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Yang Y, Liang Y, Wang C, Wang Y. MicroRNAs as potent regulators in nitrogen and phosphorus signaling transduction and their applications. STRESS BIOLOGY 2024; 4:38. [PMID: 39264517 PMCID: PMC11393275 DOI: 10.1007/s44154-024-00181-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Accepted: 06/18/2024] [Indexed: 09/13/2024]
Abstract
Nitrogen (N) and phosphorus (Pi) are essential macronutrients that affect plant growth and development by influencing the molecular, metabolic, biochemical, and physiological responses at the local and whole levels in plants. N and Pi stresses suppress the physiological activities of plants, resulting in agricultural productivity losses and severely threatening food security. Accordingly, plants have elaborated diverse strategies to cope with N and Pi stresses through maintaining N and Pi homeostasis. MicroRNAs (miRNAs) as potent regulators fine-tune N and Pi signaling transduction that are distinct and indivisible from each other. Specific signals, such as noncoding RNAs (ncRNAs), interact with miRNAs and add to the complexity of regulation. Elucidation of the mechanisms by which miRNAs regulate N and Pi signaling transduction aids in the breeding of plants with strong tolerance to N and Pi stresses and high N and Pi use efficiency by fine-tuning MIR genes or miRNAs. However, to date, there has been no detailed and systematic introduction and comparison of the functions of miRNAs in N and Pi signaling transduction from the perspective of miRNAs and their applications. Here, we summarized and discussed current advances in the involvement of miRNAs in N and Pi signaling transduction and highlighted that fine-tuning the MIR genes or miRNAs involved in maintaining N and Pi homeostasis might provide valuable sights for sustainable agriculture.
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Affiliation(s)
- Yuzhang Yang
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Yanting Liang
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Chun Wang
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Yanwei Wang
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China.
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2
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Sakuraba Y, Yang M, Yanagisawa S. HASTY-mediated miRNA dynamics modulate nitrogen starvation-induced leaf senescence in Arabidopsis. Nat Commun 2024; 15:7913. [PMID: 39256370 PMCID: PMC11387735 DOI: 10.1038/s41467-024-52339-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 08/30/2024] [Indexed: 09/12/2024] Open
Abstract
Nitrogen (N) deficiency responses are essential for plant survival and reproduction. Here, via an expression genome-wide association study (eGWAS), we reveal a mechanism that regulates microRNA (miRNA) dynamics necessary for N deficiency responses in Arabidopsis. Differential expression levels of three NAC transcription factor (TF) genes involved in leaf N deficiency responses among Arabidopsis accessions are most significantly associated with polymorphisms in HASTY (HST), which encodes an importin/exportin family protein responsible for the generation of mature miRNAs. HST acts as a negative regulator of N deficiency-induced leaf senescence, and the disruption and overexpression of HST differently modifies miRNA dynamics in response to N deficiency, altering levels of miRNAs targeting transcripts. Interestingly, N deficiency prevents the interaction of HST with HST-interacting proteins, DCL1 and RAN1, and some miRNAs. This suggests that HST-mediated regulation of miRNA dynamics collectively controls regulations mediated by multiple N deficiency response-associated NAC TFs, thereby being central to the N deficiency response network.
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Affiliation(s)
- Yasuhito Sakuraba
- Plant Functional Biotechnology, Agro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Mailun Yang
- Plant Functional Biotechnology, Agro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Shuichi Yanagisawa
- Plant Functional Biotechnology, Agro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan.
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3
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Saifi M, Ashrafi K, Qamar F, Abdin MZ. Regulatory trends in engineering bioactive-phytocompounds. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 346:112167. [PMID: 38925476 DOI: 10.1016/j.plantsci.2024.112167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 06/12/2024] [Accepted: 06/16/2024] [Indexed: 06/28/2024]
Abstract
The secondary plant metabolites are of enormous importance because of their extensive medicinal, nutraceutical, and industrial applications. In plants, these secondary metabolites are often found in extremely small amounts, therefore, following the discovery of any prospective metabolite, the main constraining element is the ability to generate enough material for use in both industrial and therapeutic settings. In order to satisfy the rising demand for value-added metabolites, researchers prefer to use different molecular approaches for scalable and sustainable production of these phytocompounds. Here, we discuss the emerging regulatory trends in engineering these bioactive-phytocompounds and provide recommendation on successful employment of these state-of-the-art technologies for translation of these academic researches into novel process and products.
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Affiliation(s)
- Monica Saifi
- Centre for Transgenic Plant Development, Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, Hamdard Nagar, New Delhi 110062, India
| | - Kudsiya Ashrafi
- Centre for Transgenic Plant Development, Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, Hamdard Nagar, New Delhi 110062, India
| | - Firdaus Qamar
- Centre for Transgenic Plant Development, Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, Hamdard Nagar, New Delhi 110062, India
| | - M Z Abdin
- Centre for Transgenic Plant Development, Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, Hamdard Nagar, New Delhi 110062, India.
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4
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Ferreira SS, Pandey S, Hemminger J, Bozdag S, Antunes MS. Early changes in microRNA expression in Arabidopsis plants infected with the fungal pathogen Fusarium graminearum. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.29.596347. [PMID: 39149262 PMCID: PMC11326132 DOI: 10.1101/2024.05.29.596347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Plants respond to biotic stressors by modulating various processes in an attempt to limit the attack by a pathogen or herbivore. Triggering these different defense processes requires orchestration of a network of proteins and RNA molecules that includes microRNAs (miRNAs). These short RNA molecules (20-22 nucleotides) have been shown to be important players in the early responses of plants to stresses because they can rapidly regulate the expression levels of a network of downstream genes. The ascomycete Fusarium graminearum is an important fungal pathogen that causes significant losses in cereal crops worldwide. Using the well-characterized Fusarium-Arabidopsis pathosystem, we investigated how plants change expression of their miRNAs globally during the early stages of infection by F. graminearum. In addition to miRNAs that have been previously implicated in stress responses, we have also identified evolutionarily young miRNAs whose levels change significantly in response to fungal infection. Some of these young miRNAs have homologs present in cereals. Thus, manipulating expression of these miRNAs may provide a unique path toward development of plants with increased resistance to fungal pathogens.
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Affiliation(s)
- Savio S. Ferreira
- Dept. of Biological Sciences, University of North Texas, Denton, TX
- BioDiscovery Institute, University of North Texas, Denton, TX
- Current address: Dept. of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, MN
| | - Suman Pandey
- Dept. of Computer Science & Engineering, University of North Texas, Denton, TX
- BioDiscovery Institute, University of North Texas, Denton, TX
- Center for Computational Life Sciences, University of North Texas, Denton, TX
| | - Jesseca Hemminger
- Dept. of Biological Sciences, University of North Texas, Denton, TX
- BioDiscovery Institute, University of North Texas, Denton, TX
| | - Serdar Bozdag
- Dept. of Computer Science & Engineering, University of North Texas, Denton, TX
- BioDiscovery Institute, University of North Texas, Denton, TX
- Dept. of Mathematics, University of North Texas, Denton, TX
- Center for Computational Life Sciences, University of North Texas, Denton, TX
| | - Mauricio S. Antunes
- Dept. of Biological Sciences, University of North Texas, Denton, TX
- BioDiscovery Institute, University of North Texas, Denton, TX
- Center for Computational Life Sciences, University of North Texas, Denton, TX
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5
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Mabry ME, Abrahams RS, Al-Shehbaz IA, Baker WJ, Barak S, Barker MS, Barrett RL, Beric A, Bhattacharya S, Carey SB, Conant GC, Conran JG, Dassanayake M, Edger PP, Hall JC, Hao Y, Hendriks KP, Hibberd JM, King GJ, Kliebenstein DJ, Koch MA, Leitch IJ, Lens F, Lysak MA, McAlvay AC, McKibben MTW, Mercati F, Moore RC, Mummenhoff K, Murphy DJ, Nikolov LA, Pisias M, Roalson EH, Schranz ME, Thomas SK, Yu Q, Yocca A, Pires JC, Harkess AE. Complementing model species with model clades. THE PLANT CELL 2024; 36:1205-1226. [PMID: 37824826 PMCID: PMC11062466 DOI: 10.1093/plcell/koad260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 09/07/2023] [Accepted: 09/22/2023] [Indexed: 10/14/2023]
Abstract
Model species continue to underpin groundbreaking plant science research. At the same time, the phylogenetic resolution of the land plant tree of life continues to improve. The intersection of these 2 research paths creates a unique opportunity to further extend the usefulness of model species across larger taxonomic groups. Here we promote the utility of the Arabidopsis thaliana model species, especially the ability to connect its genetic and functional resources, to species across the entire Brassicales order. We focus on the utility of using genomics and phylogenomics to bridge the evolution and diversification of several traits across the Brassicales to the resources in Arabidopsis, thereby extending scope from a model species by establishing a "model clade." These Brassicales-wide traits are discussed in the context of both the model species Arabidopsis and the family Brassicaceae. We promote the utility of such a "model clade" and make suggestions for building global networks to support future studies in the model order Brassicales.
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Affiliation(s)
- Makenzie E Mabry
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - R Shawn Abrahams
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
- Department of Biochemistry, Purdue University, West Lafayette, IN 47906, USA
| | | | | | - Simon Barak
- Ben-Gurion University of the Negev, French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Midreshet Ben-Gurion, 8499000, Israel
| | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Russell L Barrett
- National Herbarium of New South Wales, Australian Botanic Garden, Locked Bag 6002, Mount Annan, NSW 2567, Australia
| | - Aleksandra Beric
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, St. Louis, MO 63110, USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, St. Louis, MO 63108, USA
| | - Samik Bhattacharya
- Department of Biology, Botany, University of Osnabrück, D-49076 Osnabrück, Germany
| | - Sarah B Carey
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Gavin C Conant
- Department of Biological Sciences, Bioinformatics Research Center, Program in Genetics, North Carolina State University, Raleigh, NC 27695, USA
| | - John G Conran
- ACEBB and SGC, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Maheshi Dassanayake
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI 48864, USA
| | - Jocelyn C Hall
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Yue Hao
- Cancer and Cell Biology Division, Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Kasper P Hendriks
- Department of Biology, Botany, University of Osnabrück, D-49076 Osnabrück, Germany
- Functional Traits, Naturalis Biodiversity Center, PO Box 9517, Leiden 2300 RA, the Netherlands
| | - Julian M Hibberd
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 1TN, UK
| | - Graham J King
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW 2480, Australia
| | | | - Marcus A Koch
- Centre for Organismal Studies (COS), Heidelberg University, 69120 Heidelberg, Germany
| | - Ilia J Leitch
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
| | - Frederic Lens
- Functional Traits, Naturalis Biodiversity Center, PO Box 9517, Leiden 2300 RA, the Netherlands
- Institute of Biology Leiden, Plant Sciences, Leiden University, 2333 BE Leiden, the Netherlands
| | - Martin A Lysak
- CEITEC, and NCBR, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Alex C McAlvay
- Institute of Economic Botany, New York Botanical Garden, The Bronx, NY 10458, USA
| | - Michael T W McKibben
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Francesco Mercati
- National Research Council (CNR), Institute of Biosciences and Bioresource (IBBR), Palermo 90129, Italy
| | | | - Klaus Mummenhoff
- Department of Biology, Botany, University of Osnabrück, D-49076 Osnabrück, Germany
| | - Daniel J Murphy
- Royal Botanic Gardens Victoria, Melbourne, VIC 3004, Australia
| | | | - Michael Pisias
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Eric H Roalson
- School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
| | - M Eric Schranz
- Biosystematics Group, Wageningen University, 6708 PB Wageningen, the Netherlands
| | - Shawn K Thomas
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
- Bioinformatics and Analytics Core, University of Missouri, Columbia, MO 65211, USA
| | - Qingyi Yu
- Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Hilo, HI 96720, USA
| | - Alan Yocca
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - J Chris Pires
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523-1170, USA
| | - Alex E Harkess
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
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6
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Yang K, Huang Y, Li Z, Zeng Q, Dai X, Lv J, Zong X, Deng K, Zhang J. Overexpression of Nta-miR6155 confers resistance to Phytophthora nicotianae and regulates growth in tobacco ( Nicotiana tabacum L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1281373. [PMID: 38053762 PMCID: PMC10694243 DOI: 10.3389/fpls.2023.1281373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 10/26/2023] [Indexed: 12/07/2023]
Abstract
Tobacco black shank induced by Phytophthora nicotianae causes significant yield losses in tobacco plants. MicroRNAs (miRNAs) play a pivotal role in plant biotic stress responses and have great potential in tobacco breeding for disease resistance. However, the roles of miRNAs in tobacco plants in response to P. nicotianae infection has not been well characterized. In this study, we found that Nta-miR6155, a miRNA specific to Solanaceae crops, was significantly induced in P. nicotianae infected tobacco. Some of predicted target genes of Nta-miR6155 were also observed to be involved in disease resistance. To further investigate the function of miR6155 in tobacco during P. nicotianae infection, Nta-miR6155 overexpression plants (miR6155-OE) were generated in the Honghua Dajinyuan tobacco variety (HD, the main cultivated tobacco variety in China). We found that the Nta-miR6155 overexpression enhanced the resistance in tobacco towards P. nicotianae infections. The level of reactive oxygen species (ROS) was significantly lower and antioxidant enzyme activities were significantly higher in miR6155-OE plants than those in control HD plants during P. nicotianae infection. In addition, we found that the accumulation of salicylic acid and the expression of salicylic acid biosynthesis and signal transduction-related genes is significantly higher in miR6155-OE plants in comparison to the control HD plants. Furthermore, we found that Nta-miR6155 cleaved target genes NtCIPK18 to modulate resistance towards P. nicotianae in tobacco plants. Additionally, phenotypic analysis of miR6155-OE plants showed that Nta-miR6155 could inhibit the growth of tobacco by suppressing nitrogen uptake and photosynthesis. In conclusion, our findings indicated that miR6155 plays a crucial role in the regulation of growth and resistance against P. nicotianae infections in tobacco plants.
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Affiliation(s)
- Kaiyue Yang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Yuanyuan Huang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Zexuan Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Qian Zeng
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Xiumei Dai
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
- Chongqing Tobacco Science Research Institute, Chongqing, China
| | - Jun Lv
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
| | - Xuefeng Zong
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
| | - Kexuan Deng
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
- Chongqing Tobacco Science Research Institute, Chongqing, China
| | - Jiankui Zhang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
- Chongqing Tobacco Science Research Institute, Chongqing, China
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7
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Malhotra B, Kumar P, Bisht NC. Defense versus growth trade-offs: Insights from glucosinolates and their catabolites. PLANT, CELL & ENVIRONMENT 2023; 46:2964-2984. [PMID: 36207995 DOI: 10.1111/pce.14462] [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: 06/22/2022] [Revised: 09/14/2022] [Accepted: 10/03/2022] [Indexed: 06/16/2023]
Abstract
Specialized metabolites are a structurally diverse group of naturally occurring compounds that facilitate plant-environment interactions. Their synthesis and maintenance in plants is overall a resource-demanding process that occurs at the expense of growth and reproduction and typically incurs several costs. Evidence emerging on different specialized compounds suggests that they serve multiple auxiliary functions to influence and moderate primary metabolism in plants. These new functionalities enable them to mediate trade-offs from defenses to growth and also to offset their production and maintenance costs in plants. Recent research on glucosinolates (GSLs), which are specialized metabolites of Brassicales, demonstrates their emerging multifunctionalities to fine-tune plant growth and development under variable environments. Herein, we present findings from the septennium on individual GSLs and their catabolites (GHPs) per se, that work as mobile signals within plants to mediate precise regulations of their primary physiological functions. Both GSLs and GHPs calibrate growth-defense trade-off interactions either synergistically or directly when they function as storage compounds, abiotic stress alleviators, and one-to-one regulators of growth pathways in plants. We finally summarize the overall lessons learned from GSLs and GHPs as a model and raise the most pressing questions to address the molecular-genetic intricacies of specialized metabolite-based trade-offs in plants.
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Affiliation(s)
- Bhanu Malhotra
- National Institute of Plant Genome Research, New Delhi, India
| | - Pawan Kumar
- National Institute of Plant Genome Research, New Delhi, India
| | - Naveen C Bisht
- National Institute of Plant Genome Research, New Delhi, India
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8
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Sagwal V, Kumar U, Sihag P, Singh Y, Balyan P, Singh KP. Physiological traits and expression profile of genes associated with nitrogen and phosphorous use efficiency in wheat. Mol Biol Rep 2023; 50:5091-5103. [PMID: 37101006 DOI: 10.1007/s11033-023-08413-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 03/28/2023] [Indexed: 04/28/2023]
Abstract
BACKGROUND Nitrogen (N) and phosphorous (P) play a very important role in the growth and development of wheat as well as major constituents of biological membranes. To meet the plant's nutritional demand these nutrients are applied in the form of fertilizers. But the plant can utilize only half of the applied fertilizer whereas the rest is lost through surface runoff, leaching and volatilization. Thus, to overcome the N/P loss we need to elucidate the molecular mechanism behind the N/P uptake. METHODS In our study, we used DBW16 (low NUE), and WH147 (high NUE) wheat genotypes under different doses of N, whereas HD2967 (low PUE) and WH1100 (high PUE) genotypes were studied under different doses of P. To check the effect of different doses of N/P, the physiological parameters like total chlorophyll content, net photosynthetic rate, N/P content, and N/PUE of these genotypes were calculated. In addition, gene expression of various genes involved in N uptake, utilization, and acquisition such as Nitrite reductase (NiR), Nitrate transporter 1/Peptide transporter family (NPF2.4/2.5), Nitrate transporter (NRT1) and NIN Like Protein (NLP) and induced phosphate starvation (IPS), Phosphate Transporter (PHT1.7) and Phosphate 2 (PHO2) acquisition was studied by quantitative real-time PCR. RESULTS Statistical analysis revealed a lower percent reduction in TCC, NPR, and N/P content in N/P efficient wheat genotypes (WH147 & WH1100). A significant increase in relative fold expression of genes under low N/P concentration was observed in N/P efficient genotypes as compared to N/P deficient genotypes. CONCLUSION Significant differences in physiological data and gene expression among N/ P efficient and deficient wheat genotypes could be useful for future improvement of N/P use efficiency.
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Affiliation(s)
- Vijeta Sagwal
- Department of Molecular Biology & Biotechnology, College of Biotechnology, CCS Haryana Agricultural University, Hisar, 125004, India
| | - Upendra Kumar
- Department of Molecular Biology & Biotechnology, College of Biotechnology, CCS Haryana Agricultural University, Hisar, 125004, India.
| | - Pooja Sihag
- Department of Molecular Biology & Biotechnology, College of Biotechnology, CCS Haryana Agricultural University, Hisar, 125004, India
| | - Yogita Singh
- Department of Molecular Biology & Biotechnology, College of Biotechnology, CCS Haryana Agricultural University, Hisar, 125004, India
| | - Priyanka Balyan
- Department of Botany, Deva Nagri P.G. College, CCS University, Meerut, 245206, India
| | - Krishna Pal Singh
- Biophysics Unit, College of Basic Sciences & Humanities, GB Pant University of Agriculture & Technology, Pantnagar, 263145, India
- Vice-Chancellor's Secretariat, Mahatma Jyotiba Phule Rohilkhand University, Bareilly, 243001, India
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9
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Katz E, Knapp A, Lensink M, Keller CK, Stefani J, Li JJ, Shane E, Tuermer-Lee K, Bloom AJ, Kliebenstein DJ. Genetic variation underlying differential ammonium and nitrate responses in Arabidopsis thaliana. THE PLANT CELL 2022; 34:4696-4713. [PMID: 36130068 PMCID: PMC9709984 DOI: 10.1093/plcell/koac279] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 09/05/2022] [Indexed: 06/15/2023]
Abstract
Nitrogen is an essential element required for plant growth and productivity. Understanding the mechanisms and natural genetic variation underlying nitrogen use in plants will facilitate the engineering of plant nitrogen use to maximize crop productivity while minimizing environmental costs. To understand the scope of natural variation that may influence nitrogen use, we grew 1,135 Arabidopsis thaliana natural genotypes on two nitrogen sources, nitrate and ammonium, and measured both developmental and defense metabolite traits. By using different environments and focusing on multiple traits, we identified a wide array of different nitrogen responses. These responses are associated with numerous genes, most of which were not previously associated with nitrogen responses. Only a small portion of these genes appear to be shared between environments or traits, while most are predominantly specific to a developmental or defense trait under a specific nitrogen source. Finally, by using a large population, we were able to identify unique nitrogen responses, such as preferring ammonium or nitrate, which appear to be generated by combinations of loci rather than a few large-effect loci. This suggests that it may be possible to obtain novel phenotypes in complex nitrogen responses by manipulating sets of genes with small effects rather than solely focusing on large-effect single gene manipulations.
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Affiliation(s)
- Ella Katz
- Department of Plant Sciences, University of California Davis, Davis, California 95616, USA
| | - Anna Knapp
- Department of Plant Sciences, University of California Davis, Davis, California 95616, USA
| | - Mariele Lensink
- Department of Plant Sciences, University of California Davis, Davis, California 95616, USA
- Integrative Genetics and Genomics Graduate Group, University of California Davis, Davis, California 95616, USA
| | - Caroline Kaley Keller
- Department of Plant Sciences, University of California Davis, Davis, California 95616, USA
- Plant Biology Graduate Group, University of California Davis, Davis, California 95616, USA
| | - Jordan Stefani
- Department of Plant Sciences, University of California Davis, Davis, California 95616, USA
| | - Jia-Jie Li
- Department of Plant Sciences, University of California Davis, Davis, California 95616, USA
| | - Emily Shane
- Department of Plant Sciences, University of California Davis, Davis, California 95616, USA
| | - Kaelyn Tuermer-Lee
- Department of Plant Sciences, University of California Davis, Davis, California 95616, USA
| | - Arnold J Bloom
- Department of Plant Sciences, University of California Davis, Davis, California 95616, USA
| | - Daniel J Kliebenstein
- Department of Plant Sciences, University of California Davis, Davis, California 95616, USA
- DynaMo Center of Excellence, University of Copenhagen, 1165 Copenhagen, Denmark
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10
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Sakuraba Y. Molecular basis of nitrogen starvation-induced leaf senescence. FRONTIERS IN PLANT SCIENCE 2022; 13:1013304. [PMID: 36212285 PMCID: PMC9538721 DOI: 10.3389/fpls.2022.1013304] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 09/08/2022] [Indexed: 06/01/2023]
Abstract
Nitrogen (N), a macronutrient, is often a limiting factor in plant growth, development, and productivity. To adapt to N-deficient environments, plants have developed elaborate N starvation responses. Under N-deficient conditions, older leaves exhibit yellowing, owing to the degradation of proteins and chlorophyll pigments in chloroplasts and subsequent N remobilization from older leaves to younger leaves and developing organs to sustain plant growth and productivity. In recent years, numerous studies have been conducted on N starvation-induced leaf senescence as one of the representative plant responses to N deficiency, revealing that leaf senescence induced by N deficiency is highly complex and intricately regulated at different levels, including transcriptional, post-transcriptional, post-translational and metabolic levels, by multiple genes and proteins. This review summarizes the current knowledge of the molecular mechanisms associated with N starvation-induced leaf senescence.
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Affiliation(s)
- Yasuhito Sakuraba
- Plant Functional Biotechnology, Biotechnology Research Center, The University of Tokyo, Tokyo, Japan
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11
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Hossain R, Quispe C, Saikat ASM, Jain D, Habib A, Janmeda P, Islam MT, Radha, Daştan SD, Kumar M, Butnariu M, Cho WC, Sharifi-Rad J, Kipchakbayeva A, Calina D. Biosynthesis of Secondary Metabolites Based on the Regulation of MicroRNAs. BIOMED RESEARCH INTERNATIONAL 2022; 2022:9349897. [PMID: 35281611 PMCID: PMC8916866 DOI: 10.1155/2022/9349897] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 02/07/2022] [Indexed: 12/12/2022]
Abstract
MicroRNA (miRNA), a noncoding ribonucleic acid, is considered to be important for the progression of gene expression in plants and animals by rupture or translational repression of targeted mRNAs. Many types of miRNA regulate plant metabolism, growth, and response to biotic and abiotic factors. miRNA characterization helps to expose its function in regulating the process of post-transcriptional genetic regulation. There are a lot of factors associated with miRNA function, but the function of miRNA in the organic synthesis of by-products by natural products is not yet fully elucidated. The current review is aimed at observing and characterizing miRNAs and identifying those involved in the functioning of the biosynthesis of secondary metabolites in plants, with their use in controlled manipulation.
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Affiliation(s)
- Rajib Hossain
- Department of Pharmacy, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj 8100, Bangladesh
| | - Cristina Quispe
- Facultad de Ciencias de la Salud, Universidad Arturo Prat, Avda. Arturo Prat 2120, Iquique 1110939, Chile
| | - Abu Saim Mohammad Saikat
- Department of Biochemistry and Molecular Biology, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj 8100, Bangladesh
| | - Divya Jain
- Department of Bioscience and Biotechnology, Banasthali Vidyapith, Rajasthan, India
| | - Arslan Habib
- Lab of Infectious and Molecular Immunology, School of Life Sciences, Fudan University, Shanghai, China
| | - Pracheta Janmeda
- Department of Bioscience and Biotechnology, Banasthali Vidyapith, Rajasthan, India
| | - Muhammad Torequl Islam
- Department of Pharmacy, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj 8100, Bangladesh
| | - Radha
- School of Biological and Environmental Sciences, Shoolini University of Biotechnology and Management Sciences, Solan 173229, India
| | - Sevgi Durna Daştan
- Department of Biology, Faculty of Science, Sivas Cumhuriyet University, Sivas 58140, Turkey
- Beekeeping Development Application and Research Center, Sivas Cumhuriyet University, Sivas 58140, Turkey
| | - Manoj Kumar
- Chemical and Biochemical Processing Division, ICAR-Central Institute for Research on Cotton Technology, Mumbai 400019, India
| | - Monica Butnariu
- Banat's University of Agricultural Sciences and Veterinary Medicine “King Michael I of Romania” from Timisoara, Timisoara, Romania
| | - William C. Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Kowloon, Hong Kong
| | | | - Aliya Kipchakbayeva
- Faculty of Chemistry and Chemical Technology, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Daniela Calina
- Department of Clinical Pharmacy, University of Medicine and Pharmacy of Craiova, Craiova 200349, Romania
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12
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MicroRNA Mediated Plant Responses to Nutrient Stress. Int J Mol Sci 2022; 23:ijms23052562. [PMID: 35269700 PMCID: PMC8910084 DOI: 10.3390/ijms23052562] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/22/2022] [Accepted: 02/23/2022] [Indexed: 01/18/2023] Open
Abstract
To complete their life cycles, plants require several minerals that are found in soil. Plant growth and development can be affected by nutrient shortages or high nutrient availability. Several adaptations and evolutionary changes have enabled plants to cope with inappropriate growth conditions and low or high nutrient levels. MicroRNAs (miRNAs) have been recognized for transcript cleavage and translational reduction, and can be used for post-transcriptional regulation. Aside from regulating plant growth and development, miRNAs play a crucial role in regulating plant’s adaptations to adverse environmental conditions. Additionally, miRNAs are involved in plants’ sensory functions, nutrient uptake, long-distance root transport, and physiological functions related to nutrients. It may be possible to develop crops that can be cultivated in soils that are either deficient in nutrients or have extreme nutrient supplies by understanding how plant miRNAs are associated with nutrient stress. In this review, an overview is presented regarding recent advances in the understanding of plants’ responses to nitrogen, phosphorus, potassium, sulfur, copper, iron, boron, magnesium, manganese, zinc, and calcium deficiencies via miRNA regulation. We conclude with future research directions emphasizing the modification of crops for improving future food security.
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Miao N, Zhou J, Li M, Zhang J, Hu Y, Guo J, Zhang T, Shi L. Remodeling and protecting the membrane system to resist phosphorus deficiency in wild soybean (Glycine soja) seedling leaves. PLANTA 2022; 255:53. [PMID: 35099613 DOI: 10.1007/s00425-022-03834-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 01/17/2022] [Indexed: 06/14/2023]
Abstract
MAIN CONCLUSION The poor-soil-tolerant wild soybean resist phosphorus deficiency by remodeling membrane lipids to reuse phosphorus. The plants synthesize phenolic acids and flavonoids to remove reactive oxygen species and protect membrane stability. Poor soil largely limits plant yields, and the development and utilization of high-quality wild plant resources is an effective approach to resolving this problem. Two ecotypes of wild soybean were used as experimental materials in this experiment. We integrated metabolomics and transcriptomics to determine whether wild soybean (Glycine soja) could resist phosphorus deficiency by remodeling and protecting its membrane system. Under phosphorus-deficient conditions, the plant height and aboveground fresh and dry weight of poor-soil-tolerant wild soybean seedlings were less inhibited than those in common wild soybean. In poor-soil-tolerant wild soybean seedling leaves, the glycerol-3-phosphate content decreased significantly, while caffeic acid, ferulic acid, shikimic acid, phenylalanine, tyrosine, and tryptophan increased significantly. β-Glucosidase and chalcone synthase genes and those that encode SQD2, a crucial enzyme in thiolipid biosynthesis, were specifically up-regulated, whereas the glucosyltransferase UGT74B1 gene was down-regulated. The poor-soil-tolerant wild soybean enhanced glycerolipid metabolism to decompose phospholipids and release phosphorus for reuse to improve resistance to phosphorus deficiency. The plants synthesized thiolipids to replace phospholipids and maintain membrane structure integrity and inhibited glucosinolate biosynthesis to promote phenylpropanoid biosynthesis, leading to the production of phenolic acids and flavonoids that removed reactive oxygen species and protected membrane system stability. The experiments evaluated and provided insight into the innovative utilization of wild soybean germplasm resources.
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Affiliation(s)
- Ningning Miao
- Institute of Grassland Science, Northeast Normal University, Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun, 130024, China
| | - Ji Zhou
- Land Consolidation and Rehabilitation Centre, The Ministry of Land and Resources, Beijing, P.R. China
| | - Mingxia Li
- School of Life Sciences, ChangChun Normal University, Changchun, 130024, China
| | - Jiayi Zhang
- Institute of Grassland Science, Northeast Normal University, Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun, 130024, China
| | - Yunan Hu
- Institute of Grassland Science, Northeast Normal University, Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun, 130024, China
| | - Jixun Guo
- Institute of Grassland Science, Northeast Normal University, Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun, 130024, China
| | - Tao Zhang
- Institute of Grassland Science, Northeast Normal University, Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun, 130024, China.
| | - Lianxuan Shi
- Institute of Grassland Science, Northeast Normal University, Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun, 130024, China.
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14
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Noncoding-RNA-Mediated Regulation in Response to Macronutrient Stress in Plants. Int J Mol Sci 2021; 22:ijms222011205. [PMID: 34681864 PMCID: PMC8539900 DOI: 10.3390/ijms222011205] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/13/2021] [Accepted: 10/16/2021] [Indexed: 01/09/2023] Open
Abstract
Macronutrient elements including nitrogen (N), phosphorus (P), potassium (K), calcium (Ca), magnesium (Mg), and sulfur (S) are required in relatively large and steady amounts for plant growth and development. Deficient or excessive supply of macronutrients from external environments may trigger a series of plant responses at phenotypic and molecular levels during the entire life cycle. Among the intertwined molecular networks underlying plant responses to macronutrient stress, noncoding RNAs (ncRNAs), mainly microRNAs (miRNAs) and long ncRNAs (lncRNAs), may serve as pivotal regulators for the coordination between nutrient supply and plant demand, while the responsive ncRNA-target module and the interactive mechanism vary among elements and species. Towards a comprehensive identification and functional characterization of nutrient-responsive ncRNAs and their downstream molecules, high-throughput sequencing has produced massive omics data for comparative expression profiling as a first step. In this review, we highlight the recent findings of ncRNA-mediated regulation in response to macronutrient stress, with special emphasis on the large-scale sequencing efforts for screening out candidate nutrient-responsive ncRNAs in plants, and discuss potential improvements in theoretical study to provide better guidance for crop breeding practices.
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15
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The Novel Cucurbitaceae miRNA ClmiR86 Is Involved in Grafting-Enhanced Phosphate Utilization and Phosphate Starvation Tolerance in Watermelon. PLANTS 2021; 10:plants10102133. [PMID: 34685942 PMCID: PMC8540214 DOI: 10.3390/plants10102133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/05/2021] [Accepted: 10/05/2021] [Indexed: 11/24/2022]
Abstract
Watermelon (Citrullus lanatus) is a globally important Cucurbitaceae crop in which grafting is commonly used to improve stress tolerance and enhance nutrient utilization. However, the mechanism underlying grafting-enhanced nutrient assimilation remains unclear. Here, we demonstrate the possible involvement of a novel Cucurbitaceae miRNA, ClmiR86, in grafting-enhanced phosphate-starvation tolerance via CALCINEURIN B-LIKE INTERACTING PROTEIN KINASE 5 (ClCIPK5) suppression in watermelon. Transcript analyses revealed that the induction of ClmiR86 expression was correlated with the downregulation of ClCIPK5 in squash-grafted watermelon under phosphate starvation. In addition, the differential expression of ClmiR86 in various watermelon genotypes was consistent with their phosphate utilization efficiency. Furthermore, ClmiR86 overexpression in Arabidopsis enhanced root growth and phosphate uptake under phosphate starvation and promoted inflorescence elongation under normal conditions. These results suggest that the ClmiR86–ClCIPK5 axis is involved in phosphate starvation response as well as grafting-enhanced growth vigor and phosphate assimilation. The present study provides valuable insights for investigating long-distance signaling and nutrient utilization in plants.
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17
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Mitreiter S, Gigolashvili T. Regulation of glucosinolate biosynthesis. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:70-91. [PMID: 33313802 DOI: 10.1093/jxb/eraa479] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 10/14/2020] [Indexed: 05/18/2023]
Abstract
Glucosinolates are secondary defense metabolites produced by plants of the order Brassicales, which includes the model species Arabidopsis and many crop species. In the past 13 years, the regulation of glucosinolate synthesis in plants has been intensively studied, with recent research revealing complex molecular mechanisms that connect glucosinolate production with responses to other central pathways. In this review, we discuss how the regulation of glucosinolate biosynthesis is ecologically relevant for plants, how it is controlled by transcription factors, and how this transcriptional machinery interacts with hormonal, environmental, and epigenetic mechanisms. We present the central players in glucosinolate regulation, MYB and basic helix-loop-helix transcription factors, as well as the plant hormone jasmonate, which together with other hormones and environmental signals allow the coordinated and rapid regulation of glucosinolate genes. Furthermore, we highlight the regulatory connections between glucosinolates, auxin, and sulfur metabolism and discuss emerging insights and open questions on the regulation of glucosinolate biosynthesis.
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Affiliation(s)
- Simon Mitreiter
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
| | - Tamara Gigolashvili
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
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18
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Coleto I, Bejarano I, Marín-Peña AJ, Medina J, Rioja C, Burow M, Marino D. Arabidopsis thaliana transcription factors MYB28 and MYB29 shape ammonium stress responses by regulating Fe homeostasis. THE NEW PHYTOLOGIST 2021; 229:1021-1035. [PMID: 32901916 DOI: 10.1111/nph.16918] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 08/12/2020] [Indexed: 05/22/2023]
Abstract
Although ammonium (NH4+ ) is a key intermediate of plant nitrogen metabolism, high concentrations of NH4+ in the soil provoke physiological disorders that lead to the development of stress symptoms. Ammonium nutrition was shown to induce the accumulation of glucosinolates (GSLs) in leaves of different Brassicaceae species. To further understand the link between ammonium nutrition and GSLs, we analysed the ammonium stress response of Arabidopsis mutants impaired in GSL metabolic pathway. We showed that the MYB28 and MYB29 double mutant (myb28myb29), which is almost deprived of aliphatic GSLs, is highly hypersensitive to ammonium nutrition. Moreover, we evidenced that the stress symptoms developed were not a consequence of the lack of aliphatic GSLs. Transcriptomic analysis highlighted the induction of an iron (Fe) deficiency response in myb28myb29 under ammonium nutrition. Consistently, ammonium-grown myb28myb29 plants showed altered Fe accumulation and homeostasis. Interestingly, we showed overall that growing Arabidopsis with increased Fe availability relieved ammonium stress symptoms and that this was associated with MYB28 and MYB29 expression. Taken together, our data indicated that the control of Fe homeostasis was crucial for the Arabidopsis response to ammonium nutrition and evidenced that MYB28 and MYB29 play a role in this control.
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Affiliation(s)
- Inmaculada Coleto
- Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU), Apdo. 644, Bilbao, E-48080, Spain
| | - Iraide Bejarano
- Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU), Apdo. 644, Bilbao, E-48080, Spain
| | - Agustín Javier Marín-Peña
- Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU), Apdo. 644, Bilbao, E-48080, Spain
| | - Joaquín Medina
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo, Autopista M40 (km 38), Madrid, 28223, Spain
| | - Cristina Rioja
- Department of Plant and Environmental Sciences, DynaMo Center, University of Copenhagen, Frederiksberg, Denmark
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Meike Burow
- Department of Plant and Environmental Sciences, DynaMo Center, University of Copenhagen, Frederiksberg, Denmark
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Daniel Marino
- Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU), Apdo. 644, Bilbao, E-48080, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, E-48011, Spain
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Fukuda M, Fujiwara T, Nishida S. Roles of Non-Coding RNAs in Response to Nitrogen Availability in Plants. Int J Mol Sci 2020; 21:ijms21228508. [PMID: 33198163 PMCID: PMC7696010 DOI: 10.3390/ijms21228508] [Citation(s) in RCA: 10] [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: 10/22/2020] [Revised: 11/06/2020] [Accepted: 11/10/2020] [Indexed: 01/06/2023] Open
Abstract
Nitrogen (N) is an essential nutrient for plant growth and development; therefore, N deficiency is a major limiting factor in crop production. Plants have evolved mechanisms to cope with N deficiency, and the role of protein-coding genes in these mechanisms has been well studied. In the last decades, regulatory non-coding RNAs (ncRNAs), such as microRNAs (miRNAs), small interfering RNAs (siRNAs), and long ncRNAs (lncRNAs), have emerged as important regulators of gene expression in diverse biological processes. Recent advances in technologies for transcriptome analysis have enabled identification of N-responsive ncRNAs on a genome-wide scale. Characterization of these ncRNAs is expected to improve our understanding of the gene regulatory mechanisms of N response. In this review, we highlight recent progress in identification and characterization of N-responsive ncRNAs in Arabidopsis thaliana and several other plant species including maize, rice, and Populus.
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Affiliation(s)
- Makiha Fukuda
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, New York University Langone Health, New York, NY 10016, USA;
| | - Toru Fujiwara
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan;
| | - Sho Nishida
- Department of Bioresource Science, Faculty of Agriculture, Saga University, 1 Honjo-machi, Saga 840-8502, Japan
- Correspondence: ; Tel.: +81-952-28-8720
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20
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Fan H, Quan S, Qi S, Xu N, Wang Y. Novel Aspects of Nitrate Regulation in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2020; 11:574246. [PMID: 33362808 PMCID: PMC7758431 DOI: 10.3389/fpls.2020.574246] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 11/18/2020] [Indexed: 05/04/2023]
Abstract
Nitrogen (N) is one of the most essential macronutrients for plant growth and development. Nitrate (NO3 -), the major form of N that plants uptake from the soil, acts as an important signaling molecule in addition to its nutritional function. Over the past decade, significant progress has been made in identifying new components involved in NO3 - regulation and starting to unravel the NO3 - regulatory network. Great reviews have been made recently by scientists on the key regulators in NO3 - signaling, NO3 - effects on plant development, and its crosstalk with phosphorus (P), potassium (K), hormones, and calcium signaling. However, several novel aspects of NO3 - regulation have not been previously reviewed in detail. Here, we mainly focused on the recent advances of post-transcriptional regulation and non-coding RNA (ncRNAs) in NO3 - signaling, and NO3 - regulation on leaf senescence and the circadian clock. It will help us to extend the general picture of NO3 - regulation and provide a basis for further exploration of NO3 - regulatory network.
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Affiliation(s)
- Hongmei Fan
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai’an, China
| | - Shuxuan Quan
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai’an, China
| | - Shengdong Qi
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai’an, China
| | - Na Xu
- School of Biological Science, Jining Medical University, Rizhao, China
| | - Yong Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai’an, China
- *Correspondence: Yong Wang,
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Baek SA, Im KH, Park SU, Oh SD, Choi J, Kim JK. Dynamics of Short-Term Metabolic Profiling in Radish Sprouts ( Raphanus sativus L.) in Response to Nitrogen Deficiency. PLANTS 2019; 8:plants8100361. [PMID: 31547524 PMCID: PMC6843509 DOI: 10.3390/plants8100361] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 09/19/2019] [Accepted: 09/20/2019] [Indexed: 12/15/2022]
Abstract
Nitrogen (N) is a macronutrient important for the survival of plants. To investigate the effects of N deficiency, a time-course metabolic profiling of radish sprouts was performed. A total of 81 metabolites—including organic acids, inorganic acid, amino acids, sugars, sugar alcohols, amines, amide, sugar phosphates, policosanols, tocopherols, phytosterols, carotenoids, chlorophylls, and glucosinolates—were characterized. Principal component analysis and heat map showed distinction between samples grown under different N conditions, as well as with time. Using PathVisio, metabolic shift in biosynthetic pathways was visualized using the metabolite data obtained for 7 days. The amino acids associated with glucosinolates accumulated as an immediate response against –N condition. The synthesis of pigments and glucosinolates was decreased, but monosaccharides and γ-tocopherol were increased as antioxidants in radish sprouts grown in –N condition. These results indicate that in radish sprouts, response to N deficiency occurred quickly and dynamically. Thus, this metabolic phenotype reveals that radish responds quickly to N deficiency by increasing the content of soluble sugars and γ-tocopherol, which acts as a defense mechanism after the germination of radish seeds.
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Affiliation(s)
- Seung-A Baek
- Division of Life Sciences and Bio-Resource and Environmental Center, College of Life Sciences and Bioengineering, Incheon National University, Incheon 22012, Korea.
| | - Kyung-Hoan Im
- Division of Life Sciences and Bio-Resource and Environmental Center, College of Life Sciences and Bioengineering, Incheon National University, Incheon 22012, Korea.
| | - Sang Un Park
- Department of Crop Science, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea.
| | - Sung-Dug Oh
- National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Korea.
| | - Jaehyuk Choi
- Division of Life Sciences and Bio-Resource and Environmental Center, College of Life Sciences and Bioengineering, Incheon National University, Incheon 22012, Korea.
| | - Jae Kwang Kim
- Division of Life Sciences and Bio-Resource and Environmental Center, College of Life Sciences and Bioengineering, Incheon National University, Incheon 22012, Korea.
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Physiological responses and small RNAs changes in maize under nitrogen deficiency and resupply. Genes Genomics 2019; 41:1183-1194. [PMID: 31313105 DOI: 10.1007/s13258-019-00848-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 07/02/2019] [Indexed: 02/08/2023]
Abstract
BACKGROUND Maize is an important crop in the world, nitrogen stress severely reduces maize yield. Although a large number of studies have identified the expression changes of microRNAs (miRNAs) under N stress in several species, the miRNAs expression patterns of N-deficient plants under N resupply remain unclear. OBJECTIVE The primary objective of this study was to identify miRNAs in response to nitrogen stress and understand relevant physiological changes in nitrogen-deficient maize after nitrogen resupply. METHODS Physiological parameters were measured to study relevant physiological changes under different nitrogen conditions. Small RNA sequencing and qRT-PCR analysis were performed to understand the response of miRNAs under different nitrogen conditions. RESULTS The content of chlorophyll, soluble protein and nitrate nitrogen decreased than CK by 0.52, 0.49 and 0.82 times after N deficiency treatment and increased than ND by 0.52, 1.36 and 0.65 times after N resupply, respectively. Conversely, the activity of superoxide dismutase (SOD) and peroxidase (POD) increased by 0.67 and 1.64 times than CK after N deficiency, respectively, and decreased by 0.09 and 0.35 times than ND after N resupply. A total of 226 known miRNAs were identified by sRNA sequencing; 106 miRNAs were differentially expressed between the control and N-deficient groups, and 103 were differentially expressed between the N-deficient and N-resupply groups (P < 0.05). Real-time quantitative PCR (qPCR) was used to further validate and analyze the expression of the identified miRNAs. A total of 1609 target genes were identified by target prediction, and some differentially expressed miRNAs were predicted to target transcription factors and functional proteins. Gene Ontology (GO) analysis was used to determine the biological function of these targets and revealed that some miRNAs, such as miR169, miR1214, miR2199, miR398, miR408 and miR827 might be involved in nitrogen metabolism regulation. CONCLUSION Our study comprehensively provides important information on miRNA functions and molecular mechanisms in response to N stress. These findings may assist to improve nitrogen availability in plants.
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Chen L, Meng J, Luan Y. miR1916 plays a role as a negative regulator in drought stress resistance in tomato and tobacco. Biochem Biophys Res Commun 2019; 508:597-602. [PMID: 30514439 DOI: 10.1016/j.bbrc.2018.11.165] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 11/27/2018] [Indexed: 10/27/2022]
Abstract
MicroRNAs (miRNAs) play important roles in regulating plant responses to various environmental stresses. In our study, overexpression of miR1916 in tomato (OE-1) reduced its tolerance to drought. The miR1916-silenced transgenic plants (ST-1 and Anti-7) significantly increased resistance to drought stress. The transgenic tobacco plants also have a similar result in displaying the tolerance of drought. Physiological analysis revealed that miR1916 affected the osmoregulation and reactive oxygen species (ROS) accumulation. In addition, transcript levels of the miR1916 target genes, histone deacetylases (HDAC) and strictosidine synthase (STR), decreased in miR1916-overexpressing transgenic tobacco plants. Our results suggested that miR1916 is a passive regulator in the plant resistance to drought stress and has potentially impacting on abiotic stress responses in Solanaceae.
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Affiliation(s)
- Lei Chen
- School of Life Sciences and Biotechnology, Dalian University of Technology, Dalian, 116024, China
| | - Jun Meng
- School of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Yushi Luan
- School of Life Sciences and Biotechnology, Dalian University of Technology, Dalian, 116024, China.
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Zhang X, Lai Y, Zhang W, Ahmad J, Qiu Y, Zhang X, Duan M, Liu T, Song J, Wang H, Li X. MicroRNAs and their targets in cucumber shoot apices in response to temperature and photoperiod. BMC Genomics 2018; 19:819. [PMID: 30442111 PMCID: PMC6238408 DOI: 10.1186/s12864-018-5204-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 10/25/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The cucumber is one of the most important vegetables worldwide and is used as a research model for study of phloem transport, sex determination and temperature-photoperiod physiology. The shoot apex is the most important plant tissue in which the cell fate and organ meristems have been determined. In this study, a series of whole-genome small RNA, degradome and transcriptome analyses were performed on cucumber shoot apical tissues treated with high vs. low temperature and long vs. short photoperiod. RESULTS A total of 164 known miRNAs derived from 68 families and 203 novel miRNAs from 182 families were identified. Their 4611 targets were predicted using psRobot and TargetFinder, amongst which 349 were validated by degradome sequencing. Fourteen targets of six miRNAs were differentially expressed between the treatments. A total of eight known and 16 novel miRNAs were affected by temperature and photoperiod. Functional annotations revealed that "Plant hormone signal transduction" pathway was significantly over-represented in the miRNA targets. The miR156/157/SBP-Boxes and novel-mir153/ethylene-responsive transcription factor/senescence-related protein/aminotransferase/acyl-CoA thioesterase are the two most credible miRNA/targets combinations modulating the plant's responsive processes to the temperature-photoperiod changes. Moreover, the newly evolved, cucumber-specific novel miRNA (novel-mir153) was found to target 2087 mRNAs by prediction and has 232 targets proven by degradome analysis, accounting for 45.26-58.88% of the total miRNA targets in this plant. This is the largest sum of genes targeted by a single miRNA to the best of our knowledge. CONCLUSIONS These results contribute to a better understanding of the miRNAs mediating plant adaptation to combinations of temperature and photoperiod and sheds light on the recent evolution of new miRNAs in cucumber.
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Affiliation(s)
- Xiaohui Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture; Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yunsong Lai
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture; Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.,Institute of Pomology & Olericulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wei Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture; Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jalil Ahmad
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture; Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yang Qiu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture; Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaoxue Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture; Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Mengmeng Duan
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture; Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Tongjin Liu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture; Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jiangping Song
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture; Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Haiping Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture; Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xixiang Li
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture; Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Jung JY, Ahn JH, Schachtman DP. CC-type glutaredoxins mediate plant response and signaling under nitrate starvation in Arabidopsis. BMC PLANT BIOLOGY 2018; 18:281. [PMID: 30424734 PMCID: PMC6234535 DOI: 10.1186/s12870-018-1512-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 10/30/2018] [Indexed: 05/05/2023]
Abstract
BACKGROUND Nitrogen is an essential nutrient in plants. Despite the importance of nitrogen for plant growth and agricultural productivity, signal transduction pathways in response to nitrate starvation have not been fully elucidated in plants. RESULTS Gene expression analysis and ectopic expression were used to discover that many CC-type glutaredoxins (ROXYs) are differentially expressed in response to nitrate deprivation. A gain-of-function approach showed that ROXYs may play a role in nutrient sensing through the regulation of chlorophyll content, root hair growth, and transcription of nitrate-related genes such as NRT2.1 under low or high nitrate conditions. Reactive oxygen species (ROS) were produced in plant roots under nitrate starvation and H2O2 treatment differentially regulated the expression of the ROXYs, suggesting the involvement of ROS in signaling pathways under nitrate deficiency. CONCLUSION This work adds to what is known about nitrogen sensing and signaling through the findings that the ROXYs and ROS are likely to be involved in the nitrate deprivation signaling pathway.
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Affiliation(s)
- Ji-Yul Jung
- Department of Life Sciences, Korea University, Seoul, 02841 South Korea
| | - Ji Hoon Ahn
- Department of Life Sciences, Korea University, Seoul, 02841 South Korea
| | - Daniel P. Schachtman
- Department of Agronomy and Horticulture, Center for Biotechnology, University of Nebraska Lincoln, Lincoln, NE 68588 USA
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Park BS, Yao T, Seo JS, Wong ECC, Mitsuda N, Huang CH, Chua NH. Arabidopsis NITROGEN LIMITATION ADAPTATION regulates ORE1 homeostasis during senescence induced by nitrogen deficiency. NATURE PLANTS 2018; 4:898-903. [PMID: 30374089 DOI: 10.1038/s41477-018-0269-8] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 09/05/2018] [Indexed: 05/04/2023]
Abstract
Nitrogen is an important macronutrient in plants and its deficiency induces rapid leaf senescence. Two genes, ORE1 and NITROGEN LIMITATION ADAPTATION (NLA), have been implicated in regulating the senescence process but their relationship is unclear1,2. Here, we show that nla and pho2 (also known as ubc24) plants develop rapid leaf senescence under nitrogen-starvation condition, whereas ore1 and nla/ore1 and pho2 (ubc24)/ore1 plants stay green. These results suggest that ORE1 acts downstream of NLA and PHO2 (UBC24). NLA interacts with ORE1 in the nucleus and regulates its stability through polyubiquitination using PHO2 (UBC24) as the E2 conjugase. Our findings identified ORE1 as a downstream target of NLA/PHO2 (UBC24) and showed that post-translational regulation of ORE1 levels determines leaf senescence during nitrogen deficiency.
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Affiliation(s)
- Bong Soo Park
- Temasek Life Sciences Laboratory, National University of Singapore, 117604, Singapore
| | - Tao Yao
- Temasek Life Sciences Laboratory, National University of Singapore, 117604, Singapore
| | - Jun Sung Seo
- Temasek Life Sciences Laboratory, National University of Singapore, 117604, Singapore
| | - Eriko Chi Cheng Wong
- Temasek Life Sciences Laboratory, National University of Singapore, 117604, Singapore
| | - Nobutaka Mitsuda
- Plant Gene Regulation Research Group, Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
| | - Chung-Hao Huang
- Temasek Life Sciences Laboratory, National University of Singapore, 117604, Singapore
| | - Nam-Hai Chua
- Temasek Life Sciences Laboratory, National University of Singapore, 117604, Singapore.
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Yu C, Chen Y, Cao Y, Chen H, Wang J, Bi YM, Tian F, Yang F, Rothstein SJ, Zhou X, He C. Overexpression of miR169o, an Overlapping MicroRNA in Response to Both Nitrogen Limitation and Bacterial Infection, Promotes Nitrogen Use Efficiency and Susceptibility to Bacterial Blight in Rice. PLANT & CELL PHYSIOLOGY 2018; 59:1234-1247. [PMID: 29566243 DOI: 10.1093/pcp/pcy060] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 03/14/2018] [Indexed: 05/04/2023]
Abstract
Limiting nitrogen (N) supply contributes to improved resistance to bacterial blight (BB) caused by Xanthomonas oryzae pv. oryzae (Xoo) in susceptible rice (Oryza sativa). To understand the regulatory roles of microRNAs (miRNAs) in this phenomenon, 63 differentially expressed overlapping miRNAs in response to Xoo infection and N limitation stress in rice were identified through deep RNA sequencing and stem-loop quantitative real-time PCR. Among these, miR169o was further assessed as a typical overlapping miRNA through the overexpression of the miR169o primary gene. Osa-miR169o-OX plants were taller, and had more biomass accumulation with significantly increased nitrate and total amino acid contents in roots than the wild type (WT). Transcript level assays showed that under different N supply conditions, miR169o oppositely regulated NRT2, and this is reduced under normal N supply conditions but remarkably induced under N-limiting stress. On the other hand, osa-miR169o-OX plants also displayed increased disease lesion lengths and reduced transcriptional levels of defense gene (PR1b, PR10a, PR10b and PAL) compared with the WT after inoculation with Xoo. In addition, miR169o impeded Xoo-mediated NRT transcription. Therefore, the overlapping miR169o contributes to increase N use efficiency and negatively regulates the resistance to BB in rice. Consistently, transient expression of NF-YA genes in rice protoplasts promoted the transcripts of PR genes and NRT2 genes, while it reduced the transcripts of NRT1 genes. Our results provide novel and additional insights into the co ordinated regulatory mechanisms of cross-talk between Xoo infection and N deficiency responses in rice.
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Affiliation(s)
- Chao Yu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yutong Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yaqian Cao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Huamin Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jichun Wang
- Institute of Plant Protection, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, China
| | - Yong-Mei Bi
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Fang Tian
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Fenghuan Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Steven J Rothstein
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Xueping Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Chenyang He
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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Understanding nitrate uptake, signaling and remobilisation for improving plant nitrogen use efficiency. Semin Cell Dev Biol 2018; 74:89-96. [DOI: 10.1016/j.semcdb.2017.08.034] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 08/14/2017] [Accepted: 08/16/2017] [Indexed: 12/31/2022]
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Tian X, Song L, Wang Y, Jin W, Tong F, Wu F. miR394 Acts as a Negative Regulator of Arabidopsis Resistance to B. cinerea Infection by Targeting LCR. FRONTIERS IN PLANT SCIENCE 2018; 9:903. [PMID: 30018624 PMCID: PMC6037856 DOI: 10.3389/fpls.2018.00903] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 06/07/2018] [Indexed: 05/11/2023]
Abstract
Gray mold of tomato is caused by the pathogen Botrytis cinerea. MicroRNAs play a crucial role in the biotic and abiotic stress responses of plants and regulate their targets by gene silencing. miR394 is an ancient and conserved miRNA in plants, and it participates in the regulation of plant development and stress responses. In our previous study, miR394 was found to respond to B. cinerea infection in tomato, but the roles and regulatory mechanisms of miR394 in B. cinerea-infected tomato remain unclear. miR394 was down-regulated in tomato in response to B. cinerea infection, showing an expression pattern opposite to the previous finding that miR394 was up-regulated in tomato cv. Jinpeng 1 infected by B. cinerea. We obtained transgenic Arabidopsis overexpressing miR394, which resulted in low expression levels of its target LEAF CURLING RESPONSIVENESS (LCR). Leaf lesion size and trypan blue staining showed that miR394 overexpression led to increased sensitivity of transgenic Arabidopsis to B. cinerea compared to wild type. We also detected changes in the expression levels of stress-related miRNAs, including miR159, miR156, miR168, and miR172. In the transgenic plants, it indicated potential cross talk between these miRNAs and miR394, except for miR159. miR394 also enhanced the expression of ARGONAUTE 1 (AGO1), DSRNA-BINDING PROTEIN 4 (DRB4) and the RNA-binding protein gene DAWDLE (DDL), which are involved in the pathways of miRNA biosynthesis and regulation, suggesting that miR394 overexpression has a feedback effect on these genes. Our data indicate that overexpression of miR394 in Arabidopsis increased the susceptibility of plants to B. cinerea by affecting the expression of its target gene LCR along with a number of key genes involved in plant miRNA metabolism (AGO1). Thus, miR394 is a negative regulator of Arabidopsis resistance to B. cinerea infection by targeting LCR.
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Affiliation(s)
| | | | | | - Weibo Jin
- *Correspondence: Weibo Jin, Fudan Tong, Fangli Wu,
| | - Fudan Tong
- *Correspondence: Weibo Jin, Fudan Tong, Fangli Wu,
| | - Fangli Wu
- *Correspondence: Weibo Jin, Fudan Tong, Fangli Wu,
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30
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Saroha M, Singroha G, Sharma M, Mehta G, Gupta OP, Sharma P. sRNA and epigenetic mediated abiotic stress tolerance in plants. ACTA ACUST UNITED AC 2017. [DOI: 10.1007/s40502-017-0330-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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31
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Zhao D, Xia X, Wei M, Sun J, Meng J, Tao J. Overexpression of herbaceous peony miR156e-3p improves anthocyanin accumulation in transgenic Arabidopsis thaliana lateral branches. 3 Biotech 2017; 7:379. [PMID: 29071176 DOI: 10.1007/s13205-017-1011-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 10/14/2017] [Indexed: 12/19/2022] Open
Abstract
microRNAs (miRNAs) play critical regulatory roles in plant growth and development. In the present study, the function of herbaceous peony (Paeonia lactiflora Pall.) miR156e-3p in the regulation of color formation has been investigated. Firstly, P. lactiflora miR156e-3p precursor sequence (pre-miR156e-3p) was isolated. Subsequently, the overexpression vector of pre-miR156e-3p was constructed and transformed into Arabidopsis thaliana. Moreover, the medium screening, GUS staining, polymerase chain reaction (PCR) of the GUS region and real-time quantitative PCR (qRT-PCR) of miR156e-3p all confirmed that the purpose gene had been successfully transferred into Arabidopsis plants and expressed, which resulted in apparent purple lateral branches. And this change in color was caused by the improved anthocyanin accumulation. In addition, expression analysis had shown that the level of miR156e-3p transcript was increased, while transcription level of target gene squamosa promoter binding protein-like gene (SPL1), encoding SPL transcription factor that negatively regulated anthocyanin accumulation, was repressed in miR156e-3p-overexpressing transgenic plants, and its downstream gene dihydroflavonol 4-reductase gene (DFR) that was directly involved in anthocyanin biosynthesis was strongly expressed, which resulted in anthocyanin accumulation of Arabidopsis lateral branches. These findings would improve the understanding of miRNAs regulation of color formation in P. lactiflora.
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Affiliation(s)
- Daqiu Zhao
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009 People's Republic of China
| | - Xing Xia
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009 People's Republic of China
| | - Mengran Wei
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009 People's Republic of China
| | - Jing Sun
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009 People's Republic of China
| | - Jiasong Meng
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009 People's Republic of China
| | - Jun Tao
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009 People's Republic of China
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32
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Chien PS, Chiang CB, Wang Z, Chiou TJ. MicroRNA-mediated signaling and regulation of nutrient transport and utilization. CURRENT OPINION IN PLANT BIOLOGY 2017; 39:73-79. [PMID: 28668626 DOI: 10.1016/j.pbi.2017.06.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Revised: 06/10/2017] [Accepted: 06/12/2017] [Indexed: 05/23/2023]
Abstract
MicroRNAs (miRNAs), a group of small-RNA regulators, control diverse developmental processes and stress responses. Recent studies of nutrient-responsive miRNAs have offered novel insights into how plants regulate gene expression to coordinate endogenous demand and external availability of nutrients. Here, we review the mechanisms mediated by miRNAs to facilitate nutrient transport and utilization and show that miRNAs: first, control nutrient uptake and translocation by targeting nutrient transporters or their regulators; second, adjust nutrient metabolism by redistributing nutrients for biosynthesis of more essential compounds; and third, modulate root development and microbial symbiosis to exploit soil nutrients. We also highlight the long-distance movement of miRNAs in maintaining whole-plant nutrient homeostasis and propose several directions for future research.
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Affiliation(s)
- Pei-Shan Chien
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Chih-Bin Chiang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Zhengrui Wang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Tzyy-Jen Chiou
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan.
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33
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Li S, Castillo-González C, Yu B, Zhang X. The functions of plant small RNAs in development and in stress responses. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:654-670. [PMID: 27943457 DOI: 10.1111/tpj.13444] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 11/29/2016] [Accepted: 12/06/2016] [Indexed: 05/22/2023]
Abstract
Like metazoans, plants use small regulatory RNAs (sRNAs) to direct gene expression. Several classes of sRNAs, which are distinguished by their origin and biogenesis, exist in plants. Among them, microRNAs (miRNAs) and trans-acting small interfering RNAs (ta-siRNAs) mainly inhibit gene expression at post-transcriptional levels. In the past decades, plant miRNAs and ta-siRNAs have been shown to be essential for numerous developmental processes, including growth and development of shoots, leaves, flowers, roots and seeds, among others. In addition, miRNAs and ta-siRNAs are also involved in the plant responses to abiotic and biotic stresses, such as drought, temperature, salinity, nutrient deprivation, bacteria, virus and others. This review summarizes the roles of miRNAs and ta-siRNAs in plant physiology and development.
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Affiliation(s)
- Shengjun Li
- Center for Plant Science Innovation and School of Biological Sciences, University of Nebraska, Lincoln, NE, 68588-0660, USA
| | - Claudia Castillo-González
- Department of Biochemistry and Biophysics & Institute of Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, 77843, USA
| | - Bin Yu
- Center for Plant Science Innovation and School of Biological Sciences, University of Nebraska, Lincoln, NE, 68588-0660, USA
| | - Xiuren Zhang
- Department of Biochemistry and Biophysics & Institute of Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, 77843, USA
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34
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Regulation of miR163 and its targets in defense against Pseudomonas syringae in Arabidopsis thaliana. Sci Rep 2017; 7:46433. [PMID: 28401908 PMCID: PMC5388894 DOI: 10.1038/srep46433] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 03/20/2017] [Indexed: 02/07/2023] Open
Abstract
Small RNAs are important regulators for a variety of biological processes, including leaf development, flowering-time, embryogenesis and defense responses. miR163 is a non-conserved miRNA and its locus has evolved recently through inverted duplication of its target genes to which they belong to the SABATH family of related small-molecule methyltransferases (MTs). In Arabidopsis thaliana, previous study demonstrated that miR163 accumulation was induced by alamethicin treatment, suggesting its roles in defense response pathways. Enhanced resistance against Pseudomonas syringae pv. tomato (Pst) was observed in the mir163 mutant, whereas transgenic lines overexpressing miR163 showed increase sensitivity to Pst, suggesting that miR163 is a negative regulator of defense response. Elevated level of miR163 and its targets in A. thaliana were observed upon Pst treatment, suggesting a modulating relationship between miR163 and its targets. In addition, miR163 and histone deacetylase were found to act cooperatively in mediating defense against Pst. Transgenic plants overexpressing miR163-resistant targets suggested their different contributions in defense. Results from this study revealed that the stress-inducible miR163 and its targets act in concert to modulate defense responses against bacterial pathogen in A. thaliana.
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35
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Cui J, You C, Chen X. The evolution of microRNAs in plants. CURRENT OPINION IN PLANT BIOLOGY 2017; 35:61-67. [PMID: 27886593 PMCID: PMC5342909 DOI: 10.1016/j.pbi.2016.11.006] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 11/05/2016] [Accepted: 11/08/2016] [Indexed: 05/20/2023]
Abstract
MicroRNAs (miRNAs) are a central player in post-transcriptional regulation of gene expression and are involved in numerous biological processes in eukaryotes. Knowledge of the origins and divergence of miRNAs paves the way for a better understanding of the complexity of the regulatory networks that they participate in. The biogenesis, degradation, and regulatory activities of miRNAs are relatively better understood, but the evolutionary history of miRNAs still needs more exploration. Inverted duplication of target genes, random hairpin sequences and small transposable elements constitute three main models that explain the origination of miRNA genes (MIR). Both inter-species and intra-species divergence of miRNAs exhibits functional adaptation and adaptation to changing environments in evolution. Here we summarize recent progress in studies on the evolution of MIR and related genes.
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Affiliation(s)
- Jie Cui
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, PR China; Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, PR China
| | - Chenjiang You
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, PR China; Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, PR China; Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Xuemei Chen
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, PR China; Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA; Howard Hughes Medical Institute, University of California, Riverside, CA 92521, USA.
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36
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Augustine R, Bisht NC. Regulation of Glucosinolate Metabolism: From Model Plant Arabidopsis thaliana to Brassica Crops. REFERENCE SERIES IN PHYTOCHEMISTRY 2017. [DOI: 10.1007/978-3-319-25462-3_3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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37
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Gupta OP, Karkute SG, Banerjee S, Meena NL, Dahuja A. Contemporary Understanding of miRNA-Based Regulation of Secondary Metabolites Biosynthesis in Plants. FRONTIERS IN PLANT SCIENCE 2017; 8:374. [PMID: 28424705 PMCID: PMC5372812 DOI: 10.3389/fpls.2017.00374] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 03/03/2017] [Indexed: 05/20/2023]
Abstract
Plant's secondary metabolites such as flavonoids, terpenoids, and alkaloids etc. are known for their role in the defense against various insects-pests of plants and for medicinal benefits in human. Due to the immense biological importance of these phytochemicals, understanding the regulation of their biosynthetic pathway is crucial. In the recent past, advancement in the molecular technologies has enabled us to better understand the proteins, enzymes, genes, etc. involved in the biosynthetic pathway of the secondary metabolites. miRNAs are magical, tiny, non-coding ribonucleotides that function as critical regulators of gene expression in eukaryotes. Despite the accumulated knowledge of the miRNA-mediated regulation of several processes, the involvement of miRNAs in regulating secondary plant product biosynthesis is still poorly understood. Here, we summarize the recent progress made in the area of identification and characterizations of miRNAs involved in regulating the biosynthesis of secondary metabolites in plants and discuss the future perspectives for designing the viable strategies for their targeted manipulation.
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Affiliation(s)
- Om P. Gupta
- Division of Quality and Basic Sciences, ICAR-Indian Institute of Wheat and Barley ResearchKarnal, India
- *Correspondence: Om P. Gupta
| | - Suhas G. Karkute
- Division of Vegetable Improvement, ICAR-Indian Institute of Vegetable ResearchVaranasi, India
| | - Sagar Banerjee
- Division of Biochemistry, ICAR-Indian Agricultural Research InstituteNew Delhi, India
| | - Nand L. Meena
- Division of Basic Sciences, ICAR-Indian Institute of Millets ResearchHyderabad, India
| | - Anil Dahuja
- Division of Biochemistry, ICAR-Indian Agricultural Research InstituteNew Delhi, India
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38
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Lou D, Wang H, Liang G, Yu D. OsSAPK2 Confers Abscisic Acid Sensitivity and Tolerance to Drought Stress in Rice. FRONTIERS IN PLANT SCIENCE 2017; 8:993. [PMID: 28659944 PMCID: PMC5468418 DOI: 10.3389/fpls.2017.00993] [Citation(s) in RCA: 137] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 05/26/2017] [Indexed: 05/19/2023]
Abstract
SNF 1-RELATED PROTEIN KINASE 2 (SnRK2) is a family of plant-specific protein kinases which is the key regulator of hyper-osmotic stress signaling and abscisic acid (ABA)-dependent development in various plants. Among the rice subclass-I and -II SnRK2s, osmotic stress/ABA-activated protein kinase 2 (SAPK2) may be the primary mediator of ABA signaling. However, SAPK2 has not been comprehensively characterized. In this study, we elucidated the functional properties of SAPK2 using loss-of-function mutants produced with the CRISPR/Cas9 system. The SAPK2 expression level was strongly upregulated by drought, high-salinity, and polyethylene glycol (PEG) treatments. The sapk2 mutants exhibited an ABA-insensitive phenotype during the germination and post-germination stages, suggesting that SAPK2 had a pivotal role related to ABA-mediated seed dormancy. The sapk2 mutants were more sensitive to drought stress and reactive oxygen species (ROS) than the wild-type plants, indicating that SAPK2 was important for responses to drought conditions in rice. An additional investigation revealed that SAPK2 increased drought tolerance in the following two ways: (i) by reducing water loss via the accumulation of compatible solutes, promoting stomatal closure, and upregulating the expression levels of stress-response genes such as OsRab16b, OsRab21, OsbZIP23, OsLEA3, OsOREB1 and slow anion channel (SLAC)-associated genes such as OsSLAC1 and OsSLAC7; (ii) by inducing the expression of antioxidant enzyme genes to promote ROS-scavenging abilities that will ultimately decrease ROS damages. Moreover, we also observed that SAPK2 significantly increased the tolerance of rice plants to salt and PEG stresses. These findings imply that SAPK2 is a potential candidate gene for future crop improvement studies.
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Affiliation(s)
- Dengji Lou
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of SciencesKunming, China
- College of Life Sciences, University of Chinese Academy of SciencesBeijing, China
| | - Houping Wang
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of SciencesKunming, China
- College of Life Sciences, University of Chinese Academy of SciencesBeijing, China
| | - Gang Liang
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of SciencesKunming, China
| | - Diqiu Yu
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of SciencesKunming, China
- *Correspondence: Diqiu Yu,
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Liu Q, Yang T, Yu T, Zhang S, Mao X, Zhao J, Wang X, Dong J, Liu B. Integrating Small RNA Sequencing with QTL Mapping for Identification of miRNAs and Their Target Genes Associated with Heat Tolerance at the Flowering Stage in Rice. FRONTIERS IN PLANT SCIENCE 2017; 8:43. [PMID: 28174587 PMCID: PMC5258760 DOI: 10.3389/fpls.2017.00043] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2016] [Accepted: 01/09/2017] [Indexed: 05/03/2023]
Abstract
Although, microRNAs (miRNAs) have been reported to be associated with heat tolerance at the seedling stage in rice, their involvement in heat tolerance at the flowering stage is still unknown. In this study, small RNA profiling was conducted in a heat-tolerant variety Gan-Xiang-Nuo (GXN) and a heat-sensitive variety Hua-Jing-Xian-74 (HJX), respectively. Totally, 102 miRNAs were differentially expressed (DE) under heat stress. Compared to HJX, GXN had more DE miRNAs and its DE miRNAs changed earlier under heat stress. Plant Ontology (PO) analysis of the target genes revealed that many DE miRNAs were involved in flower development. As a parallel experiment, QTL mapping was also conducted and four QTLs for heat tolerance at the flowering stage were identified using chromosome single-segment substitution lines derived from GXN and HJX. Further, through integrating analysis of DE miRNAs with QTLs, we identified 8 target genes corresponding to 26 miRNAs within the four QTL regions. Some meaningful target genes such as LOC_Os12g42400, SGT1, and pectinesterase were within the QTL regions. The negative correlation between miR169r-5p and its target gene LOC_Os12g42400 was confirmed under heat stress, and overexpression of miR169r-5p enhanced heat tolerance at flowering stage in rice. Our results demonstrate that the integrated analysis of genome-wide miRNA profiling with QTL mapping can facilitate identification of miRNAs and their target genes associated with the target traits and the limited candidates identified in this study offer an important source for further functional analysis and molecular breeding for heat tolerance in rice.
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Affiliation(s)
- Qing Liu
- Guangdong Key Laboratory of New Technology in Rice BreedingGuangzhou, China
- Rice Research Institute, Guangdong Academy of Agricultural SciencesGuangzhou, China
| | - Tifeng Yang
- Guangdong Key Laboratory of New Technology in Rice BreedingGuangzhou, China
- Rice Research Institute, Guangdong Academy of Agricultural SciencesGuangzhou, China
| | - Ting Yu
- Agro-biological Gene Research Center, Guangdong Academy of Agricultural SciencesGuangzhou, China
| | - Shaohong Zhang
- Guangdong Key Laboratory of New Technology in Rice BreedingGuangzhou, China
- Rice Research Institute, Guangdong Academy of Agricultural SciencesGuangzhou, China
| | - Xingxue Mao
- Guangdong Key Laboratory of New Technology in Rice BreedingGuangzhou, China
- Rice Research Institute, Guangdong Academy of Agricultural SciencesGuangzhou, China
| | - Junliang Zhao
- Guangdong Key Laboratory of New Technology in Rice BreedingGuangzhou, China
- Rice Research Institute, Guangdong Academy of Agricultural SciencesGuangzhou, China
| | - Xiaofei Wang
- Guangdong Key Laboratory of New Technology in Rice BreedingGuangzhou, China
- Rice Research Institute, Guangdong Academy of Agricultural SciencesGuangzhou, China
| | - Jingfang Dong
- Guangdong Key Laboratory of New Technology in Rice BreedingGuangzhou, China
- Rice Research Institute, Guangdong Academy of Agricultural SciencesGuangzhou, China
| | - Bin Liu
- Guangdong Key Laboratory of New Technology in Rice BreedingGuangzhou, China
- Rice Research Institute, Guangdong Academy of Agricultural SciencesGuangzhou, China
- *Correspondence: Bin Liu
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Beatty PH, Klein MS, Fischer JJ, Lewis IA, Muench DG, Good AG. Understanding Plant Nitrogen Metabolism through Metabolomics and Computational Approaches. PLANTS 2016; 5:plants5040039. [PMID: 27735856 PMCID: PMC5198099 DOI: 10.3390/plants5040039] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 09/21/2016] [Accepted: 09/30/2016] [Indexed: 01/24/2023]
Abstract
A comprehensive understanding of plant metabolism could provide a direct mechanism for improving nitrogen use efficiency (NUE) in crops. One of the major barriers to achieving this outcome is our poor understanding of the complex metabolic networks, physiological factors, and signaling mechanisms that affect NUE in agricultural settings. However, an exciting collection of computational and experimental approaches has begun to elucidate whole-plant nitrogen usage and provides an avenue for connecting nitrogen-related phenotypes to genes. Herein, we describe how metabolomics, computational models of metabolism, and flux balance analysis have been harnessed to advance our understanding of plant nitrogen metabolism. We introduce a model describing the complex flow of nitrogen through crops in a real-world agricultural setting and describe how experimental metabolomics data, such as isotope labeling rates and analyses of nutrient uptake, can be used to refine these models. In summary, the metabolomics/computational approach offers an exciting mechanism for understanding NUE that may ultimately lead to more effective crop management and engineered plants with higher yields.
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Affiliation(s)
- Perrin H Beatty
- Department of Biological Sciences, University of Alberta, 85 Avenue NW, Edmonton, AB T6G 2E9, Canada.
| | - Matthias S Klein
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada.
| | - Jeffrey J Fischer
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada.
| | - Ian A Lewis
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada.
| | - Douglas G Muench
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada.
| | - Allen G Good
- Department of Biological Sciences, University of Alberta, 85 Avenue NW, Edmonton, AB T6G 2E9, Canada.
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Saminathan T, Bodunrin A, Singh NV, Devarajan R, Nimmakayala P, Jeff M, Aradhya M, Reddy UK. Genome-wide identification of microRNAs in pomegranate (Punica granatum L.) by high-throughput sequencing. BMC PLANT BIOLOGY 2016; 16:122. [PMID: 27230657 PMCID: PMC4880961 DOI: 10.1186/s12870-016-0807-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 05/17/2016] [Indexed: 05/04/2023]
Abstract
BACKGROUND MicroRNAs (miRNAs), a class of small non-coding endogenous RNAs that regulate gene expression post-transcriptionally, play multiple key roles in plant growth and development and in biotic and abiotic stress response. Knowledge and roles of miRNAs in pomegranate fruit development have not been explored. RESULTS Pomegranate, which accumulates a large amount of anthocyanins in skin and arils, is valuable to human health, mainly because of its antioxidant properties. In this study, we developed a small RNA library from pooled RNA samples from young seedlings to mature fruits and identified both conserved and pomegranate-specific miRNA from 29,948,480 high-quality reads. For the pool of 15- to 30-nt small RNAs, ~50 % were 24 nt. The miR157 family was the most abundant, followed by miR156, miR166, and miR168, with variants within each family. The base bias at the first position from the 5' end had a strong preference for U for most 18- to 26-nt sRNAs but a preference for A for 18-nt sRNAs. In addition, for all 24-nt sRNAs, the nucleotide U was preferred (97 %) in the first position. Stem-loop RT-qPCR was used to validate the expression of the predominant miRNAs and novel miRNAs in leaves, male and female flowers, and multiple fruit developmental stages; miR156, miR156a, miR159a, miR159b, and miR319b were upregulated during the later stages of fruit development. Higher expression of miR156 in later fruit developmental may positively regulate anthocyanin biosynthesis by reducing SPL transcription factor. Novel miRNAs showed variation in expression among different tissues. These novel miRNAs targeted different transcription factors and hormone related regulators. Gene ontology and KEGG pathway analyses revealed predominant metabolic processes and catalytic activities, important for fruit development. In addition, KEGG pathway analyses revealed the involvement of miRNAs in ascorbate and linolenic acid, starch and sucrose metabolism; RNA transport; plant hormone signaling pathways; and circadian clock. CONCLUSION Our first and preliminary report of miRNAs will provide information on the synthesis of biochemical compounds of pomegranate for future research. The functions of the targets of the novel miRNAs need further investigation.
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Affiliation(s)
- Thangasamy Saminathan
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV, 25112-1000, USA
| | - Abiodun Bodunrin
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV, 25112-1000, USA
| | - Nripendra V Singh
- ICAR-National Research Center on Pomegranate, Kegaon, Solapur, Maharashtra, 413255, India
| | - Ramajayam Devarajan
- ICAR-Indian Institute of Oil Palm Research, Pedavegi, West Godavari, Andhra Pradesh, 534450, India
| | - Padma Nimmakayala
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV, 25112-1000, USA
| | - Moersfelder Jeff
- National Clonal Germplasm Repository, USDA-ARS, University of California, Davis, CA, 95616, USA
| | - Mallikarjuna Aradhya
- National Clonal Germplasm Repository, USDA-ARS, University of California, Davis, CA, 95616, USA
| | - Umesh K Reddy
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV, 25112-1000, USA.
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Li H, Hu B, Wang W, Zhang Z, Liang Y, Gao X, Li P, Liu Y, Zhang L, Chu C. Identification of microRNAs in rice root in response to nitrate and ammonium. J Genet Genomics 2016; 43:651-661. [PMID: 27372185 DOI: 10.1016/j.jgg.2015.12.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 12/15/2015] [Accepted: 12/18/2015] [Indexed: 01/03/2023]
Abstract
Nitrate and ammonium are two major nitrogen (N) sources for higher plants, but they differ in utilization and signaling. MicroRNAs (miRNAs) play an essential role in N signal transduction; however, knowledge remains limited about the regulatory role of miRNAs responsive to different N sources, especially in crop plants. To get global overview on miRNAs involved in N response in rice, we performed high-throughput small RNA-sequencing under different nitrate and ammonium treatments. The results demonstrated that only 16 and 11 miRNAs were significantly induced by nitrate and ammonium under short-term treatment, respectively. However, 60 differentially expressed miRNAs were found between nitrate and ammonium under long-term cultivation. These results suggested that miRNA response greatly differentiates between nitrate and ammonium treatments. Furthermore, 44 miRNAs were found to be differentially expressed between high- and low-N conditions. Our study reveals comprehensive expression profiling of miRNAs responsive to different N sources and different N treatments, which advances our understanding on the regulation of different N signaling and homeostasis mediated by miRNAs.
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Affiliation(s)
- Hua Li
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bin Hu
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wei Wang
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhihua Zhang
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan Liang
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaokai Gao
- School of Agriculture, Henan University of Science and Technology, Luoyang 471023, China
| | - Peng Li
- School of Agriculture, Henan University of Science and Technology, Luoyang 471023, China
| | - Yongqiang Liu
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lianhe Zhang
- School of Agriculture, Henan University of Science and Technology, Luoyang 471023, China
| | - Chengcai Chu
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
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Marino D, Ariz I, Lasa B, Santamaría E, Fernández-Irigoyen J, González-Murua C, Aparicio Tejo PM. Quantitative proteomics reveals the importance of nitrogen source to control glucosinolate metabolism in Arabidopsis thaliana and Brassica oleracea. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:3313-23. [PMID: 27085186 PMCID: PMC4892723 DOI: 10.1093/jxb/erw147] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Accessing different nitrogen (N) sources involves a profound adaptation of plant metabolism. In this study, a quantitative proteomic approach was used to further understand how the model plant Arabidopsis thaliana adjusts to different N sources when grown exclusively under nitrate or ammonium nutrition. Proteome data evidenced that glucosinolate metabolism was differentially regulated by the N source and that both TGG1 and TGG2 myrosinases were more abundant under ammonium nutrition, which is generally considered to be a stressful situation. Moreover, Arabidopsis plants displayed glucosinolate accumulation and induced myrosinase activity under ammonium nutrition. Interestingly, these results were also confirmed in the economically important crop broccoli (Brassica oleracea var. italica). Moreover, these metabolic changes were correlated in Arabidopsis with the differential expression of genes from the aliphatic glucosinolate metabolic pathway. This study underlines the importance of nitrogen nutrition and the potential of using ammonium as the N source in order to stimulate glucosinolate metabolism, which may have important applications not only in terms of reducing pesticide use, but also for increasing plants' nutritional value.
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Affiliation(s)
- Daniel Marino
- Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU), Apdo. 644, E-48080 Bilbao, Spain Ikerbasque, Basque Foundation for Science, E-48011 Bilbao, Spain
| | - Idoia Ariz
- Departamento de Ciencias del Medio Natural, Universidad Pública de Navarra, Pamplona, Spain Faculdade de Ciências, Centro Ecologia Evolução e Alterações Ambientais, Universidade de Lisboa, Lisboa, Portugal
| | - Berta Lasa
- Departamento de Ciencias del Medio Natural, Universidad Pública de Navarra, Pamplona, Spain
| | - Enrique Santamaría
- Proteomics Unit, Navarrabiomed, Fundación Miguel Servet, Proteored-ISCIII, Instituto de investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
| | - Joaquín Fernández-Irigoyen
- Proteomics Unit, Navarrabiomed, Fundación Miguel Servet, Proteored-ISCIII, Instituto de investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
| | - Carmen González-Murua
- Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU), Apdo. 644, E-48080 Bilbao, Spain
| | - Pedro M Aparicio Tejo
- Departamento de Ciencias del Medio Natural, Universidad Pública de Navarra, Pamplona, Spain
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Nath M, Tuteja N. NPKS uptake, sensing, and signaling and miRNAs in plant nutrient stress. PROTOPLASMA 2016; 253:767-786. [PMID: 26085375 DOI: 10.1007/s00709-015-0845-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 06/08/2015] [Indexed: 05/24/2023]
Abstract
Sessile nature of higher plants consequently makes it highly adaptable for nutrient absorption and acquisition from soil. Plants require 17 essential elements for their growth and development which include 14 minerals (macronutrients: N, P, K, Mg, Ca, S; micronutrients: Cl, Fe, B, Mn, Zn, Cu, Ni, Mo) and 3 non-mineral (C, H, O) elements. The roots of higher plants must acquire these macronutrients and micronutrients from rhizosphere and further allocate to other plant parts for completing their life cycle. Plants evolved an intricate series of signaling and sensing cascades to maintain nutrient homeostasis and to cope with nutrient stress/availability. The specific receptors for nutrients in root, root system architecture, and internal signaling pathways help to develop plasticity in response to the nutrient starvation. Nitrogen (N), phosphorus (P), potassium (K), and sulfur (S) are essential for various metabolic processes, and their deficiency negatively effects the plant growth and yield. Genes coding for transporters and receptors for nutrients as well as some small non-coding RNAs have been implicated in nutrient uptake and signaling. This review summarizes the N, P, K, and S uptake, sensing and signaling events in nutrient stress condition especially in model plant Arabidopsis thaliana and involvement of microRNAs in nutrient deficiency. This article also provides a framework of uptake, sensing, signaling and to highlight the microRNA as an emerging major players in nutrient stress condition. Nutrient-plant-miRNA cross talk may help plant to cope up nutrient stress, and understanding their precise mechanism(s) will be necessary to develop high yielding smart crop with low nutrient input.
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Affiliation(s)
- Manoj Nath
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, 110067, New Delhi, India
| | - Narendra Tuteja
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, 110067, New Delhi, India.
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Jain A, Das S. Synteny and comparative analysis of miRNA retention, conservation, and structure across Brassicaceae reveals lineage- and sub-genome-specific changes. Funct Integr Genomics 2016; 16:253-68. [PMID: 26873704 DOI: 10.1007/s10142-016-0484-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Revised: 02/01/2016] [Accepted: 02/04/2016] [Indexed: 12/22/2022]
Abstract
The recent availability of genome sequences together with syntenic block information for Brassicaceae offers an opportunity to study microRNA (miRNA) evolution across this family. We employed a synteny-based comparative genomics strategy to unambiguously identify miRNA homologs from the genome sequence of members of Brassicaceae. Such an analysis of miRNA across Brassicaceae allowed us to classify miRNAs as conserved, lineage-, karyotype- and sub-genome-specific. The differential loss of miRNA from sub-genomes in polyploid genomes of Brassica rapa and Brassica oleracea shows that miRNA also follows the rules of gene fractionation as observed in the case of protein-coding genes. The study of mature and miR* region of precursors revealed instances of in-dels and SNPs which reflect the evolutionary history of the genomes. High level of conservation in miR* regions in some cases points to their functional relevance which needs to be further investigated. We further show that sequence and length variability in precursor sequences can affect the free energy and foldback structure of miRNA which may ultimately affect their biogenesis and expression in the biological system.
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Affiliation(s)
- Aditi Jain
- Department of Botany, Faculty of Science, University of Delhi, New Delhi, Delhi, 110007, India
| | - Sandip Das
- Department of Botany, Faculty of Science, University of Delhi, New Delhi, Delhi, 110007, India.
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Bakshi M, Vahabi K, Bhattacharya S, Sherameti I, Varma A, Yeh KW, Baldwin I, Johri AK, Oelmüller R. WRKY6 restricts Piriformospora indica-stimulated and phosphate-induced root development in Arabidopsis. BMC PLANT BIOLOGY 2015; 15:305. [PMID: 26718529 PMCID: PMC4697310 DOI: 10.1186/s12870-015-0673-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Accepted: 12/03/2015] [Indexed: 05/07/2023]
Abstract
BACKGROUND Arabidopsis root growth is stimulated by Piriformospora indica, phosphate limitation and inactivation of the WRKY6 transcription factor. Combinations of these factors induce unexpected alterations in root and shoot growth, root architecture and root gene expression profiles. RESULTS The results demonstrate that P. indica promotes phosphate uptake and root development under Pi limitation in wrky6 mutant. This is associated with the stimulation of PHOSPHATE1 expression and ethylene production. Expression profiles from the roots of wrky6 seedlings identified genes involved in hormone metabolism, transport, meristem, cell and plastid proliferation, and growth regulation. 25 miRNAs were also up-regulated in these roots. We generated and discuss here a list of common genes which are regulated in growing roots and which are common to all three growth stimuli investigated in this study. CONCLUSION Since root development of wrky6 plants exposed to P. indica under phosphate limitation is strongly promoted, we propose that common genes which respond to all three growth stimuli are central for the control of root growth and architecture. They can be tested for optimizing root growth in model and agricultural plants.
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Affiliation(s)
- Madhunita Bakshi
- Institute of General Botany and Plant Physiology, Friedrich-Schiller-University Jena, Dornburgerstr. 159, D-07743, Jena, Germany.
| | - Khabat Vahabi
- Institute of General Botany and Plant Physiology, Friedrich-Schiller-University Jena, Dornburgerstr. 159, D-07743, Jena, Germany.
| | - Samik Bhattacharya
- Max-Planck-Institute for Chemical Ecology, Beutenberg Campus, Hans-Knöll-Straße 8, D-07745, Jena, Germany.
| | - Irena Sherameti
- Institute of General Botany and Plant Physiology, Friedrich-Schiller-University Jena, Dornburgerstr. 159, D-07743, Jena, Germany.
| | - Ajit Varma
- Amity Institute of Microbial Technology, AUUP, Noida, India.
| | - Kai-Wun Yeh
- Institute of Plant Biology, Taiwan National University, Taipei, Taiwan.
| | - Ian Baldwin
- Max-Planck-Institute for Chemical Ecology, Beutenberg Campus, Hans-Knöll-Straße 8, D-07745, Jena, Germany.
| | - Atul Kumar Johri
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
| | - Ralf Oelmüller
- Institute of General Botany and Plant Physiology, Friedrich-Schiller-University Jena, Dornburgerstr. 159, D-07743, Jena, Germany.
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Li WW, Chen M, Zhong L, Liu JM, Xu ZS, Li LC, Zhou YB, Guo CH, Ma YZ. Overexpression of the autophagy-related gene SiATG8a from foxtail millet (Setaria italica L.) confers tolerance to both nitrogen starvation and drought stress in Arabidopsis. Biochem Biophys Res Commun 2015; 468:800-6. [PMID: 26577407 DOI: 10.1016/j.bbrc.2015.11.035] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 11/05/2015] [Indexed: 10/22/2022]
Abstract
Autophagy is an evolutionarily conserved biological process in all eukaryotes for the degradation of intracellular components for nutrient recycling. Autophagy is known to be involved in responses to low nitrogen stress in Arabidopsis. Foxtail millet has strong abiotic stress resistance to both low nutrient and drought stress. However, to date, there have only been a few genes reported to be related with abiotic stress resistance in foxtail millet. In this study, we identified an autophagy-related gene, SiATG8a, from foxtail millet. SiATG8a is mainly expressed in stems and its expression was dramatically induced by drought stress and nitrogen starvation treatments. SiATG8a was localized in the membrane and cytoplasm of foxtail millet. Overexpression of SiATG8a in Arabidopsis conferred tolerance to both nitrogen starvation and to drought stress. Under nitrogen starvation conditions, the SiATG8a transgenic plants had larger root and leaf areas and accumulated more total nitrogen than wild-type plants. The transgenic plants had lower total protein concentrations than did the WT plants. Under drought stress, the SiATG8a transgenic plants had higher survival rates, chlorophyll content, and proline content, but had lower MDA content than wild type plants. Taken together, our results represent the first identified case where overexpression of autophagy related gene can simultaneously improve plant resistance to low nitrogen and drought stresses. These findings implicate plant autophagy in plant stress responses to low nitrogen and drought and should be helpful in efforts to improve stresses resistance to nitrogen starvation and drought of crops by genetic transformation.
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Affiliation(s)
- Wei-wei Li
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, Heilongjiang 150025, China
| | - Ming Chen
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Li Zhong
- Guizhou Institute of Prataculture, Gui Academy of Agricultural Sciences, Guiyang, Guizhou 550006, China
| | - Jia-ming Liu
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, Heilongjiang 150025, China
| | - Zhao-shi Xu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Lian-cheng Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yong-Bin Zhou
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Chang-Hong Guo
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, Heilongjiang 150025, China.
| | - You-Zhi Ma
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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Wei X, Zhang X, Yao Q, Yuan Y, Li X, Wei F, Zhao Y, Zhang Q, Wang Z, Jiang W, Zhang X. The miRNAs and their regulatory networks responsible for pollen abortion in Ogura-CMS Chinese cabbage revealed by high-throughput sequencing of miRNAs, degradomes, and transcriptomes. FRONTIERS IN PLANT SCIENCE 2015; 6:894. [PMID: 26557132 PMCID: PMC4617173 DOI: 10.3389/fpls.2015.00894] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 10/08/2015] [Indexed: 05/23/2023]
Abstract
Chinese cabbage (Brassica rapa ssp. pekinensis) is one of the most important vegetables in Asia and is cultivated across the world. Ogura-type cytoplasmic male sterility (Ogura-CMS) has been widely used in the hybrid breeding industry for Chinese cabbage and many other cruciferous vegetables. Although, the cause of Ogura-CMS has been localized to the orf138 locus in the mitochondrial genome, however, the mechanism by which nuclear genes respond to the mutation of the mitochondrial orf138 locus is unclear. In this study, a series of whole genome small RNA, degradome and transcriptome analyses were performed on both Ogura-CMS and its maintainer Chinese cabbage buds using deep sequencing technology. A total of 289 known miRNAs derived from 69 families (including 23 new families first reported in B. rapa) and 426 novel miRNAs were identified. Among these novel miRNAs, both 3-p and 5-p miRNAs were detected on the hairpin arms of 138 precursors. Ten known and 49 novel miRNAs were down-regulated, while one known and 27 novel miRNAs were up-regulated in Ogura-CMS buds compared to the fertile plants. Using degradome analysis, a total of 376 mRNAs were identified as targets of 30 known miRNA families and 100 novel miRNAs. A large fraction of the targets were annotated as reproductive development related. Our transcriptome profiling revealed that the expression of the targets was finely tuned by the miRNAs. Two novel miRNAs were identified that were specifically highly expressed in Ogura-CMS buds and sufficiently suppressed two pollen development essential genes: sucrose transporter SUC1 and H (+) -ATPase 6. These findings provide clues for the contribution of a potential miRNA regulatory network to bud development and pollen engenderation. This study contributes new insights to the communication between the mitochondria and chromosome and takes one step toward filling the gap in the regulatory network from the orf138 locus to pollen abortion in Ogura-CMS plants from a miRNA perspective.
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Affiliation(s)
- Xiaochun Wei
- Institute of Horticulture, Henan Academy of Agricultural SciencesZhengzhou, China
| | - Xiaohui Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijing, China
| | - Qiuju Yao
- Institute of Horticulture, Henan Academy of Agricultural SciencesZhengzhou, China
| | - Yuxiang Yuan
- Institute of Horticulture, Henan Academy of Agricultural SciencesZhengzhou, China
| | - Xixiang Li
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijing, China
| | - Fang Wei
- College of Life Science, Zhengzhou UniversityZhengzhou, China
| | - Yanyan Zhao
- Institute of Horticulture, Henan Academy of Agricultural SciencesZhengzhou, China
| | - Qiang Zhang
- Institute of Horticulture, Henan Academy of Agricultural SciencesZhengzhou, China
| | - Zhiyong Wang
- Institute of Horticulture, Henan Academy of Agricultural SciencesZhengzhou, China
| | - Wusheng Jiang
- Institute of Horticulture, Henan Academy of Agricultural SciencesZhengzhou, China
| | - Xiaowei Zhang
- Institute of Horticulture, Henan Academy of Agricultural SciencesZhengzhou, China
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Nguyen GN, Rothstein SJ, Spangenberg G, Kant S. Role of microRNAs involved in plant response to nitrogen and phosphorous limiting conditions. FRONTIERS IN PLANT SCIENCE 2015; 6:629. [PMID: 26322069 PMCID: PMC4534779 DOI: 10.3389/fpls.2015.00629] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 07/30/2015] [Indexed: 05/22/2023]
Abstract
Plant microRNAs (miRNAs) are a class of small non-coding RNAs which target and regulate the expression of genes involved in several growth, development, and metabolism processes. Recent researches have shown involvement of miRNAs in the regulation of uptake and utilization of nitrogen (N) and phosphorus (P) and more importantly for plant adaptation to N and P limitation conditions by modifications in plant growth, phenology, and architecture and production of secondary metabolites. Developing strategies that allow for the higher efficiency of using both N and P fertilizers in crop production is important for economic and environmental benefits. Improved crop varieties with better adaptation to N and P limiting conditions could be a key approach to achieve this effectively. Furthermore, understanding on the interactions between N and P uptake and use and their regulation is important for the maintenance of nutrient homeostasis in plants. This review describes the possible functions of different miRNAs and their cross-talk relevant to the plant adaptive responses to N and P limiting conditions. In addition, a comprehensive understanding of these processes at molecular level and importance of biological adaptation for improved N and P use efficiency is discussed.
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Affiliation(s)
- Giao N. Nguyen
- Biosciences Research, Department of Economic DevelopmentHorsham, VIC, Australia
| | - Steven J. Rothstein
- Department of Molecular and Cellular Biology, College of Biological Science, University of GuelphGuelph, ON, Canada
| | - German Spangenberg
- Biosciences Research, Department of Economic Development, AgriBio, Centre for AgriBioscienceBundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe UniversityBundoora, VIC, Australia
| | - Surya Kant
- Biosciences Research, Department of Economic DevelopmentHorsham, VIC, Australia
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Wang J, Wang Y, Yang J, Ma C, Zhang Y, Ge T, Qi Z, Kang Y. Arabidopsis ROOT HAIR DEFECTIVE3 is involved in nitrogen starvation-induced anthocyanin accumulation. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2015; 57:708-21. [PMID: 25494721 DOI: 10.1111/jipb.12320] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 12/05/2014] [Indexed: 05/07/2023]
Abstract
Anthocyanin accumulation is a common phenomenon seen in plants under environmental stress. In this study, we identified a new allele of ROOT HAIR DEFECTIVE3 (RHD3) showing an anthocyanin overaccumulation phenotype under nitrogen starvation conditions. It is known that ethylene negatively regulates light- and sucrose-induced anthocyanin biosynthesis. We hypothesized that RHD3 achieves its negative effect on anthocyanin biosynthesis via an ethylene-regulating pathway. In support of this, similar to rhd3 mutants, the Arabidopsis ethylene signaling mutants etr1, ein2, and ein3/eil1 showed an anthocyanin overaccumulation phenotype under nitrogen starvation conditions. The ethylene precursor ACC strongly suppressed anthocyanin accumulation, dependent on ETR1, EIN2, EIN3/EIL1, and, partially, RHD3. In addition, inactivating RHD3 partially reversed the suppressive effect of ETO1 inactivation-evoked endogenous ethylene production on anthocyanin accumulation. The expression of nitrogen starvation-induced anthocyanin biosynthesis genes was negatively regulated by RHD3, but ethylene response genes were positively regulated by RHD3. Wild-type seedlings overexpressing RHD3 showed similar phenotypes to rhd3 mutants, indicating the existence of a fine-tuned relationship between gene expression and function. RHD3 was initially identified as a gene involved in root hair development. This study uncovered a new physiological function of RHD3 in nitrogen starvation-induced anthocyanin accumulation and ethylene homeostasis. [Correction added on 6 August 2015, after first online publication: "RND3" corrected to "RHD3".].
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Affiliation(s)
- Jing Wang
- College of Life Sciences, Inner Mongolia University, Hohhot, 010021, China
| | - Yan Wang
- College of Life Sciences, Inner Mongolia University, Hohhot, 010021, China
| | - Ju Yang
- College of Life Sciences, Inner Mongolia University, Hohhot, 010021, China
| | - Chunli Ma
- College of Life Sciences, Inner Mongolia University, Hohhot, 010021, China
| | - Ying Zhang
- College of Life Sciences, Inner Mongolia University, Hohhot, 010021, China
| | - Ting Ge
- College of Life Sciences, Inner Mongolia University, Hohhot, 010021, China
| | - Zhi Qi
- College of Life Sciences, Inner Mongolia University, Hohhot, 010021, China
| | - Yan Kang
- College of Life Sciences, Inner Mongolia University, Hohhot, 010021, China
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