelator type, Fe uptake type, and WRKY and other co-expression type. Next, we explored CREs within these four clusters of gene expression types using a machine-learning method called microarray-associated motif analyzer (MAMA), which we previously established. Through a comprehensive bioinformatics approach, we identified a total of 560 CRE candidates extracted by MAMA analyses and 42 important conserved sequences of CREs directly related to the Fe excess response in various rice tissues. We explored several novel cis-elements as candidate Fe excess CREs including GCWGCWGC, CGACACGC, and Myb binding-like motifs. Based on the presence or absence of candidate CREs using MAMA and known PLACE CREs, we found that the Boruta-XGBoost model explained expression patterns with high accuracy of about 83%. Enriched sequences of both novel MAMA CREs and known PLACE CREs led to high accuracy expression patterns. We also found new roles of known CREs in the Fe excess response, including the DCEp2 motif, IDEF1-, Zinc Finger-, WRKY-, Myb-, AP2/ERF-, MADS- box-, bZIP and bHLH- binding sequence-containing motifs among Fe excess-responsive genes. In addition, we built a molecular model and promoter structures regulating Fe excess-responsive genes based on new finding CREs. Together, our findings about Fe excess-related CREs and conserved sequences will provide a comprehensive resource for discovery of genes and transcription factors involved in Fe excess-responsive pathways, clarification of the Fe excess response mechanism in rice, and future application of the promoter sequences to produce genotypes tolerant of Fe excess.
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Affiliation(s)
- Yusuke Kakei
- Institute of Vegetable and Floriculture Science, Research Center for Agricultural Information Technology, National Agriculture and Food Research Organization, Ibaraki, Japan
| | - Hiroshi Masuda
- Faculty of Bioresource Sciences, Department of Biological Production, Akita Prefectural University, Akita, Japan
| | - Naoko K. Nishizawa
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Ishikawa, Japan
| | - Hiroyuki Hattori
- Faculty of Bioresource Sciences, Department of Biological Production, Akita Prefectural University, Akita, Japan
| | - May Sann Aung
- Faculty of Bioresource Sciences, Department of Biological Production, Akita Prefectural University, Akita, Japan
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Ishikawa, Japan
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16
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Salavati J, Fallah H, Niknejad Y, Barari Tari D. Methyl jasmonate ameliorates lead toxicity in Oryza sativa by modulating chlorophyll metabolism, antioxidative capacity and metal translocation. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:1089-1104. [PMID: 34092952 PMCID: PMC8140021 DOI: 10.1007/s12298-021-00993-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 03/15/2021] [Accepted: 04/07/2021] [Indexed: 05/21/2023]
Abstract
Lead (Pb) not only negatively alters plant growth and yield but may also have potentially toxic risks to human health. Nevertheless, the interaction between rice (Oryza sativa L.) plants and the molecular cell dynamics induced by lead-methyl jasmonate (MJ) remains unknown. Here, plants were hydroponically exposed to Pb (150 and 300 µM) alone or in combination with 0.5 and 1 µM MJ. The application of MJ modulated the expression of the HMAs, PCS1, PCS2 and ABCC1 genes, thereby immobilizing the Pb in the roots and lessening its translocation to the aerial parts of the rice plant. The supplementation of MJ improved the growth and yield of Pb-stressed rice by adjusting the proline and chlorophyll metabolism, increasing the phytochelatins (PCs) accumulation and diminishing the accumulation of Pb in the shoots. the application of MJ alleviated the oxidative stress of rice plants exposed to Pb toxicity by enhancing the activity of antioxidant enzymes and enzymes of the glyoxalase system (glyoxalase I and II) and decreasing the endogenous levels of malondialdehyde (MDA), hydrogen peroxide (H2O2) and methylglyoxal (MG). Therefore, the results of the present study could provide a molecular insight and cellular interplay scheme for the development of a promising strategy in Pb-contaminated areas to produce healthy food.
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Affiliation(s)
- Javad Salavati
- Department of Agronomy, Islamic Azad University of Ayatollah Amoli Branch, Islamic Azad University, Amol, Iran
| | - Hormoz Fallah
- Department of Agronomy, Islamic Azad University of Ayatollah Amoli Branch, Islamic Azad University, Amol, Iran
| | - Yosoof Niknejad
- Department of Agronomy, Islamic Azad University of Ayatollah Amoli Branch, Islamic Azad University, Amol, Iran
| | - Davood Barari Tari
- Department of Agronomy, Islamic Azad University of Ayatollah Amoli Branch, Islamic Azad University, Amol, Iran
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17
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Bashir K, Ahmad Z, Kobayashi T, Seki M, Nishizawa NK. Roles of subcellular metal homeostasis in crop improvement. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:2083-2098. [PMID: 33502492 DOI: 10.1093/jxb/erab018] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 01/25/2021] [Indexed: 06/12/2023]
Abstract
Improvement of crop production in response to rapidly changing environmental conditions is a serious challenge facing plant breeders and biotechnologists. Iron (Fe), zinc (Zn), manganese (Mn), and copper (Cu) are essential micronutrients for plant growth and reproduction. These minerals are critical to several cellular processes including metabolism, photosynthesis, and cellular respiration. Regulating the uptake and distribution of these minerals could significantly improve plant growth and development, ultimately leading to increased crop production. Plant growth is limited by mineral deficiency, but on the other hand, excess Fe, Mn, Cu, and Zn can be toxic to plants; therefore, their uptake and distribution must be strictly regulated. Moreover, the distribution of these metals among subcellular organelles is extremely important for maintaining optimal cellular metabolism. Understanding the mechanisms controlling subcellular metal distribution and availability would enable development of crop plants that are better adapted to challenging and rapidly changing environmental conditions. Here, we describe advances in understanding of subcellular metal homeostasis, with a particular emphasis on cellular Fe homeostasis in Arabidopsis and rice, and discuss strategies for regulating cellular metabolism to improve plant production.
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Affiliation(s)
- Khurram Bashir
- Department of Biology, Syed Babar Ali School of Science and Engineering, Lahore, Pakistan
- Plant Genomics Network Research Team, Center for Sustainable Resource Science, Suehiro, Tsurumi Ku, Yokohama, Kanagawa, Japan
| | - Zarnab Ahmad
- Plant Genomics Network Research Team, Center for Sustainable Resource Science, Suehiro, Tsurumi Ku, Yokohama, Kanagawa, Japan
| | - Takanori Kobayashi
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi, Ishikawa, Japan
| | - Motoaki Seki
- Plant Genomics Network Research Team, Center for Sustainable Resource Science, Suehiro, Tsurumi Ku, Yokohama, Kanagawa, Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
- Plant Epigenome Regulation Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
| | - Naoko K Nishizawa
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi, Ishikawa, Japan
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, Japan
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18
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Lu X, Liu S, Zhi S, Chen J, Ye G. Comparative transcriptome profile analysis of rice varieties with different tolerance to zinc deficiency. PLANT BIOLOGY (STUTTGART, GERMANY) 2021; 23:375-390. [PMID: 33296551 DOI: 10.1111/plb.13227] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 11/30/2020] [Indexed: 06/12/2023]
Abstract
Zinc (Zn) is an indispensable element for rice growth. Zn deficiency results in brown blotches and streaks 2-3 weeks after transplanting, as well as stunting, reduced tillering, and low productivity of rice plants. These processes are controlled by different families of expressed genes. A comparative transcriptome profile analysis was conducted using the roots of two Zn deficiency tolerant varieties (UCP122 and KALIBORO26) and two sensitive varieties (IR26 and IR64) by merging data from untreated control (CK) and Zn deficiency treated samples. Results revealed a total of 4,688 differentially expressed genes (DEGs) between the normal Zn and deficient conditions, with 2,702 and 1,489 unique DEGs upregulated and downregulated, respectively. Functional enrichment analysis identified transcription factors (TFs), such as WRKY, MYB, ERF, and bHLH which are important in the regulation of the Zn deficiency response. Furthermore, chitinases, jasmonic acid, and phenylpropanoid pathways were found to be important in the Zn deficiency response. The metal tolerance protein (MTP) genes also appeared to play an important role in conferring tolerance to Zn deficiency. A heavy metal-associated domain-containing protein 7 was associated with tolerance to Zn deficiency and negatively regulated downstream genes. Collectively, our findings provide valuable expression patterns and candidate genes for the study of molecular mechanisms underlying the response to Zn deficiency and for improvements in breeding for tolerance to Zn deficiency in rice.
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Affiliation(s)
- X Lu
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute in Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - S Liu
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute in Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Group of Crop Genetics and Breeding, Jiangxi Agricultural University, Nanchang, China
| | - S Zhi
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute in Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- College of Resources and Environment, Henan Agricultural University, Zhengzhou, China
| | - J Chen
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute in Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - G Ye
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute in Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Group of Crop Genetics and Breeding, Jiangxi Agricultural University, Nanchang, China
- Strategic Innovation Platform, International Rice Research Institute, Metro Manila, Philippines
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19
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Kumar S, Kumar S, Mohapatra T. Interaction Between Macro- and Micro-Nutrients in Plants. FRONTIERS IN PLANT SCIENCE 2021; 12:665583. [PMID: 34040623 PMCID: PMC8141648 DOI: 10.3389/fpls.2021.665583] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 04/06/2021] [Indexed: 05/03/2023]
Abstract
Nitrogen (N), phosphorus (P), sulfur (S), zinc (Zn), and iron (Fe) are some of the vital nutrients required for optimum growth, development, and productivity of plants. The deficiency of any of these nutrients may lead to defects in plant growth and decreased productivity. Plant responses to the deficiency of N, P, S, Fe, or Zn have been studied mainly as a separate event, and only a few reports discuss the molecular basis of biological interaction among the nutrients. Macro-nutrients like N, P, and/or S not only show the interacting pathways for each other but also affect micro-nutrient pathways. Limited reports are available on the investigation of two-by-two or multi-level nutrient interactions in plants. Such studies on the nutrient interaction pathways suggest that an MYB-like transcription factor, phosphate starvation response 1 (PHR1), acts as a master regulator of N, P, S, Fe, and Zn homeostasis. Similarly, light-responsive transcription factors were identified to be involved in modulating nutrient responses in Arabidopsis. This review focuses on the recent advances in our understanding of how plants coordinate the acquisition, transport, signaling, and interacting pathways for N, P, S, Fe, and Zn nutrition at the molecular level. Identification of the important candidate genes for interactions between N, P, S, Fe, and/or Zn metabolic pathways might be useful for the breeders to improve nutrient use efficiency and yield/quality of crop plants. Integrated studies on pathways interactions/cross-talks between macro- and micro-nutrients in the agronomically important crop plants would be essential for sustainable agriculture around the globe, particularly under the changing climatic conditions.
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Affiliation(s)
- Suresh Kumar
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
- *Correspondence: Suresh Kumar, ; , orcid.org/0000-0002-7127-3079
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20
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Huang S, Sasaki A, Yamaji N, Okada H, Mitani-Ueno N, Ma JF. The ZIP Transporter Family Member OsZIP9 Contributes To Root Zinc Uptake in Rice under Zinc-Limited Conditions. PLANT PHYSIOLOGY 2020; 183:1224-1234. [PMID: 32371522 PMCID: PMC7333685 DOI: 10.1104/pp.20.00125] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 04/24/2020] [Indexed: 05/21/2023]
Abstract
Zinc (Zn) is an important essential micronutrient for plants and humans; however, the exact transporter responsible for root zinc uptake from soil has not been identified. Here, we found that OsZIP9, a member of the ZRT-IRT-related protein, is involved in Zn uptake in rice (Oryza sativa) under Zn-limited conditions. OsZIP9 was mainly localized to the plasma membrane and showed transport activity for Zn in yeast (Saccharomyces cerevisiae). Expression pattern analysis showed that OsZIP9 was mainly expressed in the roots throughout all growth stages and its expression was upregulated by Zn-deficiency. Furthermore, OsZIP9 was expressed in the exodermis and endodermis of root mature regions. For plants grown in a hydroponic solution with low Zn concentration, knockout of OsZIP9 significantly reduced plant growth, which was accompanied by decreased Zn concentrations in both the root and shoot. However, plant growth and Zn accumulation did not differ between knockout lines and wild-type rice under Zn-sufficient conditions. When grown in soil, Zn concentrations in the shoots and grains of knockout lines were decreased to half of wild-type rice, whereas the concentrations of other mineral nutrients were not altered. A short-term kinetic experiment with stable isotope 67Zn showed that 67Zn uptake in knockout lines was much lower than that in wild-type rice. Combined, these results indicate that OsZIP9 localized at the root exodermis and endodermis functions as an influx transporter of Zn and contributes to Zn uptake under Zn-limited conditions in rice.
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Affiliation(s)
- Sheng Huang
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046 Japan
| | - Akimasa Sasaki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046 Japan
| | - Naoki Yamaji
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046 Japan
| | - Haruka Okada
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046 Japan
| | - Namiki Mitani-Ueno
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046 Japan
| | - Jian Feng Ma
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046 Japan
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21
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Ajeesh Krishna TP, Maharajan T, Victor Roch G, Ignacimuthu S, Antony Ceasar S. Structure, Function, Regulation and Phylogenetic Relationship of ZIP Family Transporters of Plants. FRONTIERS IN PLANT SCIENCE 2020; 11:662. [PMID: 32536933 PMCID: PMC7267038 DOI: 10.3389/fpls.2020.00662] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 04/29/2020] [Indexed: 05/24/2023]
Abstract
Zinc (Zn) is an essential micronutrient for plants and humans. Nearly 50% of the agriculture soils of world are Zn-deficient. The low availability of Zn reduces the yield and quality of the crops. The zinc-regulated, iron-regulated transporter-like proteins (ZIP) family and iron-regulated transporters (IRTs) are involved in cellular uptake of Zn, its intracellular trafficking and detoxification in plants. In addition to Zn, ZIP family transporters also transport other divalent metal cations (such as Cd2+, Fe2+, and Cu2+). ZIP transporters play a crucial role in biofortification of grains with Zn. Only a very limited information is available on structural features and mechanism of Zn transport of plant ZIP family transporters. In this article, we present a detailed account on structure, function, regulations and phylogenetic relationships of plant ZIP transporters. We give an insight to structure of plant ZIPs through homology modeling and multiple sequence alignment with Bordetella bronchiseptica ZIP (BbZIP) protein whose crystal structure has been solved recently. We also provide details on ZIP transporter genes identified and characterized in rice and other plants till date. Functional characterization of plant ZIP transporters will help for the better crop yield and human health in future.
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Affiliation(s)
- T. P. Ajeesh Krishna
- Division of Plant Biotechnology, Entomology Research Institute, Loyola College, University of Madras, Chennai, India
| | - T. Maharajan
- Division of Plant Biotechnology, Entomology Research Institute, Loyola College, University of Madras, Chennai, India
| | - G. Victor Roch
- Division of Plant Biotechnology, Entomology Research Institute, Loyola College, University of Madras, Chennai, India
| | | | - Stanislaus Antony Ceasar
- Division of Plant Biotechnology, Entomology Research Institute, Loyola College, University of Madras, Chennai, India
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22
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Morina F, Mishra A, Mijovilovich A, Matoušková Š, Brückner D, Špak J, Küpper H. Interaction Between Zn Deficiency, Toxicity and Turnip Yellow Mosaic Virus Infection in Noccaea ochroleucum. FRONTIERS IN PLANT SCIENCE 2020; 11:739. [PMID: 32582260 PMCID: PMC7290001 DOI: 10.3389/fpls.2020.00739] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 05/08/2020] [Indexed: 05/08/2023]
Abstract
Zinc is essential for the functioning of numerous proteins in plants. To investigate how Zn homeostasis interacts with virus infection, Zn-tolerant Noccaea ochroleucum plants exposed to deficient (Zn'0'), optimal (Zn10), and excess Zn (Zn100) concentrations, as well as Cd amendment, were infected with Turnip yellow mosaic virus (TYMV). Imaging analysis of fluorescence kinetics from the μs (OJIP) to the minutes (Kautsky effect, quenching analysis) time domain revealed strong patchiness of systemic virus-induced photosystem II (PSII) inhibition. That was more pronounced in Zn-deficient plants, while Zn excess acted synergistically with TYMV, in both cases resulting in reduced PSII reaction centers. Infected Cd-treated plants, already severely stressed, showed inhibited non-photochemical quenching and PSII activity. Quantitative in situ hybridization at the cellular level showed increased gene expression of ZNT5 and downregulation of HMA4 in infected Zn-deficient leaves. In Zn10 and Zn100 infected leaves, vacuolar sequestration of Zn increased by activation of HMA3 (mesophyll) and MTP1 (epidermis). This correlated with Zn accumulation in the mesophyll and formation of biomineralization dots in the cell wall (Zn100) visible by micro X-ray fluorescence tomography. The study reveals the importance of adequate Zn supply and distribution in the maintenance of photosynthesis under TYMV infection, achieved by tissue-targeted activation of metal transporter gene expression.
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Affiliation(s)
- Filis Morina
- Department of Plant Biophysics and Biochemistry, Biology Centre, Institute of Plant Molecular Biology, Czech Academy of Sciences, České Budějovice, Czechia
| | - Archana Mishra
- Department of Plant Biophysics and Biochemistry, Biology Centre, Institute of Plant Molecular Biology, Czech Academy of Sciences, České Budějovice, Czechia
| | - Ana Mijovilovich
- Department of Plant Biophysics and Biochemistry, Biology Centre, Institute of Plant Molecular Biology, Czech Academy of Sciences, České Budějovice, Czechia
| | - Šárka Matoušková
- Department of Geological Processes, Czech Academy of Sciences, Institute of Geology, Rozvojová, Czechia
| | - Dennis Brückner
- Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
- Department of Physics, University of Hamburg, Hamburg, Germany
- Faculty of Chemistry and Biochemistry, Ruhr-University Bochum, Bochum, Germany
| | - Josef Špak
- Department of Plant Virology, Biology Centre, Institute of Plant Molecular Biology, Czech Academy of Sciences, České Budějovice, Czechia
| | - Hendrik Küpper
- Department of Plant Biophysics and Biochemistry, Biology Centre, Institute of Plant Molecular Biology, Czech Academy of Sciences, České Budějovice, Czechia
- Department of Experimental Plant Biology, University of South Bohemia, České Budějovice, Czechia
- *Correspondence: Hendrik Küpper,
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23
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Raza Q, Riaz A, Sabar M, Atif RM, Bashir K. Meta-analysis of grain iron and zinc associated QTLs identified hotspot chromosomal regions and positional candidate genes for breeding biofortified rice. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 288:110214. [PMID: 31521222 DOI: 10.1016/j.plantsci.2019.110214] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 07/13/2019] [Accepted: 08/06/2019] [Indexed: 05/09/2023]
Abstract
Biofortification of staple crops with essential micronutrients is the sustainable way to overcome the hidden hunger. A large number of quantitative trait loci (QTL) linked with grain micronutrient contents have been reported in different mapping studies. Identification of consistent QTLs across diverse genetic backgrounds is useful for candidate gene analysis and marker assisted selection of target traits. In this study, an up to date meta-analysis of grain iron and zinc associated QTLs was performed and 48 meta-QTLs (MQTLs) distributed across 12 rice chromosomes were identified. The 95% confidence intervals of identified genomic regions were significantly narrower than the average of their corresponding original QTLs. A total of 9308 genes/transcripts physically located within or near MQTL regions were retrieved and through prioritization of candidate genes (CGs) 663 non-redundant iron and zinc CGs were selected and studied in detailed. Several functionally characterized iron and zinc homoeostasis related genes e.g OsATM3, OsDMAS1, OsFRO2, OsNAS1-3, OsVIT2, OsYSL16, OsZIP3 and OsZIP7 were also included in our MQTL analysis. More than 64% genes were enriched with zinc and iron binding gene ontology terms and were involved in oxidation reduction process, carbohydrate metabolic process, regulation of transcription, trans-membrane transport, response to oxidative stress, cell redox homeostasis and proteolysis etc. In-silico transcriptomic analysis of rice identified 260 CGs which were regulated in response to iron and zinc stresses. We also identified at least 37 genes which were differentially expressed under both stress conditions and majority of these have not been studied in detailed before. Our results strongly indicate that majority of the MQTLs identified in this study are hotspots for grain iron and zinc concentration and are worth of intensive functional studies in near future.
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Affiliation(s)
- Qasim Raza
- Molecular Breeding Laboratory, Division of Plant Breeding and Genetics, Rice Research Institute, Kala Shah Kaku, Sheikhupura, Pakistan.
| | - Awais Riaz
- Molecular Breeding Laboratory, Division of Plant Breeding and Genetics, Rice Research Institute, Kala Shah Kaku, Sheikhupura, Pakistan
| | - Muhammad Sabar
- Molecular Breeding Laboratory, Division of Plant Breeding and Genetics, Rice Research Institute, Kala Shah Kaku, Sheikhupura, Pakistan
| | - Rana Muhammad Atif
- Department of Plant Breeding and Genetics, University of Agriculture Faisalabad, Pakistan; US-Pak Centre for Advanced Studies in Food and Agricultural Security, University of Agriculture Faisalabad, Pakistan
| | - Khurram Bashir
- Plant Genomic Network Research Team, Center for Sustainable Resource Science, RIKEN, Yokohama Campus, Yokohama, Japan.
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da Cruz TNM, Savassa SM, Montanha GS, Ishida JK, de Almeida E, Tsai SM, Lavres Junior J, Pereira de Carvalho HW. A new glance on root-to-shoot in vivo zinc transport and time-dependent physiological effects of ZnSO 4 and ZnO nanoparticles on plants. Sci Rep 2019; 9:10416. [PMID: 31320668 PMCID: PMC6639404 DOI: 10.1038/s41598-019-46796-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 05/02/2019] [Indexed: 11/25/2022] Open
Abstract
Understanding nanoparticle root uptake and root-to-shoot transport might contribute to the use of nanotechnology in plant nutrition. This study performed time resolved experiments to probe Zn uptake, biotransformation and physiological effects on Phaseolus vulgaris (L.). Plants roots were exposed to ZnO nanoparticles (40 and 300 nm) dispersions and ZnSO4(aq) (100 and 1000 mg Zn L−1) for 48 h. Near edge X-ray absorption spectroscopy showed that 40 nm ZnO was more easily dissolved by roots than 300 nm ZnO. It also showed that in the leaves Zn was found as a mixture Zn3(PO4)2 and Zn-histidine complex. X-ray fluorescence spectroscopy showed that root-to-shoot Zn-translocation presented a decreasing gradient of concentration and velocity, it seems radial Zn movement occurs simultaneously to the axial xylem transport. Below 100 mg Zn L−1, the lower stem tissue section served as a buffer preventing Zn from reaching the leaves. Conversely, it was not observed for 1000 mg Zn L−1 ZnSO4(aq). Transcriptional analysis of genes encoding metal carriers indicated higher expression levels of tonoplast-localized transporters, suggesting that the mechanism trend to accumulate Zn in the lower tissues may be associated with an enhanced of Zn compartmentalization in vacuoles. The photosynthetic rate, transpiration, and water conductance were impaired by treatments.
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Affiliation(s)
- Tatiana N M da Cruz
- University of São Paulo, Nuclear Instrumentation Laboratory, Center for Nuclear Energy in Agriculture, Piracicaba, 13416000, Brazil
| | - Susilaine M Savassa
- University of São Paulo, Nuclear Instrumentation Laboratory, Center for Nuclear Energy in Agriculture, Piracicaba, 13416000, Brazil
| | - Gabriel S Montanha
- University of São Paulo, Nuclear Instrumentation Laboratory, Center for Nuclear Energy in Agriculture, Piracicaba, 13416000, Brazil
| | - Juliane K Ishida
- University of São Paulo, Cellular and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, Piracicaba, 13416000, Brazil
| | - Eduardo de Almeida
- University of São Paulo, Nuclear Instrumentation Laboratory, Center for Nuclear Energy in Agriculture, Piracicaba, 13416000, Brazil
| | - Siu M Tsai
- University of São Paulo, Cellular and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, Piracicaba, 13416000, Brazil
| | - José Lavres Junior
- University of Sao Paulo, Center for Nuclear Energy in Agriculture, Plant Nutrition Laboratory, Piracicaba, 13416000, Brazil
| | - Hudson W Pereira de Carvalho
- University of São Paulo, Nuclear Instrumentation Laboratory, Center for Nuclear Energy in Agriculture, Piracicaba, 13416000, Brazil.
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25
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Cong W, Miao Y, Xu L, Zhang Y, Yuan C, Wang J, Zhuang T, Lin X, Jiang L, Wang N, Ma J, Sanguinet KA, Liu B, Rustgi S, Ou X. Transgenerational memory of gene expression changes induced by heavy metal stress in rice (Oryza sativa L.). BMC PLANT BIOLOGY 2019; 19:282. [PMID: 31248374 PMCID: PMC6598230 DOI: 10.1186/s12870-019-1887-7] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 06/13/2019] [Indexed: 05/22/2023]
Abstract
BACKGROUND Heavy metal toxicity has become a major threat to sustainable crop production worldwide. Thus, considerable interest has been placed on deciphering the mechanisms that allow plants to combat heavy metal stress. Strategies to deal with heavy metals are largely focused on detoxification, transport and/or sequestration. The P1B subfamily of the Heavy Metal-transporting P-type ATPases (HMAs) was shown to play a crucial role in the uptake and translocation of heavy metals in plants. Here, we report the locus-specific expression changes in the rice HMA genes together with several low-copy cellular genes and transposable elements upon the heavy metal treatment and monitored the transgenerational inheritance of the altered expression states. We reveal that plants cope with heavy metal stress by making heritable changes in gene expression and further determined gene-specific responses to heavy metal stress. RESULTS We found most HMA genes were upregulated in response to heavy metal stress, and furthermore found evidence of transgenerational memory via changes in gene regulation even after the removal of heavy metals. To explore whether DNA methylation was also altered in response to the heavy metal stress, we selected a Tos17 retrotransposon for bisulfite sequencing and studied its methylation state across three generations. We found the DNA methylation state of Tos17 was altered in response to the heavy metal stress and showed transgenerational inheritance. CONCLUSIONS Collectively, the present study elucidates heritable changes in gene expression and DNA methylation in rice upon exposure to heavy metal stress and discusses implications of this knowledge in breeding for heavy metal tolerant crops.
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Affiliation(s)
- Weixuan Cong
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, 130024 China
| | - Yiling Miao
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, 130024 China
| | - Lei Xu
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, 130024 China
| | - Yunhong Zhang
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, 130024 China
| | - Chunlei Yuan
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, 130024 China
| | - Junmeng Wang
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, 130024 China
| | - Tingting Zhuang
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, 130024 China
| | - Xiuyun Lin
- Jilin Academy of Agricultural Sciences, Changchun, 130033 China
| | - Lili Jiang
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, 130024 China
| | - Ningning Wang
- Jilin Agriculture University, Changchun, 130000 China
| | - Jian Ma
- Jilin Agriculture University, Changchun, 130000 China
| | - Karen A. Sanguinet
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164 USA
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, 130024 China
| | - Sachin Rustgi
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164 USA
- Department of Plant and Environmental Sciences, Clemson University, Pee Dee Research and Education Center, Florence, SC 29506 USA
| | - Xiufang Ou
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, 130024 China
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26
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Cai H, Huang S, Che J, Yamaji N, Ma JF. The tonoplast-localized transporter OsHMA3 plays an important role in maintaining Zn homeostasis in rice. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:2717-2725. [PMID: 30840766 PMCID: PMC6506766 DOI: 10.1093/jxb/erz091] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 02/13/2019] [Indexed: 05/20/2023]
Abstract
In order to respond to fluctuating zinc (Zn) in the environment, plants must have a system to control Zn homeostasis. However, how plants maintain an appropriate level of Zn during their growth and development is still poorly understood. In this study, we found that OsHMA3, a tonoplast-localized transporter for Zn/Cd, plays an important role in Zn homeostasis in rice. Accessions with the functional allele of OsHMA3 showed greater tolerance to high Zn than those with the non-functional allele based on root elongation test. A 67Zn-labeling experiment showed that accessions with loss of function of OsHMA3 had lower Zn accumulation in the roots but similar concentrations in the shoots compared with functional OsHMA3 accessions. When exposed to Zn-free growing medium, the concentration in the root cell sap was rapidly decreased in accessions with functional OsHMA3, but less dramatic changes were observed in non-functional accessions. A mobility experiment showed that more Zn in the roots was translocated to the shoots in accessions with functional OsHMA3. Higher expression levels of OsZIP4, OsZIP5, OsZIP8, and OsZIP10 were found in the roots of accessions with functional OsHMA3 in response to Zn deficiency. Taken together, our results indicate that OsHMA3 plays an important role in rice roots in both Zn detoxification and storage by sequestration into the vacuoles, depending on Zn concentration in the environment.
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Affiliation(s)
- Hongmei Cai
- Institute of Plant Science and Resources, Okayama University, Chuo, Kurashiki, Japan
- Research Center of Microelement, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Sheng Huang
- Institute of Plant Science and Resources, Okayama University, Chuo, Kurashiki, Japan
| | - Jing Che
- Institute of Plant Science and Resources, Okayama University, Chuo, Kurashiki, Japan
| | - Naoki Yamaji
- Institute of Plant Science and Resources, Okayama University, Chuo, Kurashiki, Japan
| | - Jian Feng Ma
- Institute of Plant Science and Resources, Okayama University, Chuo, Kurashiki, Japan
- Correspondence:
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Muhammad I, Jing XQ, Shalmani A, Ali M, Yi S, Gan PF, Li WQ, Liu WT, Chen KM. Comparative in Silico Analysis of Ferric Reduction Oxidase (FRO) Genes Expression Patterns in Response to Abiotic Stresses, Metal and Hormone Applications. Molecules 2018; 23:molecules23051163. [PMID: 29757203 PMCID: PMC6099960 DOI: 10.3390/molecules23051163] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 05/04/2018] [Accepted: 05/09/2018] [Indexed: 02/01/2023] Open
Abstract
The ferric reduction oxidase (FRO) gene family is involved in various biological processes widely found in plants and may play an essential role in metal homeostasis, tolerance and intricate signaling networks in response to a number of abiotic stresses. Our study describes the identification, characterization and evolutionary relationships of FRO genes families. Here, total 50 FRO genes in Plantae and 15 ‘FRO like’ genes in non-Plantae were retrieved from 16 different species. The entire FRO genes have been divided into seven clades according to close similarity in biological and functional behavior. Three conserved domains were common in FRO genes while in two FROs sub genome have an extra NADPH-Ox domain, separating the function of plant FROs. OsFRO1 and OsFRO7 genes were expressed constitutively in rice plant. Real-time RT-PCR analysis demonstrated that the expression of OsFRO1 was high in flag leaf, and OsFRO7 gene expression was maximum in leaf blade and flag leaf. Both genes showed vigorous expressions level in response to different abiotic and hormones treatments. Moreover, the expression of both genes was also substantial under heavy metal stresses. OsFRO1 gene expression was triggered following 6 h under Zn, Pb, Co and Ni treatments, whereas OsFRO7 gene expression under Fe, Pb and Ni after 12 h, Zn and Cr after 6 h, and Mn and Co after 3 h treatments. These findings suggest the possible involvement of both the genes under abiotic and metal stress and the regulation of phytohormones. Therefore, our current work may provide the foundation for further functional characterization of rice FRO genes family.
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Affiliation(s)
- Izhar Muhammad
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, China.
| | - Xiu-Qing Jing
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, China.
| | - Abdullah Shalmani
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, China.
| | - Muhammad Ali
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
| | - Shi Yi
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, China.
| | - Peng-Fei Gan
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, China.
| | - Wen-Qiang Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, China.
| | - Wen-Ting Liu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, China.
| | - Kun-Ming Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, China.
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28
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Neeraja CN, Kulkarni KS, Madhu Babu P, Sanjeeva Rao D, Surekha K, Ravindra Babu V. Transporter genes identified in landraces associated with high zinc in polished rice through panicle transcriptome for biofortification. PLoS One 2018; 13:e0192362. [PMID: 29394277 PMCID: PMC5796704 DOI: 10.1371/journal.pone.0192362] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 01/21/2018] [Indexed: 11/27/2022] Open
Abstract
Polished rice is poor source of micronutrients, however wide genotypic variability exists for zinc uptake and remobilization and zinc content in brown and polished grains in rice. Two landraces (Chittimutyalu and Kala Jeera Joha) and one popular improved variety (BPT 5204) were grown under zinc sufficient soil and their analyses showed high zinc in straw of improved variety, but high zinc in polished rice in landraces suggesting better translocation ability of zinc into the grain in landraces. Transcriptome analyses of the panicle tissue showed 41182 novel transcripts across three samples. Out of 1011 differentially expressed exclusive transcripts by two landraces, 311 were up regulated and 534 were down regulated. Phosphate transporter-exporter (PHO), proton-coupled peptide transporters (POT) and vacuolar iron transporter (VIT) showed enhanced and significant differential expression in landraces. Out of 24 genes subjected to quantitative real time analyses for confirmation, eight genes showed significant differential expression in landraces. Through mapping, six rice microsatellite markers spanning the genomic regions of six differentially expressed genes were validated for their association with zinc in brown and polished rice using recombinant inbred lines (RIL) of BPT 5204/Chittimutyalu. Thus, this study reports repertoire of genes associated with high zinc in polished rice and a proof concept for deployment of transcriptome information for validation in mapping population and its use in marker assisted selection for biofortification of rice with zinc.
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Affiliation(s)
- C. N. Neeraja
- Department of Crop Improvement, ICAR-Indian Institute of Rice Research, Rajendranagar, Telangana, Hyderabad, India
| | - Kalyani S. Kulkarni
- Department of Crop Improvement, ICAR-Indian Institute of Rice Research, Rajendranagar, Telangana, Hyderabad, India
| | - P. Madhu Babu
- Department of Crop Improvement, ICAR-Indian Institute of Rice Research, Rajendranagar, Telangana, Hyderabad, India
| | - D. Sanjeeva Rao
- Department of Crop Improvement, ICAR-Indian Institute of Rice Research, Rajendranagar, Telangana, Hyderabad, India
| | - K. Surekha
- Department of Crop Improvement, ICAR-Indian Institute of Rice Research, Rajendranagar, Telangana, Hyderabad, India
| | - V Ravindra Babu
- Department of Crop Improvement, ICAR-Indian Institute of Rice Research, Rajendranagar, Telangana, Hyderabad, India
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29
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Evens NP, Buchner P, Williams LE, Hawkesford MJ. The role of ZIP transporters and group F bZIP transcription factors in the Zn-deficiency response of wheat (Triticum aestivum). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 92:291-304. [PMID: 28771859 PMCID: PMC5656842 DOI: 10.1111/tpj.13655] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 07/25/2017] [Accepted: 07/28/2017] [Indexed: 05/12/2023]
Abstract
Understanding the molecular basis of zinc (Zn) uptake and transport in staple cereal crops is critical for improving both Zn content and tolerance to low-Zn soils. This study demonstrates the importance of group F bZIP transcription factors and ZIP transporters in responses to Zn deficiency in wheat (Triticum aestivum). Seven group F TabZIP genes and 14 ZIPs with homeologs were identified in hexaploid wheat. Promoter analysis revealed the presence of Zn-deficiency-response elements (ZDREs) in a number of the ZIPs. Functional complementation of the zrt1/zrt2 yeast mutant by TaZIP3, -6, -7, -9 and -13 supported an ability to transport Zn. Group F TabZIPs contain the group-defining cysteine-histidine-rich motifs, which are the predicted binding site of Zn2+ in the Zn-deficiency response. Conservation of these motifs varied between the TabZIPs suggesting that individual TabZIPs may have specific roles in the wheat Zn-homeostatic network. Increased expression in response to low Zn levels was observed for several of the wheat ZIPs and bZIPs; this varied temporally and spatially suggesting specific functions in the response mechanism. The ability of the group F TabZIPs to bind to specific ZDREs in the promoters of TaZIPs indicates a conserved mechanism in monocots and dicots in responding to Zn deficiency. In support of this, TabZIPF1-7DL and TabZIPF4-7AL afforded a strong level of rescue to the Arabidopsis hypersensitive bzip19 bzip23 double mutant under Zn deficiency. These results provide a greater understanding of Zn-homeostatic mechanisms in wheat, demonstrating an expanded repertoire of group F bZIP transcription factors, adding to the complexity of Zn homeostasis.
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Affiliation(s)
- Nicholas P. Evens
- Rothamsted ResearchWest CommonHarpenden, HertfordshireAL5 2JQUK
- Biological ScienceUniversity of SouthamptonLife Sciences Building 85, Highfield CampusSouthamptonSO17 1BJUK
| | - Peter Buchner
- Rothamsted ResearchWest CommonHarpenden, HertfordshireAL5 2JQUK
| | - Lorraine E. Williams
- Biological ScienceUniversity of SouthamptonLife Sciences Building 85, Highfield CampusSouthamptonSO17 1BJUK
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30
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Bandyopadhyay T, Mehra P, Hairat S, Giri J. Morpho-physiological and transcriptome profiling reveal novel zinc deficiency-responsive genes in rice. Funct Integr Genomics 2017; 17:565-581. [DOI: 10.1007/s10142-017-0556-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 02/28/2017] [Accepted: 03/01/2017] [Indexed: 11/28/2022]
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31
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Nanda AK, Pujol V, Wissuwa M. Patterns of stress response and tolerance based on transcriptome profiling of rice crown tissue under zinc deficiency. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:1715-1729. [PMID: 28369468 DOI: 10.1093/jxb/erx039] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Zinc (Zn) deficiency is the most prevalent micronutrient disorder in rice and leads to delayed development and decreased yield. Several studies have investigated how rice plants respond to Zn deficiency and examined the differences between Zn-efficient (ZE) and Zn-inefficient (ZI) genotypes. ZE genotypes reallocate more Zn to roots and are better at maintaining crown root development than ZI genotypes in response to Zn deficiency. However, little is known about the molecular mechanisms controlling these differences. Moreover, the role of the crown, the part of the stem from which crown roots emerge, has yet to be examined. In this study we highlight the molecular mechanisms triggered by early Zn deficiency in crown tissue through RNA sequencing of two contrasting groups of several ZE and ZI genotypes. This method allowed us to (i) identify several novel and well-known Zn transporters involved in Zn retranslocation from the crown to the shoot and roots in response to Zn deficiency; (ii) determine that Zn deficiency triggers the conversion of soluble sugars into starch; and (iii) detect several candidate genes possibly conferring Zn efficiency, including a monosaccharide transporter, a Zn finger domain-containing protein, a gibberellin-stimulated family protein and a plasma membrane polypeptide family protein.
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Affiliation(s)
- Amrit K Nanda
- Crop, Livestock and Environment Division, Japan International Research Center for Agricultural Sciences, Tsukuba, Japan
| | - Vincent Pujol
- Crop, Livestock and Environment Division, Japan International Research Center for Agricultural Sciences, Tsukuba, Japan
| | - Matthias Wissuwa
- Crop, Livestock and Environment Division, Japan International Research Center for Agricultural Sciences, Tsukuba, Japan
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Bashir K, Rasheed S, Kobayashi T, Seki M, Nishizawa NK. Regulating Subcellular Metal Homeostasis: The Key to Crop Improvement. FRONTIERS IN PLANT SCIENCE 2016; 7:1192. [PMID: 27547212 PMCID: PMC4974246 DOI: 10.3389/fpls.2016.01192] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 07/25/2016] [Indexed: 05/21/2023]
Abstract
Iron (Fe), zinc (Zn), manganese (Mn), and copper (Cu) are essential micronutrient mineral elements for living organisms, as they regulate essential cellular processes, such as chlorophyll synthesis and photosynthesis (Fe, Cu, and Mn), respiration (Fe and Cu), and transcription (Zn). The storage and distribution of these minerals in various cellular organelles is strictly regulated to ensure optimal metabolic rates. Alteration of the balance in uptake, distribution, and/or storage of these minerals severely impairs cellular metabolism and significantly affects plant growth and development. Thus, any change in the metal profile of a cellular compartment significantly affects metabolism. Different subcellular compartments are suggested to be linked through complex retrograde signaling networks to regulate cellular metal homeostasis. Various genes regulating cellular and subcellular metal distribution have been identified and characterized. Understanding the role of these transporters is extremely important to elaborate the signaling between various subcellular compartments. Moreover, modulation of the proteins involved in cellular metal homeostasis may help in the regulation of metabolism, adaptability to a diverse range of environmental conditions, and biofortification. Here, we review progress in the understanding of different subcellular metal transport components in plants and discuss the prospects of regulating cellular metabolism and strategies to develop biofortified crop plants.
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Affiliation(s)
- Khurram Bashir
- Plant Genomics Network Research Team, Center for Sustainable Resource Science, RIKEN, Yokohama Campus, YokohamaJapan
| | - Sultana Rasheed
- Plant Genomics Network Research Team, Center for Sustainable Resource Science, RIKEN, Yokohama Campus, YokohamaJapan
- Kihara Institute for Biological Research, Yokohama City University, YokohamaJapan
| | - Takanori Kobayashi
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, NonoichiJapan
| | - Motoaki Seki
- Plant Genomics Network Research Team, Center for Sustainable Resource Science, RIKEN, Yokohama Campus, YokohamaJapan
- Kihara Institute for Biological Research, Yokohama City University, YokohamaJapan
- Core Research for Evolutional Science and Technology – Japan Science and Technology Agency, KawaguchiJapan
| | - Naoko K. Nishizawa
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, NonoichiJapan
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, TokyoJapan
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Fang X, Wang L, Deng X, Wang P, Ma Q, Nian H, Wang Y, Yang C. Genome-wide characterization of soybean P 1B -ATPases gene family provides functional implications in cadmium responses. BMC Genomics 2016; 17:376. [PMID: 27207280 PMCID: PMC4874001 DOI: 10.1186/s12864-016-2730-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 05/12/2016] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND The P1B-ATPase subfamily is an important group involved in transporting heavy metals and has been extensively studied in model plants, such as Arabidopsis thaliana and Oryza sativa. Emerging evidence indicates that one homolog in Glycine max is also involved in cadmium (Cd) stress, but the gene family has not been fully investigated in soybean. RESULTS Here, we identified 20 heavy metal ATPase (HMA) family members in the soybean genome, presented as 10 paralogous pairs, which is significantly greater than the number in Arabidopsis or rice, and was likely caused by the latest whole genome duplication event in soybean. A phylogenetic analysis divided the 20 members into six groups, each having conserved or divergent gene structures and protein motif patterns. The integration of RNA-sequencing and qRT-PCR data from multiple tissues provided an overall expression pattern for the HMA family in soybean. Further comparisons of expression patterns and the single nucleotide polymorphism distribution between paralogous pairs suggested functional conservation and the divergence of HMA genes during soybean evolution. Finally, analyses of the HMAs expressed in response to Cd stress provided evidence on how plants manage Cd tolerance, at least in the two contrasting soybean genotypes examined. CONCLUSIONS The genome-wide identification, chromosomal distribution, gene structures, and evolutionary and expression analyses of the 20 HMA genes in soybean provide an overall insight into their potential involvement in Cd responses. These results will facilitate further research on the HMA gene family, and their conserved and divergent biological functions in soybean.
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Affiliation(s)
- Xiaolong Fang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, Guangdong Sub-center of National Center for Soybean Improvement, College of Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- State Key Laboratory of Genetic Engineering and Institute of Genetics, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Lei Wang
- College of Life Sciences, Xinyang Normal University, Xinyang, 464000, Henan, China
| | - Xiaojuan Deng
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, Guangdong Sub-center of National Center for Soybean Improvement, College of Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Peng Wang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, Guangdong Sub-center of National Center for Soybean Improvement, College of Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Qibin Ma
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, Guangdong Sub-center of National Center for Soybean Improvement, College of Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Hai Nian
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, Guangdong Sub-center of National Center for Soybean Improvement, College of Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Yingxiang Wang
- State Key Laboratory of Genetic Engineering and Institute of Genetics, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China.
| | - Cunyi Yang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, Guangdong Sub-center of National Center for Soybean Improvement, College of Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, China.
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34
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Krithika S, Balachandar D. Expression of Zinc Transporter Genes in Rice as Influenced by Zinc-Solubilizing Enterobacter cloacae Strain ZSB14. FRONTIERS IN PLANT SCIENCE 2016; 7:446. [PMID: 27092162 PMCID: PMC4822286 DOI: 10.3389/fpls.2016.00446] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Accepted: 03/21/2016] [Indexed: 05/09/2023]
Abstract
Zinc (Zn) deficiency in major food crops has been considered as an important factor affecting the crop production and subsequently the human health. Rice (Oryza sativa) is sensitive to Zn deficiency and thereby causes malnutrition to most of the rice-eating Asian populations. Application of zinc solubilizing bacteria (ZSB) could be a sustainable agronomic approach to increase the soil available Zn which can mitigate the yield loss and consequently the nutritional quality of rice. Understanding the molecular interactions between rice and unexplored ZSB is useful for overcoming Zn deficiency problems. In the present study, the role of zinc solubilizing bacterial strain Enterobacter cloacae strain ZSB14 on regulation of Zn-regulated transporters and iron (Fe)-regulated transporter-like protein (ZIP) genes in rice under iron sufficient and deficient conditions was assessed by quantitative real-time reverse transcription PCR. The expression patterns of OsZIP1, OsZIP4, and OsZIP5 in root and shoot of rice were altered due to the Zn availability as dictated by Zn sources and ZSB inoculation. Fe sufficiency significantly reduced the root and shoot OsZIP1 expression, but not the OsZIP4 and OsZIP5 levels. Zinc oxide in the growth medium up-regulated all the assessed ZIP genes in root and shoot of rice seedlings. When ZSB was inoculated to rice seedlings grown with insoluble zinc oxide in the growth medium, the expression of root and shoot OsZIP1, OsZIP4, and OsZIP5 was reduced. In the absence of zinc oxide, ZSB inoculation up-regulated OsZIP1 and OsZIP5 expressions. Zinc nutrition provided to the rice seedling through ZSB-bound zinc oxide solubilization was comparable to the soluble zinc sulfate application which was evident through the ZIP genes' expression and the Zn accumulation in root and shoot of rice seedlings. These results demonstrate that ZSB could play a crucial role in zinc fertilization and fortification of rice.
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Zhang W, Tan NGJ, Fu B, Li SFY. Metallomics and NMR-based metabolomics of Chlorella sp. reveal the synergistic role of copper and cadmium in multi-metal toxicity and oxidative stress. Metallomics 2015; 7:426-38. [DOI: 10.1039/c4mt00253a] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Bashir K, Hanada K, Shimizu M, Seki M, Nakanishi H, Nishizawa NK. Transcriptomic analysis of rice in response to iron deficiency and excess. RICE (NEW YORK, N.Y.) 2014; 7:18. [PMID: 26224551 PMCID: PMC4884027 DOI: 10.1186/s12284-014-0018-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 07/23/2014] [Indexed: 05/20/2023]
Abstract
BACKGROUND Iron (Fe) is essential micronutrient for plants and its deficiency as well as toxicity is a serious agricultural problem. The mechanisms of Fe deficiency are reasonably understood, however our knowledge about plants response to excess Fe is limited. Moreover, the regulation of small open reading frames (sORFs) in response to abiotic stress has not been reported in rice. Understanding the regulation of rice transcriptome in response to Fe deficiency and excess could provide bases for developing strategies to breed plants tolerant to Fe deficiency as well as excess Fe. RESULTS We used a novel rice 110 K microarray harbouring ~48,620 sORFs to understand the transcriptomic changes that occur in response to Fe deficiency and excess. In roots, 36 genes were upregulated by excess Fe, of which three were sORFs. In contrast, 1509 genes were upregulated by Fe deficiency, of which 90 (6%) were sORFs. Co-expression analysis revealed that the expression of some sORFs was positively correlated with the genes upregulated by Fe deficiency. In shoots, 50 (19%) of the genes upregulated by Fe deficiency and 1076 out of 2480 (43%) genes upregulated by excess Fe were sORFs. These results suggest that excess Fe may significantly alter metabolism, particularly in shoots. CONCLUSION These data not only reveal the genes regulated by excess Fe, but also suggest that sORFs might play an important role in the response of plants to Fe deficiency and excess.
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Affiliation(s)
- Khurram Bashir
- />Laboratory of Plant Biotechnology, Department of Global Agricultural Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
- />Plant Genomics Network Research Team, Center for Sustainable Resource Science, RIKEN Yokohama Campus, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, 230-0045 Kanagawa, Japan
| | - Kousuke Hanada
- />Gene Discovery Research Group, Center for Sustainable Resource Science, RIKEN Yokohama Campus, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, 230-0045 Kanagawa, Japan
- />Frontier Research Academy for Young Researchers, Department of Bioscience and Bioinformatics, Kyusyu Institute of Technology, Iizuka, 820-8502 Fukuoka, Japan
| | - Minami Shimizu
- />Frontier Research Academy for Young Researchers, Department of Bioscience and Bioinformatics, Kyusyu Institute of Technology, Iizuka, 820-8502 Fukuoka, Japan
| | - Motoaki Seki
- />Plant Genomics Network Research Team, Center for Sustainable Resource Science, RIKEN Yokohama Campus, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, 230-0045 Kanagawa, Japan
- />Kihara Institute for Biological Research, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama, 236-0027 Japan
| | - Hiromi Nakanishi
- />Laboratory of Plant Biotechnology, Department of Global Agricultural Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Naoko K Nishizawa
- />Laboratory of Plant Biotechnology, Department of Global Agricultural Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
- />Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, 1-308 Suematsu, Nonoichi-shi, 921-8836 Ishikawa, Japan
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Zheng J, Wang Y, He Y, Zhou J, Li Y, Liu Q, Xie X. Overexpression of an S-like ribonuclease gene, OsRNS4, confers enhanced tolerance to high salinity and hyposensitivity to phytochrome-mediated light signals in rice. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2014; 214:99-105. [PMID: 24268167 DOI: 10.1016/j.plantsci.2013.10.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 08/26/2013] [Accepted: 10/05/2013] [Indexed: 05/15/2023]
Abstract
S-like ribonucleases (S-like RNases) are homologous to S-ribonucleases (S-RNases), but are not involved in self-incompatibility. In dicotyledonous plants, S-like RNases play an important role in phosphate recycling during senescence and are induced by inorganic phosphate-starvation and in response to defense and mechanical wounding. However, little information about the functions of the S-like RNase in monocots has been reported. Here, we investigated the expression patterns and roles of an S-like RNase gene, OsRNS4, in abscisic acid (ABA)-mediated responses and phytochrome-mediated light responses as well as salinity tolerance in rice. The OsRNS4 gene was expressed at relatively high levels in leaves although its transcripts were detected in various organs. OsRNS4 expression was regulated by salt, PEG and ABA. The seedlings overexpressing OsRNS4 had longer coleoptiles and first leaves than wild-type seedlings under red light (R) and far-red light (FR), suggesting negative regulation of OsRNS4 in photomorphogenesis in rice seedlings. Moreover, ABA-induced growth inhibition of rice seedlings was significantly increased in the OsRNS4-overexpression (OsRNS4-OX) lines compared with that in WT, suggesting that OsRNS4 probably acts as a positive regulator in ABA responses in rice seedlings. In addition, our results demonstrate that OsRNS4-OX lines have enhanced tolerance to high salinity compared to WT. Our findings supply new evidence on the functions of monocot S-like RNase in regulating photosensitivity and abiotic stress responses.
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Affiliation(s)
- Jun Zheng
- Shandong Rice Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, 250100 Jinan, China.
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Kakei Y, Ogo Y, Itai RN, Kobayashi T, Yamakawa T, Nakanishi H, Nishizawa NK. Development of a novel prediction method of cis-elements to hypothesize collaborative functions of cis-element pairs in iron-deficient rice. RICE (NEW YORK, N.Y.) 2013; 6:22. [PMID: 24279975 PMCID: PMC4883709 DOI: 10.1186/1939-8433-6-22] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Accepted: 09/13/2013] [Indexed: 05/20/2023]
Abstract
BACKGROUND Cis-acting elements are essential genomic sequences that control gene expression. In higher eukaryotes, a series of cis-elements function cooperatively. However, further studies are required to examine the co-regulation of multiple cis-elements on a promoter. The aim of this study was to propose a model of cis-element networks that cooperatively regulate gene expression in rice under iron (Fe) deficiency. RESULTS We developed a novel clustering-free method, microarray-associated motif analyzer (MAMA), to predict novel cis-acting elements based on weighted sequence similarities and gene expression profiles in microarray analyses. Simulation of gene expression was performed using a support vector machine and based on the presence of predicted motifs and motif pairs. The accuracy of simulated gene expression was used to evaluate the quality of prediction and to optimize the parameters used in this method. Based on sequences of Oryza sativa genes upregulated by Fe deficiency, MAMA returned experimentally identified cis-elements responsible for Fe deficiency in O. sativa. When this method was applied to O. sativa subjected to zinc deficiency and Arabidopsis thaliana subjected to salt stress, several novel candidate cis-acting elements that overlap with known cis-acting elements, such as ZDRE, ABRE, and DRE, were identified. After optimization, MAMA accurately simulated more than 87% of gene expression. Predicted motifs strongly co-localized in the upstream regions of regulated genes and sequences around transcription start sites. Furthermore, in many cases, the separation (in bp) between co-localized motifs was conserved, suggesting that predicted motifs and the separation between them were important in the co-regulation of gene expression. CONCLUSIONS Our results are suggestive of a typical sequence model for Fe deficiency-responsive promoters and some strong candidate cis-elements that function cooperatively with known cis-elements.
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Affiliation(s)
- Yusuke Kakei
- />Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, 113-8657 Bunkyo-ku Tokyo, Japan
- />Plant Biotechnology Division, Yokohama City University, Kihara Institute for Biological Research Maiokacho, 641-12, Totsuka, Yokohama, Kanagawa 244-0813 Japan
| | - Yuko Ogo
- />Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, 113-8657 Bunkyo-ku Tokyo, Japan
- />Functional Transgenic Crops Research Unit, Genetically Modified Organism Research Center National Institute of Agrobiological Sciences, Kannondai 2-1-2, 305-8602 Tsukuba, Ibaraki Japan
| | - Reiko N Itai
- />Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, 113-8657 Bunkyo-ku Tokyo, Japan
| | - Takanori Kobayashi
- />Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, 113-8657 Bunkyo-ku Tokyo, Japan
- />Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, 1-308 Suematsu, 921-8836 Nonoichi-machi, Ishikawa Japan
- />Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, 1-308 Suematsu, 921-8836 Nonoichi-machi, Ishikawa Japan
| | - Takashi Yamakawa
- />Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, 113-8657 Bunkyo-ku Tokyo, Japan
| | - Hiromi Nakanishi
- />Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, 113-8657 Bunkyo-ku Tokyo, Japan
| | - Naoko K Nishizawa
- />Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, 113-8657 Bunkyo-ku Tokyo, Japan
- />Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, 1-308 Suematsu, 921-8836 Nonoichi-machi, Ishikawa Japan
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Bashir K, Takahashi R, Nakanishi H, Nishizawa NK. The road to micronutrient biofortification of rice: progress and prospects. FRONTIERS IN PLANT SCIENCE 2013; 4:15. [PMID: 23404425 PMCID: PMC3567483 DOI: 10.3389/fpls.2013.00015] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Accepted: 01/21/2013] [Indexed: 05/20/2023]
Abstract
Biofortification (increasing the contents of vitamins and minerals through plant breeding or biotechnology) of food crops with micronutrient elements has the potential to combat widespread micronutrient deficiencies in humans. Rice (Oryza sativa L.) feeds more than half of the world's population and is used as a staple food in many parts of Asia. As in other plants, micronutrient transport in rice is controlled at several stages, including uptake from soil, transport from root to shoot, careful control of subcellular micronutrient transport, and finally, and most importantly, transport to seeds. To enhance micronutrient accumulation in rice seeds, we need to understand and carefully regulate all of these processes. During the last decade, numerous attempts such as increasing the contents/expression of genes encoding metal chelators (mostly phytosiderophores) and metal transporters; Fe storage protein ferritin and phytase were successfully undertaken to significantly increase the micronutrient content of rice. However, despite the rapid progress in biofortification of rice, the commercialization of biofortified crops has not yet been achieved. Here, we briefly review the progress in biofortification of rice with micronutrient elements (Fe, Zn, and Mn) and discuss future prospects to mitigate widespread micronutrient deficiencies in humans.
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Affiliation(s)
- Khurram Bashir
- Laboratory of Plant Biotechnology, Department of Global Agricultural Sciences, Graduate School of Agricultural and Life Sciences, The University of TokyoTokyo, Japan
| | - Ryuichi Takahashi
- Laboratory of Plant Biotechnology, Department of Global Agricultural Sciences, Graduate School of Agricultural and Life Sciences, The University of TokyoTokyo, Japan
| | - Hiromi Nakanishi
- Laboratory of Plant Biotechnology, Department of Global Agricultural Sciences, Graduate School of Agricultural and Life Sciences, The University of TokyoTokyo, Japan
| | - Naoko K. Nishizawa
- Laboratory of Plant Biotechnology, Department of Global Agricultural Sciences, Graduate School of Agricultural and Life Sciences, The University of TokyoTokyo, Japan
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural UniversityIshikawa, Japan
- *Correspondence: Naoko K. Nishizawa, Laboratory of Plant Biotechnology, Department of Global Agricultural Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan. e-mail:
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Takahashi R, Bashir K, Ishimaru Y, Nishizawa NK, Nakanishi H. The role of heavy-metal ATPases, HMAs, in zinc and cadmium transport in rice. PLANT SIGNALING & BEHAVIOR 2012; 7:1605-7. [PMID: 23072989 PMCID: PMC3578901 DOI: 10.4161/psb.22454] [Citation(s) in RCA: 111] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The P(1B)-type heavy metal ATPases (HMAs) are diverse in terms of tissue distribution, subcellular localization, and metal specificity. Functional studies of HMAs have shown that these transporters can be divided into two subgroups based on their metal-substrate specificity: a copper (Cu)/silver (Ag) group and a zinc (Zn)/cobalt (Co)/cadmium (Cd)/lead (Pb) group. Studies on Arabidopsis thaliana and metal hyperaccumulator plants indicate that HMAs play an important role in the translocation or detoxification of Zn and Cd in plants. Rice possesses nine HMA genes, of which OsHMA1-OsHMA3 belong to the Zn/Co/Cd/Pb subgroup. OsHMA2 plays an important role in root-to-shoot translocation of Zn and Cd, and participates in Zn and Cd transport to developing seeds in rice. OsHMA3 transports Cd and plays a role in the sequestration of Cd into vacuoles in root cells. Modification of the expression of these genes might be an effective approach for reducing the Cd concentration in rice grains.
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Affiliation(s)
- Ryuichi Takahashi
- Graduate School of Agricultural and Life Sciences; The University of Tokyo; Tokyo, Japan
| | - Khurram Bashir
- Graduate School of Agricultural and Life Sciences; The University of Tokyo; Tokyo, Japan
| | - Yasuhiro Ishimaru
- Graduate School of Agricultural and Life Sciences; The University of Tokyo; Tokyo, Japan
- Graduate School of Science; Tohoku University; Sendai, Miyagi, Japan
| | - Naoko K. Nishizawa
- Graduate School of Agricultural and Life Sciences; The University of Tokyo; Tokyo, Japan
- Research Institute for Bioresources and Biotechnology; Ishikawa Prefectural University; Ishikawa, Japan
| | - Hiromi Nakanishi
- Graduate School of Agricultural and Life Sciences; The University of Tokyo; Tokyo, Japan
- * Correspondence to: Hiromi Nakanisihi;
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