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Pei L, Gao X, Tian X, Liu N, Chen M, Fernie AR, Li H. A microRNA528-ZmLac3 module regulates low phosphate tolerance in maize. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:2233-2248. [PMID: 38569011 DOI: 10.1111/tpj.16741] [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: 11/07/2023] [Revised: 03/08/2024] [Accepted: 03/19/2024] [Indexed: 04/05/2024]
Abstract
MicroRNAs are known to play a crucial role in plant development and physiology and become a target for investigating the regulatory mechanism underlying plant low phosphate tolerance. ZmmiR528 has been shown to display significantly different expression levels between wild-type and low Pi-tolerant maize mutants. However, its functional role in maize low Pi tolerance remains unknown. In the present study, we studied the role and underlying molecular mechanism of miR528 in maize with low Pi tolerance. Overexpression of ZmmiR528 in maize resulted in impaired root growth, reduced Pi uptake capacity and compromised resistance to Pi deficiency. By contrast, transgenic maize plants suppressing ZmmiR528 expression showed enhanced low Pi tolerance. Furthermore, ZmLac3 and ZmLac5 which encode laccase were identified and verified as targets of ZmmiR528. ZmLac3 transgenic plants were subsequently generated and were also found to play key roles in regulating maize root growth, Pi uptake and low Pi tolerance. Furthermore, auxin transport was found to be potentially involved in ZmLac3-mediated root growth. Moreover, we conducted genetic complementary analysis through the hybridization of ZmmiR528 and ZmLac3 transgenic plants and found a favorable combination with breeding potential, namely anti-miR528:ZmLac3OE hybrid maize, which exhibited significantly increased low Pi tolerance and markedly alleviated yield loss caused by low Pi stress. Our study has thus identified a ZmmiR528-ZmLac3 module regulating auxin transport and hence root growth, thereby determining Pi uptake and ultimately low Pi tolerance, providing an effective approach for low Pi tolerance improvement through manipulating the expression of miRNA and its target in maize.
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Affiliation(s)
- Laming Pei
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Xiaomei Gao
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Xiao Tian
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Ning Liu
- Shandong Zhongnong Tiantai Seed Co., Ltd, Linyi, 273300, China
| | - Minghao Chen
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm, 14476, Germany
| | - Hui Li
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
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Upadhyay SK. Phosphate Deficiency: A Tale from the End of PILNCR2. Noncoding RNA 2023; 9:40. [PMID: 37624032 PMCID: PMC10457764 DOI: 10.3390/ncrna9040040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 07/18/2023] [Accepted: 07/24/2023] [Indexed: 08/26/2023] Open
Abstract
A deficiency in inorganic phosphate (Pi) induces the expression of miRNA399 and the accumulation of its target Pi transporters (PHT1s) mRNA, which is contrary to the goal of miRNA-mediated gene regulation. Recently, a novel mechanism of RNA/RNA-duplex formation between the transcripts of a Pi deficiency-induced long non-coding RNA (PILNCR2) and PHT1s has been reported, which prevents the binding and cleavage of miRNA399 to PHT1 mRNAs, thereby providing tolerance of Pi-deficient conditions. Moreover, the way in which ribosomes move through the RNA/RNA-duplex for the translation of PHT1 transporter proteins remains elusive.
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Kumar K, Yadava P, Gupta M, Choudhary M, Jha AK, Wani SH, Dar ZA, Kumar B, Rakshit S. Narrowing down molecular targets for improving phosphorus-use efficiency in maize (Zea mays L.). Mol Biol Rep 2022; 49:12091-12107. [PMID: 35752697 DOI: 10.1007/s11033-022-07679-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 06/06/2022] [Indexed: 10/17/2022]
Abstract
Conventional agricultural practices rely heavily on chemical fertilizers to boost production. Among the fertilizers, phosphatic fertilizers are copiously used to ameliorate low-phosphate availability in the soil. However, phosphorus-use efficiency (PUE) for major cereals, including maize, is less than 30%; resulting in more than half of the applied phosphate being lost to the environment. Rock phosphate reserves are finite and predicted to exhaust in near future with the current rate of consumption. Thus, the dependence of modern agriculture on phosphatic fertilizers poses major food security and sustainability challenges. Strategies to optimize and improve PUE, like genetic interventions to develop high PUE cultivars, could have a major impact in this area. Here, we present the current understanding and recent advances in the biological phenomenon of phosphate uptake, translocation, and adaptive responses of plants under phosphate deficiency, with special reference to maize. Maize is one of the most important cereal crops that is cultivated globally under diverse agro-climatic conditions. It is an industrial, feed and food crop with multifarious uses and a fast-rising global demand and consumption. The interesting aspects of diversity in the root system architecture traits, the interplay between signaling pathways contributing to PUE, and an in-depth discussion on promising candidate genes for improving PUE in maize are elaborated.
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Affiliation(s)
- Krishan Kumar
- Delhi Unit Office, ICAR - Indian Institute of Maize Research, Pusa Campus, New Delhi, 110012, India.
| | - Pranjal Yadava
- ICAR - Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110012, India
| | - Mamta Gupta
- ICAR - Indian Institute of Maize Research, PAU Campus, Ludhiana, 141004, India
| | - Mukesh Choudhary
- ICAR - Indian Institute of Maize Research, PAU Campus, Ludhiana, 141004, India.,School of Agriculture and Environment, The University of Western Australia, Perth, WA, 6009, Australia
| | - Abhishek Kumar Jha
- Delhi Unit Office, ICAR - Indian Institute of Maize Research, Pusa Campus, New Delhi, 110012, India
| | - Shabir Hussain Wani
- Mountain Research Center for Field Crops, Sher-e-Kashmir University of Agricultural Sciences and Technology, Khudwani, Srinagar, Jammu and Kashmir, India
| | - Zahoor Ahmed Dar
- Dryland Agriculture Research Station, Sher-e-Kashmir University of Agricultural Sciences and Technology Srinagar, Khudwani, Srinagar, Jammu and Kashmir, India
| | - Bhupender Kumar
- Delhi Unit Office, ICAR - Indian Institute of Maize Research, Pusa Campus, New Delhi, 110012, India
| | - Sujay Rakshit
- ICAR - Indian Institute of Maize Research, PAU Campus, Ludhiana, 141004, India.
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Pei L, Liu J, Zhou Y, Jiang Y, Li H. Transcriptomic and metabolomic profiling reveals the protective role of anthocyanins in alleviating low phosphate stress in maize. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:889-905. [PMID: 34108822 PMCID: PMC8140177 DOI: 10.1007/s12298-021-00981-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 03/22/2021] [Accepted: 03/23/2021] [Indexed: 05/15/2023]
Abstract
UNLABELLED Anthocyanin accumulation is a characteristic response to phosphate (Pi) deficiency in plants. In the present study, we investigated the role of maize anthocyanins (MA) in alleviating low Pi (LP) stress in maize (Zea mays L). To this end, maize plants were exposed to LP conditions and treated with or without (control) MA. Interestingly, MA-treated maize plants showed relieved growth inhibition, reproductive development retardation, and yield loss compared to control plants under LP stress. Moreover, the level of oxidative destruction was significantly alleviated in MA-treated plants compared to the untreated control under conditions of LP stress. Acid phosphatase (APase) activity was significantly higher in MA-treated plants than in control plants, resulting in enhanced Pi mobilization and recycling. The results of the transcriptome analysis suggested that genes involved in photosynthesis, photosystem light harvesting, Pi transport, and recycling were differentially expressed between MA-treated plants and control plants. Moreover, metabolome analysis indicated higher sugar and organic acid levels and lower phosphorylated metabolite contents in MA-treated plants than in control plants, which was consistent with the results of the comparative transcriptome analysis. Taken together, our findings indicate that MA plays critical roles in alleviating LP stress in maize plants, probably by improving photosynthetic performance and increasing Pi mobilization and recycling. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-00981-9.
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Affiliation(s)
- Laming Pei
- School of Biological Science and Technology, University of Jinan, Jinan, 250022 China
| | - Jiajia Liu
- School of Biological Science and Technology, University of Jinan, Jinan, 250022 China
| | - Yuanyuan Zhou
- School of Biological Science and Technology, University of Jinan, Jinan, 250022 China
| | - Yuhang Jiang
- School of Biological Science and Technology, University of Jinan, Jinan, 250022 China
| | - Hui Li
- School of Biological Science and Technology, University of Jinan, Jinan, 250022 China
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Zhang J, Lin Y, Wu F, Zhang Y, Cheng L, Huang M, Tong Z. Profiling of MicroRNAs and Their Targets in Roots and Shoots Reveals a Potential MiRNA-Mediated Interaction Network in Response to Phosphate Deficiency in the Forestry Tree Betula luminifera. Front Genet 2021; 12:552454. [PMID: 33584823 PMCID: PMC7876418 DOI: 10.3389/fgene.2021.552454] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 01/06/2021] [Indexed: 01/14/2023] Open
Abstract
Inorganic phosphate (Pi) is often lacking in natural and agro-climatic environments, which impedes the growth of economically important woody species. Plants have developed strategies to cope with low Pi (LP) availability. MicroRNAs (miRNAs) play important roles in responses to abiotic stresses, including nutrition stress, by regulating target gene expression. However, the miRNA-mediated regulation of these adaptive responses and their underlying coordinating signals are still poorly understood in forestry trees such as Betula luminifera. Transcriptomic libraries, small RNA (sRNA) libraries, and a mixed degradome cDNA library of B. luminifera roots and shoots treated under LP and normal conditions (CK) were constructed and sequenced using next-generation deep sequencing. A comprehensive B. luminifera transcriptome derived from its roots and shoots was constructed, and a total of 76,899 unigenes were generated. Analysis of the transcriptome identified 8,095 and 5,584 differentially expressed genes in roots and shoots, respectively, under LP conditions. sRNA sequencing analyses indicated that 66 and 60 miRNAs were differentially expressed in roots and shoots, respectively, under LP conditions. A total of 109 and 112 miRNA-target pairs were further validated in the roots and shoots, respectively, using degradome sequencing. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis of differential miRNA targets indicated that the "ascorbate and aldarate metabolism" pathway responded to LP, suggesting miRNA-target pairs might participating in the removing of reactive oxidative species under LP stress. Moreover, a putative network of miRNA-target interactions involved in responses to LP stress in B. luminifera is proposed. Taken together, these findings provide useful information to decipher miRNA functions and establish a framework for exploring P signaling networks regulated by miRNAs in B. luminifera and other woody plants. It may provide new insights into the genetic engineering of high use efficiency of Pi in forestry trees.
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Affiliation(s)
- Junhong Zhang
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Bio-Technology, Zhejiang A&F University, Hangzhou, China
| | | | | | | | | | | | - Zaikang Tong
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Bio-Technology, Zhejiang A&F University, Hangzhou, China
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Yu J, Xu F, Wei Z, Zhang X, Chen T, Pu L. Epigenomic landscape and epigenetic regulation in maize. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1467-1489. [PMID: 31965233 DOI: 10.1007/s00122-020-03549-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Accepted: 01/14/2020] [Indexed: 05/12/2023]
Abstract
Epigenetic regulation has been implicated in the control of multiple agronomic traits in maize. Here, we review current advances in our understanding of epigenetic regulation, which has great potential for improving agronomic traits and the environmental adaptability of crops. Epigenetic regulation plays vital role in the control of complex agronomic traits. Epigenetic variation could contribute to phenotypic diversity and can be used to improve the quality and productivity of crops. Maize (Zea mays L.), one of the most widely cultivated crops for human food, animal feed, and ethanol biofuel, is a model plant for genetic studies. Recent advances in high-throughput sequencing technology have made possible the study of epigenetic regulation in maize on a genome-wide scale. In this review, we discuss recent epigenetic studies in maize many achieved by Chinese research groups. These studies have explored the roles of DNA methylation, posttranslational modifications of histones, chromatin remodeling, and noncoding RNAs in the regulation of gene expression in plant development and environment response. We also provide our future prospects for manipulating epigenetic regulation to improve crops.
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Affiliation(s)
- Jia Yu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fan Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ziwei Wei
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Xiangxiang Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tao Chen
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Li Pu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.
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Huen A, Bally J, Smith P. Identification and characterisation of microRNAs and their target genes in phosphate-starved Nicotiana benthamiana by small RNA deep sequencing and 5'RACE analysis. BMC Genomics 2018; 19:940. [PMID: 30558535 PMCID: PMC6296076 DOI: 10.1186/s12864-018-5258-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 11/16/2018] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Phosphorus is an important macronutrient that is severely lacking in soils. In plants, specific microRNAs (miRNAs) essential for nutrient management and the regulation of stress responses are responsible for the control of many phosphate starvation responses. Further understanding of conserved and species-specific microRNA species has potential implications for the development of crops tolerant to soils with low phosphate. RESULTS This study identified and characterised phosphate starvation-responsive miRNAs in the native Australian tobacco Nicotiana benthamiana. Small RNA libraries were constructed and sequenced from phosphate-starved plant leaves, stems and roots. Twenty-four conserved miRNA families and 36 species-specific miRNAs were identified. The majority of highly phosphate starvation-responsive miRNAs were highly conserved, comprising of members from the miR399, miR827, and miR2111 families. In addition, two miRNA-star species were identified to be phosphate starvation-responsive. A total of seven miRNA targets were confirmed using RLM-5'RACE to be cleaved by five miRNA families, including two confirmed cleavage targets for Nbe-miR399 species, one for Nbe-miR2111, and two for Nbe-miR398. A number of N. benthamiana-specific features for conserved miRNAs were identified, including species-specific miRNA targets predicted or confirmed for miR399, miR827, and miR398. CONCLUSIONS Our results give an insight into the phosphate starvation-responsive miRNAs of Nicotiana benthamiana, and indicate that the phosphate starvation response pathways in N. benthamiana contain both highly conserved and species-specific components.
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Affiliation(s)
- Amanda Huen
- School of Life and Environmental Sciences, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - Julia Bally
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, QLD, Brisbane, 4000, Australia
| | - Penelope Smith
- Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, VIC, 3086, Australia.
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9
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Balyan S, Kumar M, Mutum RD, Raghuvanshi U, Agarwal P, Mathur S, Raghuvanshi S. Identification of miRNA-mediated drought responsive multi-tiered regulatory network in drought tolerant rice, Nagina 22. Sci Rep 2017; 7:15446. [PMID: 29133823 PMCID: PMC5684420 DOI: 10.1038/s41598-017-15450-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 10/23/2017] [Indexed: 11/21/2022] Open
Abstract
Comparative characterization of microRNA-mediated stress regulatory networks in contrasting rice cultivars is critical to decipher plant stress response. Consequently, a multi-level comparative analysis, using sRNA sequencing, degradome analysis, enzymatic and metabolite assays and metal ion analysis, in drought tolerant and sensitive rice cultivars was conducted. The study identified a group of miRNAs "Cultivar-specific drought responsive" (CSDR)-miRNAs (osa-miR159f, osa-miR1871, osa-miR398b, osa-miR408-3p, osa-miR2878-5p, osa-miR528-5p and osa-miR397a) that were up-regulated in the flag-leaves of tolerant cultivar, Nagina 22 (N22) and Vandana, but down-regulated in the sensitive cultivar, Pusa Basmati 1 (PB1) and IR64, during drought. Interestingly, CSDR-miRNAs target several copper-protein coding transcripts like plantacyanins, laccases and Copper/Zinc superoxide dismutases (Cu/Zn SODs) and are themselves found to be similarly induced under simulated copper-starvation in both N22 and PB1. Transcription factor OsSPL9, implicated in Cu-homeostasis also interacted with osa-miR408-3p and osa-miR528-5p promoters. Further, N22 flag leaves showed lower SOD activity, accumulated ROS and had a higher stomata closure. Interestingly, compared to PB1, internal Cu levels significantly decreased in the N22 flag-leaves, during drought. Thus, the study identifies the unique drought mediated dynamism and interplay of Cu and ROS homeostasis, in the flag leaves of drought tolerant rice, wherein CSDR-miRNAs play a pivotal role.
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Affiliation(s)
- Sonia Balyan
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Mukesh Kumar
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Roseeta Devi Mutum
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Utkarsh Raghuvanshi
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Priyanka Agarwal
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Saloni Mathur
- National Institute of Plant Genome Research, Aruna Asaf Ali Road, New Delhi, 110067, India
| | - Saurabh Raghuvanshi
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India.
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Genome-wide analysis of miRNAs and Tasi-RNAs in Zea mays in response to phosphate deficiency. Funct Integr Genomics 2017; 17:335-351. [PMID: 28070736 DOI: 10.1007/s10142-016-0538-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 11/28/2016] [Accepted: 12/05/2016] [Indexed: 12/12/2022]
Abstract
Globally important cereal crop maize provides important nutritions and starch in dietary foods. Low phosphate (LPi) availability in the soil frequently limits the maize quality and yield across the world. Small non-coding RNAs (Snc-RNAs) play crucial roles in growth and adaptation of plants to the environment. Snc-RNAs like microRNAs (miRs) and trans-acting small interfering RNAs (Tasi-Rs) play important functions in posttranscriptional regulation of gene expression, which controls plant development, reproduction, and biotic/abiotic stress responses. In order to identify the miR and Tasi-R alterations in leaf and root of maize in response to sufficient phosphate and LPi at 3LS and 4LS, the snc-RNA population libraries for 0th, 1st, 2nd, 4th, and 8th day were constructed. These libraries were used for genome-wide alignment and RNA-fold analysis for possible prediction of potential miRs and Tasi-Rs. This study reported 174 known and conserved differentially expressed miRs of 27 miR families of maize plant. In addition, leaf and root specific potential novel miRs representing 155 new families were also discovered. Differentially expressed conserved as well as novel miR functions in root and leaf during early stage of Pi starvation were extensively discussed. Leaf and root specific miRs as well as common miRs with their target genes, participating in different biological, cellular, and metabolic processes were explored. Further, four miR390-directed Tasi-Rs which belong to TAS3 gene family along with other orthologs of Tasi-Rs were also identified. Finally, the study provides an insight into the composite regulatory mechanism of miRs in maize in response to Pi deficiency.
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Kumar S, Verma S, Trivedi PK. Involvement of Small RNAs in Phosphorus and Sulfur Sensing, Signaling and Stress: Current Update. FRONTIERS IN PLANT SCIENCE 2017; 8:285. [PMID: 28344582 PMCID: PMC5344913 DOI: 10.3389/fpls.2017.00285] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Accepted: 02/16/2017] [Indexed: 05/14/2023]
Abstract
Plants require several essential mineral nutrients for their growth and development. These nutrients are required to maintain physiological processes and structural integrity in plants. The root architecture has evolved to absorb nutrients from soil and transport them to other parts of the plant. Nutrient deficiency affects several physiological and biological processes in plants and leads to reduction in crop productivity and yield. To compensate this adversity, plants have developed adaptive mechanisms to enhance the acquisition, conservation, and mobilization of these nutrients under deficient or adverse conditions. In addition, plants have evolved an intricate nexus of complex signaling cascades, which help in nutrient sensing and uptake as well as to maintain nutrient homeostasis. In recent years, small non-coding RNAs such as micro RNAs (miRNAs) and endogenous small interfering RNAs have emerged as important component in regulating plant stress responses. A set of these small RNAs (sRNAs) have been implicated in regulating various processes involved in nutrient uptake, assimilation, and deficiency. In response to phosphorus (P) and sulphur (S) deficiencies, role of sRNAs, miR395 and miR399, have been identified to be instrumental; however, many more miRNAs might be involved in regulating the plant response to these nutrient stresses. These sRNAs modulate expression of target genes in response to P and S deficiencies and regulate their uptake and utilization for proper growth and development of the plant. This review summarizes the current understanding of uptake, sensing, and signaling of P and S and highlights the regulatory role of sRNAs in adaptive responses to these nutrient stresses in plants.
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Affiliation(s)
- Smita Kumar
- Council of Scientific and Industrial Research – National Botanical Research InstituteLucknow, India
- Centre of Bio-Medical ResearchSanjay Gandhi Post-Graduate Institute of Medical Sciences Lucknow, India
- *Correspondence: Prabodh K. Trivedi, ; Smita Kumar,
| | - Saurabh Verma
- Council of Scientific and Industrial Research – National Botanical Research InstituteLucknow, India
- Department of Biotechnology, Babasaheb Bhimrao Ambedkar UniversityLucknow, India
| | - Prabodh K. Trivedi
- Council of Scientific and Industrial Research – National Botanical Research InstituteLucknow, India
- *Correspondence: Prabodh K. Trivedi, ; Smita Kumar,
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Sun Y, Mu C, Chen Y, Kong X, Xu Y, Zheng H, Zhang H, Wang Q, Xue Y, Li Z, Ding Z, Liu X. Comparative transcript profiling of maize inbreds in response to long-term phosphorus deficiency stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2016; 109:467-481. [PMID: 27825075 DOI: 10.1016/j.plaphy.2016.10.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 10/18/2016] [Accepted: 10/18/2016] [Indexed: 05/25/2023]
Abstract
Maize (Zea mays L.) is an important food and energy crop, and low phosphate (Pi) availability is one of the major constraints in maize production worldwide. Plants adapt suitably to acclimate to low Pi stress. However, the underlying molecular mechanism of Pi deficiency response is still unclear. In this study, comparative transcriptomic analyses were conducted to investigate the differences of transcriptional responses in two maize genotypes with different tolerances to low phosphorus (LP) stress. LP-tolerant genotype QXN233 maintained higher P and Pi levels in shoots than LP-sensitive genotype QXH0121 suffering from Pi deficiency at seedling stage. Moreover, the transcriptomic analysis identified a total of 1391 Pi-responsive genes differentially expressed between QXN233 and QXH0121 under LP stress. Among these genes, 468 (321 up- and 147 down-regulated) were identified in leaves, and 923 (626 up- and 297 down-regulated) were identified in roots. These Pi-responsive genes were involved in various metabolic pathways, the biosynthesis of secondary metabolites, ion transport, phytohormone regulation, and other adverse stress responses. Consistent with the differential tolerance to LP stress, five maize inorganic Pi transporter genes were more highly up-regulated in QXN233 than in QXH0121. Results provide important information to further study the changes in global gene expression between LP-tolerant and LP-sensitive maize genotypes and to understand the molecular mechanisms underlying maize's long-term response to Pi deficiency.
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Affiliation(s)
- Yanling Sun
- Maize Research Institute, Shandong Academy of Agricultural Science, Jinan, Shandong, China
| | - Chunhua Mu
- Maize Research Institute, Shandong Academy of Agricultural Science, Jinan, Shandong, China
| | - Yu Chen
- College of Agriculture, Xinjiang Agricultural University, Xinjiang, China
| | - Xiangpei Kong
- College of Life Sciences, Shandong University, Jinan, Shandong, China
| | - Yuanchao Xu
- School of Bioengineering, Qilu University of Technology, Jinan, Shandong, China
| | - Hongxia Zheng
- College of Life Sciences, Shandong University, Jinan, Shandong, China
| | - Hui Zhang
- Maize Research Institute, Shandong Academy of Agricultural Science, Jinan, Shandong, China
| | - Qingcheng Wang
- Maize Research Institute, Shandong Academy of Agricultural Science, Jinan, Shandong, China
| | - Yanfang Xue
- Maize Research Institute, Shandong Academy of Agricultural Science, Jinan, Shandong, China
| | - Zongxin Li
- Maize Research Institute, Shandong Academy of Agricultural Science, Jinan, Shandong, China
| | - Zhaojun Ding
- College of Life Sciences, Shandong University, Jinan, Shandong, China
| | - Xia Liu
- Maize Research Institute, Shandong Academy of Agricultural Science, Jinan, Shandong, China; College of Life Sciences, Shandong University, Jinan, Shandong, China.
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Liu H, Able AJ, Able JA. SMARTER De-Stressed Cereal Breeding. TRENDS IN PLANT SCIENCE 2016; 21:909-925. [PMID: 27514453 DOI: 10.1016/j.tplants.2016.07.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 06/30/2016] [Accepted: 07/05/2016] [Indexed: 05/06/2023]
Abstract
In cereal breeding programs, improved yield potential and stability are ultimate goals when developing new varieties. To facilitate achieving these goals, reproductive success under stressful growing conditions is of the highest priority. In recent times, small RNA (sRNA)-mediated pathways have been associated with the regulation of genes involved in stress adaptation and reproduction in both model plants and several cereals. Reproductive and physiological traits such as flowering time, reproductive branching, and root architecture can be manipulated by sRNA regulatory modules. We review sRNA-mediated pathways that could be exploited to expand crop diversity with adaptive traits and, in particular, the development of high-yielding stress-tolerant cereals: SMARTER cereal breeding through 'Small RNA-Mediated Adaptation of Reproductive Targets in Epigenetic Regulation'.
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Affiliation(s)
- Haipei Liu
- School of Agriculture, Food and Wine, University of Adelaide, Waite Research Institute, PMB 1, Glen Osmond, South Australia 5064, Australia
| | - Amanda J Able
- School of Agriculture, Food and Wine, University of Adelaide, Waite Research Institute, PMB 1, Glen Osmond, South Australia 5064, Australia
| | - Jason A Able
- School of Agriculture, Food and Wine, University of Adelaide, Waite Research Institute, PMB 1, Glen Osmond, South Australia 5064, Australia.
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Li Z, Zhang X, Liu X, Zhao Y, Wang B, Zhang J. miRNA alterations are important mechanism in maize adaptations to low-phosphate environments. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 252:103-117. [PMID: 27717445 DOI: 10.1016/j.plantsci.2016.07.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 07/13/2016] [Accepted: 07/16/2016] [Indexed: 05/26/2023]
Abstract
Maize is a globally important crop, and a low phosphate (LP) supply frequently limits maize yields in many areas. microRNAs (miRNAs) play important roles in plant development and environmental adaptation. In this study, spatio-temporal miRNA transcript profiling and some of the target genes in the roots and leaves of the maize inbred line Q319 were analyzed in response to LP. Complex small RNA populations were detected after LP culture, and they displayed different patterns in the roots and leaves. Differentially expressed miRNAs can be grouped into 'early' miRNAs, which respond rapidly and are often non-specific to phosphate deficiency, and 'late' miRNAs, which alter the morphology, physiology or metabolism of plants upon prolonged phosphate deficiency. miR827 and miR399-mediated posttranscriptional pathway responses to phosphate availability were conserved and species-specific in maize. Abiotic stress-related miRNAs were engaged in interactions with different signaling and/or metabolic pathways. Auxin-related miRNAs and their targets' expression may be involved in root architecture modification and upland growth retardation in maize when subjected to LP. The changes that were found in the expression of miRNAs and their target genes suggested that miRNA regulation/alterations are pivotal mechanisms in maize adaptations to LP environments. A complex regulatory mechanism involving miRNAs in response to the LP environment is present in maize.
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Affiliation(s)
- Zhaoxia Li
- School of Life Science, Shandong University, 27 Shanda South Road, Jinan, Shandong 250100 PR China.
| | - Xinrui Zhang
- School of Life Science, Shandong University, 27 Shanda South Road, Jinan, Shandong 250100 PR China.
| | - Xiuxia Liu
- School of Life Science, Shandong University, 27 Shanda South Road, Jinan, Shandong 250100 PR China.
| | - Yajie Zhao
- School of Life Science, Shandong University, 27 Shanda South Road, Jinan, Shandong 250100 PR China.
| | - Baomei Wang
- School of Life Science, Shandong University, 27 Shanda South Road, Jinan, Shandong 250100 PR China.
| | - Juren Zhang
- School of Life Science, Shandong University, 27 Shanda South Road, Jinan, Shandong 250100 PR China.
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15
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Nie Z, Ren Z, Wang L, Su S, Wei X, Zhang X, Wu L, Liu D, Tang H, Liu H, Zhang S, Gao S. Genome-wide identification of microRNAs responding to early stages of phosphate deficiency in maize. PHYSIOLOGIA PLANTARUM 2016; 157:161-74. [PMID: 26572939 DOI: 10.1111/ppl.12409] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Revised: 10/03/2015] [Accepted: 10/08/2015] [Indexed: 05/18/2023]
Abstract
Phosphorus (P) is an essential element involved in numerous biochemical reactions. In plants, stress responses, such as the expression of microRNAs (miRNAs), are induced to help them adapt to low phosphate (Pi) concentrations. In this study, deep sequencing was performed using the roots and leaves of maize seedlings grown under low Pi concentrations to identify miRNAs that are differentially expressed during the early stages of Pi deficiency. Eight small RNA libraries were constructed, and 159 known miRNAs representing 32 miRNA families and 10 novel miRNAs. Members of the miR396 family were extremely abundant. Further, 28 Pi-responsive miRNAs were identified (27 known and 1 novel) of which 8 and 7 were significantly expressed exclusively in leaf and root tissues, respectively. The analysis of Pi-responsive miRNAs target genes suggested that most target genes functioning as transcription factors were involved in root and leaf development. The expression profiles of selected Pi-responsive miRNAs and target genes were confirmed by quantitative real-time polymerase chain reaction (qRT-PCR). Moreover, we discuss the significance of the differences in expression patterns of these miRNAs during the early and later stages of Pi starvation. This study provides useful information concerning the role of miRNAs in response to Pi starvation and will further our understanding of the mechanisms governing Pi homeostasis in maize.
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Affiliation(s)
- Zhi Nie
- Key laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zhiyong Ren
- Key laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Libo Wang
- Key laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Shunzong Su
- Key laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xuan Wei
- Key laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiao Zhang
- Key laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ling Wu
- Key laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Dan Liu
- Key laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Haitao Tang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
| | - Hailan Liu
- Key laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Suzhi Zhang
- Key laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Shibin Gao
- Key laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
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Li D, Liu Z, Gao L, Wang L, Gao M, Jiao Z, Qiao H, Yang J, Chen M, Yao L, Liu R, Kan Y. Genome-Wide Identification and Characterization of microRNAs in Developing Grains of Zea mays L. PLoS One 2016; 11:e0153168. [PMID: 27082634 PMCID: PMC4833412 DOI: 10.1371/journal.pone.0153168] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 03/24/2016] [Indexed: 11/23/2022] Open
Abstract
The development and maturation of maize kernel involves meticulous and fine gene regulation at transcriptional and post-transcriptional levels, and miRNAs play important roles during this process. Although a number of miRNAs have been identified in maize seed, the ones involved in the early development of grains and in different lines of maize have not been well studied. Here, we profiled four small RNA libraries, each constructed from groups of immature grains of Zea mays inbred line Chang 7–2 collected 4–6, 7–9, 12–14, and 18–23 days after pollination (DAP). A total of 40 known (containing 111 unique miRNAs) and 162 novel (containing 196 unique miRNA candidates) miRNA families were identified. For conserved and novel miRNAs with over 100 total reads, 44% had higher accumulation before the 9th DAP, especially miR166 family members. 42% of miRNAs had highest accumulation during 12–14 DAP (which is the transition stage from embryogenesis to nutrient storage). Only 14% of miRNAs had higher expression 18–23 DAP. Prediction of potential targets of all miRNAs showed that 165 miRNA families had 377 target genes. For miR164 and miR166, we showed that the transcriptional levels of their target genes were significantly decreased when co-expressed with their cognate miRNA precursors in vivo. Further analysis shows miR159, miR164, miR166, miR171, miR390, miR399, and miR529 families have putative roles in the embryogenesis of maize grain development by participating in transcriptional regulation and morphogenesis, while miR167 and miR528 families participate in metabolism process and stress response during nutrient storage. Our study is the first to present an integrated dynamic expression pattern of miRNAs during maize kernel formation and maturation.
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Affiliation(s)
- Dandan Li
- China-UK-NYNU-RRes Joint Libratory of insect biology, Nanyang Normal University, Nanyang, Henan, China
| | - Zongcai Liu
- China-UK-NYNU-RRes Joint Libratory of insect biology, Nanyang Normal University, Nanyang, Henan, China
| | - Lei Gao
- Department of Botany and Plant Sciences, University of California, Riverside, California, United States of America
| | - Lifang Wang
- China-UK-NYNU-RRes Joint Libratory of insect biology, Nanyang Normal University, Nanyang, Henan, China
| | - Meijuan Gao
- China-UK-NYNU-RRes Joint Libratory of insect biology, Nanyang Normal University, Nanyang, Henan, China
| | - Zhujin Jiao
- China-UK-NYNU-RRes Joint Libratory of insect biology, Nanyang Normal University, Nanyang, Henan, China
| | - Huili Qiao
- China-UK-NYNU-RRes Joint Libratory of insect biology, Nanyang Normal University, Nanyang, Henan, China
| | - Jianwei Yang
- China-UK-NYNU-RRes Joint Libratory of insect biology, Nanyang Normal University, Nanyang, Henan, China
| | - Min Chen
- China-UK-NYNU-RRes Joint Libratory of insect biology, Nanyang Normal University, Nanyang, Henan, China
| | - Lunguang Yao
- China-UK-NYNU-RRes Joint Libratory of insect biology, Nanyang Normal University, Nanyang, Henan, China
| | - Renyi Liu
- Department of Botany and Plant Sciences, University of California, Riverside, California, United States of America
- * E-mail: (RYL); (YCK)
| | - Yunchao Kan
- China-UK-NYNU-RRes Joint Libratory of insect biology, Nanyang Normal University, Nanyang, Henan, China
- * E-mail: (RYL); (YCK)
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17
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Shriram V, Kumar V, Devarumath RM, Khare TS, Wani SH. MicroRNAs As Potential Targets for Abiotic Stress Tolerance in Plants. FRONTIERS IN PLANT SCIENCE 2016; 7:817. [PMID: 27379117 PMCID: PMC4906921 DOI: 10.3389/fpls.2016.00817] [Citation(s) in RCA: 174] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 05/25/2016] [Indexed: 05/19/2023]
Abstract
The microRNAs (miRNAs) are small (20-24 nt) sized, non-coding, single stranded riboregulator RNAs abundant in higher organisms. Recent findings have established that plants assign miRNAs as critical post-transcriptional regulators of gene expression in sequence-specific manner to respond to numerous abiotic stresses they face during their growth cycle. These small RNAs regulate gene expression via translational inhibition. Usually, stress induced miRNAs downregulate their target mRNAs, whereas, their downregulation leads to accumulation and function of positive regulators. In the past decade, investigations were mainly aimed to identify plant miRNAs, responsive to individual or multiple environmental factors, profiling their expression patterns and recognizing their roles in stress responses and tolerance. Altered expressions of miRNAs implicated in plant growth and development have been reported in several plant species subjected to abiotic stress conditions such as drought, salinity, extreme temperatures, nutrient deprivation, and heavy metals. These findings indicate that miRNAs may hold the key as potential targets for genetic manipulations to engineer abiotic stress tolerance in crop plants. This review is aimed to provide recent updates on plant miRNAs, their biogenesis and functions, target prediction and identification, computational tools and databases available for plant miRNAs, and their roles in abiotic stress-responses and adaptive mechanisms in major crop plants. Besides, the recent case studies for overexpressing the selected miRNAs for miRNA-mediated enhanced abiotic stress tolerance of transgenic plants have been discussed.
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Affiliation(s)
- Varsha Shriram
- Department of Botany, Prof. Ramkrishna More Arts, Commerce and Science College, Savitribai Phule Pune UniversityPune, India
| | - Vinay Kumar
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune UniversityPune, India
- *Correspondence: Vinay Kumar
| | - Rachayya M. Devarumath
- Molecular Biology and Genetic Engineering Section, Vasantdada Sugar InstitutePune, India
| | - Tushar S. Khare
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune UniversityPune, India
| | - Shabir H. Wani
- Division of Genetics and Plant Breeding, Faculty of Agriculture WADURA, Sher-e-Kashmir University of Agricultural Sciences and TechnologyKashmir, India
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18
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Lu YB, Qi YP, Yang LT, Guo P, Li Y, Chen LS. Boron-deficiency-responsive microRNAs and their targets in Citrus sinensis leaves. BMC PLANT BIOLOGY 2015; 15:271. [PMID: 26538180 PMCID: PMC4634795 DOI: 10.1186/s12870-015-0642-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2015] [Accepted: 10/08/2015] [Indexed: 05/22/2023]
Abstract
BACKGROUND MicroRNAs play important roles in the adaptive responses of plants to nutrient deficiencies. Most research, however, has focused on nitrogen (N), phosphorus (P), sulfur (S), copper (Cu) and iron (Fe) deficiencies, limited data are available on the differential expression of miRNAs and their target genes in response to deficiencies of other nutrient elements. In this study, we identified the known and novel miRNAs as well as the boron (B)-deficiency-responsive miRNAs from citrus leaves in order to obtain the potential miRNAs related to the tolerance of citrus to B-deficiency. METHODS Seedlings of 'Xuegan' [Citrus sinensis (L.) Osbeck] were supplied every other day with B-deficient (0 μM H3BO3) or -sufficient (10 μM H3BO3) nutrient solution for 15 weeks. Thereafter, we sequenced two small RNA libraries from B-deficient and -sufficient (control) citrus leaves, respectively, using Illumina sequencing. RESULTS Ninety one (83 known and 8 novel) up- and 81 (75 known and 6 novel) down-regulated miRNAs were isolated from B-deficient leaves. The great alteration of miRNA expression might contribute to the tolerance of citrus to B-deficiency. The adaptive responses of miRNAs to B-deficiency might related to several aspects: (a) attenuation of plant growth and development by repressing auxin signaling due to decreased TIR1 level and ARF-mediated gene expression by altering the expression of miR393, miR160 and miR3946; (b) maintaining leaf phenotype and enhancing the stress tolerance by up-regulating NACs targeted by miR159, miR782, miR3946 and miR7539; (c) activation of the stress responses and antioxidant system through down-regulating the expression of miR164, miR6260, miR5929, miR6214, miR3946 and miR3446; (d) decreasing the expression of major facilitator superfamily protein genes targeted by miR5037, thus lowering B export from plants. Also, B-deficiency-induced down-regulation of miR408 might play a role in plant tolerance to B-deficiency by regulating Cu homeostasis and enhancing superoxide dismutase activity. CONCLUSIONS Our study reveals some novel responses of citrus to B-deficiency, which increase our understanding of the adaptive mechanisms of citrus to B-deficiency at the miRNA (post-transcriptional) level.
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Affiliation(s)
- Yi-Bin Lu
- College of Resource and Environmental Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Institute of Horticultural Plant Physiology, Biochemistry and Molecular Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yi-Ping Qi
- Institute of Materia Medica, Fujian Academy of Medical Sciences, Fuzhou, 350001, China.
| | - Lin-Tong Yang
- College of Resource and Environmental Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- Institute of Horticultural Plant Physiology, Biochemistry and Molecular Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Peng Guo
- College of Resource and Environmental Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- Institute of Horticultural Plant Physiology, Biochemistry and Molecular Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Yan Li
- College of Resource and Environmental Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Li-Song Chen
- College of Resource and Environmental Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- Institute of Horticultural Plant Physiology, Biochemistry and Molecular Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- The Higher Educational Key Laboratory of Fujian Province for Soil Ecosystem Health and Regulation, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- Fujian Key Laboratory for Plant Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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19
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Budak H, Kantar M, Bulut R, Akpinar BA. Stress responsive miRNAs and isomiRs in cereals. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 235:1-13. [PMID: 25900561 DOI: 10.1016/j.plantsci.2015.02.008] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2014] [Revised: 02/12/2015] [Accepted: 02/13/2015] [Indexed: 05/18/2023]
Abstract
Abiotic and biotic stress conditions are vital determinants in the production of cereals, the major caloric source in human nutrition. Small RNAs, miRNAs and isomiRs are central to post-transcriptional regulation of gene expression in a variety of cellular processes including development and stress responses. Several miRNAs have been identified using new technologies and have roles in stress responses in plants, including cereals. The overall knowledge about the cereal miRNA repertoire, as well as an understanding of complex miRNA mediated mechanisms of target regulation in response to stress conditions, is far from complete. Ongoing efforts that add to our understanding of complex miRNA machinery have implications in plant response to stress conditions. Additionally, sequence variants of miRNAs (isomiRNAs or isomiRs), regulation of their expression through dissection of upstream regulatory elements, the role of Processing-bodies (P-bodies) in miRNA exerted gene regulation and yet unveiled organellar plant miRNAs are newly emerging topics, which will contribute to the elucidation of the miRNA machinery and its role in cereal tolerance against abiotic and biotic stresses.
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Affiliation(s)
- Hikmet Budak
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, 34956 Istanbul, Turkey.
| | - Melda Kantar
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, 34956 Istanbul, Turkey
| | - Reyyan Bulut
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, 34956 Istanbul, Turkey
| | - Bala Ani Akpinar
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, 34956 Istanbul, Turkey
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20
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Paul S, Datta SK, Datta K. miRNA regulation of nutrient homeostasis in plants. FRONTIERS IN PLANT SCIENCE 2015; 6:232. [PMID: 25914709 PMCID: PMC4392614 DOI: 10.3389/fpls.2015.00232] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 03/23/2015] [Indexed: 05/02/2023]
Abstract
Small RNAs including micro RNAs (miRNA) play an indispensable role in cell signaling mechanisms. Generally, miRNAs that are 20-24 nucleotides long bind to specific complementary transcripts, attenuating gene expression at the post-transcriptional level or via translational inhibition. In plants, miRNAs have emerged as the principal regulator of various stress responses, including low nutrient availability. It has been reported that miRNAs are vital for maintaining nutrient homeostasis in plants by regulating the expression of transporters that are involved in nutrient uptake and mobilization. The present review highlights the role of various miRNAs in several macro- or micronutrient deficiencies in plants. Understanding the regulation of different transporters by miRNAs will aid in elucidating the underlying molecular signal transduction mechanisms during nutritional stress. Recent findings regarding nutrient related-miRNAs and their gene regulation machinery may delineate a novel platform for improving the nutritional status of cereal grains or crop biofortification programs in the future.
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Affiliation(s)
| | | | - Karabi Datta
- Translational Research Laboratory of Transgenic Rice, Department of Botany, University of CalcuttaKolkata, India
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21
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Wang YG, An M, Zhou SF, She YH, Li WC, Fu FL. Expression profile of maize microRNAs corresponding to their target genes under drought stress. Biochem Genet 2014. [PMID: 25027834 DOI: 10.1007/s10535-016-0590-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Microarray assay of four inbred lines was used to identify 303 microRNAs differentially expressed under drought stress. The microRNAs were used for bioinformatics prediction of their target genes. The majority of the differentially expressed microRNA families showed different expression profiles at different time points of the stress process among the four inbred lines. Digital gene expression profiling revealed 54 genes targeted by 128 of the microRNAs differentially expressed under the same stress conditions. The differential expression of miR159 and miR168 was further validated by locked nucleic acid northern hybridization. These results indicated that miR159 and miR168, as well as numerous other microRNAs, play critical roles in signaling pathways of maize response to drought stress. However, the level of the post-transcriptional regulation mediated by microRNAs had different responses among genotypes, and the gene expression related to signaling pathways under drought stress is also regulated, possibly by multiple mechanisms.
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Affiliation(s)
- Ying-Ge Wang
- Maize Research Institute, Sichuan Agricultural University, Huimin Road 211, Wenjiang, Chengdu, 611130, Sichuan, China
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22
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Liu TY, Lin WY, Huang TK, Chiou TJ. MicroRNA-mediated surveillance of phosphate transporters on the move. TRENDS IN PLANT SCIENCE 2014; 19:647-55. [PMID: 25001521 DOI: 10.1016/j.tplants.2014.06.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 05/29/2014] [Accepted: 06/06/2014] [Indexed: 05/06/2023]
Abstract
Phosphate (Pi), which is indispensable for the structural and metabolic needs of plants, is acquired and translocated by Pi transporters. Deciphering the regulatory network of Pi signaling and homeostasis that involves the control of Pi transporters trafficking to, and their activity at, the plasma membrane provides insight into how plants adapt to environmental changes in Pi availability. Here, we review recent studies that revealed the involvement of microRNA399-PHOSPHATE 2 (PHO2) and microR827-NITROGEN LIMITATION ADAPTATION (NLA) modules in mediating the ubiquitination and degradation of PHOSPHATE TRANSPORTER 1 (PHT1) and/or PHOSPHATE 1 (PHO1). These discoveries show that miRNAs are an effective way for plants to monitor the turnover of Pi transporters in the membrane system by modulating the functioning of the membrane-associated ubiquitin machinery.
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Affiliation(s)
- Tzu-Yin Liu
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Wei-Yi Lin
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Teng-Kuei Huang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan; Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica, Taipei 115, Taiwan; Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung 402, Taiwan
| | - Tzyy-Jen Chiou
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan; Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica, Taipei 115, Taiwan; Biotechnology Center, National Chung-Hsing University, Taichung 402, Taiwan.
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23
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Kong X, Zhang M, Xu X, Li X, Li C, Ding Z. System analysis of microRNAs in the development and aluminium stress responses of the maize root system. PLANT BIOTECHNOLOGY JOURNAL 2014; 12:1108-21. [PMID: 24985700 DOI: 10.1111/pbi.12218] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2014] [Revised: 05/21/2014] [Accepted: 05/23/2014] [Indexed: 05/04/2023]
Abstract
MicroRNAs (miRNAs) are a class of regulatory small RNAs (sRNAs) that down-regulate target genes through mRNA cleavage or translational inhibition. miRNA is known to play an important role in the root development and environmental responses in both the Arabidopsis and rice. However, little information is available to form a complete view of miRNAs in the development of the maize root system and Al stress responses in maize. Four sRNA libraries were generated and sequenced from the early developmental stage of primary roots (PRY), the later developmental stage of maize primary roots (PRO), seminal roots (SR) and crown roots (CR). Through integrative analysis, we identified 278 miRNAs (246 conserved and 32 novel ones) and found that the expression patterns of miRNAs differed dramatically in different maize roots. The potential targets of the identified conserved and novel miRNAs were also predicted. In addition, our data showed that CR is more resistant to Al stress compared with PR and SR, and the differentially expressed miRNAs are likely to play significant roles in different roots in response to environmental stress such as Al stress. Here, we demonstrate that the expression patterns of miRNAs are highly diversified in different maize roots. The differentially expressed miRNAs are correlated with both the development and environmental responses in the maize root. This study not only improves our knowledge about the roles of miRNAs in maize root development but also reveals the potential role of miRNAs in the environmental responses of different maize roots.
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Affiliation(s)
- Xiangpei Kong
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, College of Life Sciences, Shandong University, Jinan, China
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24
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Sun R, Wang Q, Ma J, He Q, Zhang B. Differentiated expression of microRNAs may regulate genotype-dependent traits in cotton. Gene 2014; 547:233-8. [PMID: 24971502 DOI: 10.1016/j.gene.2014.06.052] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 05/03/2014] [Accepted: 06/23/2014] [Indexed: 10/25/2022]
Abstract
miRNA is an exogenous non-coding RNA with 21-24nt in length, which plays a crucial role in almost all biological processes. In plants, miRNAs regulate organ development, phase change, signal transduction and response to different biotic and abiotic stresses at the post-transcriptional levels. Although there are many studies on plant miRNAs, no studies have been focused on the genotype dependence. Genotype-dependent traits may be controlled by the differential expression of certain miRNAs. To test this hypothesis, we investigated the expression profile patterns of 11 selected miRNAs in 5 different organs in 5 different cotton cultivars and their implication on plant development. Our results demonstrate that miRNAs have different expression patterns in different plant organs in different genotypes, which implicate their different traits, including early flowering. miR172 is a miRNA controlling floral development and phase change; our results show that miR172 has a higher expression level in the flower bud than in any other organ, our results also show that Baimian cultivars have a higher expression of miR172 than TM-1. This suggests that Baimian cultivars have an earlier transition from vegetable growth to reproductive growth, which is confirmed by our development data on floral branch development. Our result also shows that several miRNAs, including miR159 and miR162, were highly expressed in Baimian cultivars. The results obtained in this study would provide new insight for improving cotton using miRNA-based biotechnology.
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Affiliation(s)
- Runrun Sun
- Henan Institute of Sciences and Technology, Xinxiang, Henan 453003, China; Department of Biology, East Carolina University, Greenville, NC 27858, USA
| | - Qinglian Wang
- Henan Institute of Sciences and Technology, Xinxiang, Henan 453003, China
| | - Jun Ma
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
| | - Qiuling He
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
| | - Baohong Zhang
- Henan Institute of Sciences and Technology, Xinxiang, Henan 453003, China; Department of Biology, East Carolina University, Greenville, NC 27858, USA.
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