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Zhong C, Smith NA, Zhang D, Gou X, Greaves IK, Millar AA, Walsh TK, Shan W, Wang MB. G-U base-paired hpRNA confers potent inhibition of small RNA function in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:1206-1222. [PMID: 38038953 DOI: 10.1111/tpj.16555] [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: 07/24/2023] [Revised: 10/31/2023] [Accepted: 11/06/2023] [Indexed: 12/02/2023]
Abstract
MicroRNA (miRNA) target mimicry technologies, utilizing naturally occurring miRNA decoy molecules, represent a potent tool for analyzing miRNA function. In this study, we present a highly efficient small RNA (sRNA) target mimicry design based on G-U base-paired hairpin RNA (hpG:U), which allows for the simultaneous targeting of multiple sRNAs. The hpG:U constructs consistently generate high amounts of intact, polyadenylated stem-loop (SL) RNA outside the nuclei, in contrast to traditional hairpin RNA designs with canonical base pairing (hpWT), which were predominantly processed resulting in a loop. By incorporating a 460-bp G-U base-paired double-stranded stem and a 312-576 nt loop carrying multiple miRNA target mimicry sites (GUMIC), the hpG:U construct displayed effective repression of three Arabidopsis miRNAs, namely miR165/166, miR157, and miR160, both individually and in combination. Additionally, a GUMIC construct targeting a prominent cluster of siRNAs derived from cucumber mosaic virus (CMV) Y-satellite RNA (Y-Sat) effectively inhibited Y-Sat siRNA-directed silencing of the chlorophyll biosynthetic gene CHLI, thereby reducing the yellowing symptoms in infected Nicotiana plants. Therefore, the G-U base-paired hpRNA, characterized by differential processing compared to traditional hpRNA, acts as an efficient decoy for both miRNAs and siRNAs. This technology holds great potential for sRNA functional analysis and the management of sRNA-mediated diseases.
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Affiliation(s)
- Chengcheng Zhong
- CSIRO Agriculture and Food, Canberra, 2601, ACT, Australia
- Stake Key Laboratory for Crop Stress Resistance and High-Efficiency Production and College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Neil A Smith
- CSIRO Agriculture and Food, Canberra, 2601, ACT, Australia
| | - Daai Zhang
- CSIRO Agriculture and Food, Canberra, 2601, ACT, Australia
| | - Xiuhong Gou
- Stake Key Laboratory for Crop Stress Resistance and High-Efficiency Production and College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Ian K Greaves
- CSIRO Agriculture and Food, Canberra, 2601, ACT, Australia
| | - Anthony A Millar
- Division of Plant Science, Research School of Biology, The Australian National University, Canberra, 2601, ACT, Australia
| | - Tom K Walsh
- CSIRO Environment, Canberra, 2601, ACT, Australia
| | - Weixing Shan
- Stake Key Laboratory for Crop Stress Resistance and High-Efficiency Production and College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Ming-Bo Wang
- CSIRO Agriculture and Food, Canberra, 2601, ACT, Australia
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Wang L, Hou J, Xu H, Zhang Y, Huang R, Wang D, He XQ. The PtoTCP20-miR396d-PtoGRF15 module regulates secondary vascular development in Populus. PLANT COMMUNICATIONS 2023; 4:100494. [PMID: 36419363 PMCID: PMC10030372 DOI: 10.1016/j.xplc.2022.100494] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 09/07/2022] [Accepted: 11/18/2022] [Indexed: 05/04/2023]
Abstract
Secondary vascular development is a key biological characteristic of woody plants and the basis of wood formation. Our understanding of gene expression regulation and dynamic changes in microRNAs (miRNAs) during secondary vascular development is still limited. Here we present an integrated analysis of the miRNA and mRNA transcriptome of six phase-specific tissues-the shoot apex, procambium, primary vascular tissue, cambium, secondary phloem, and secondary xylem-in Populus tomentosa. Several novel regulatory modules, including the PtoTCP20-miR396d-PtoGRF15 module, were identified during secondary vascular development in Populus. A series of biochemical and molecular experiments confirmed that PtoTCP20 activated transcription of the miR396d precursor gene and that miR396d targeted PtoGRF15 to downregulate its expression. Plants overexpressing miR396d (35S:miR396d) showed enhanced secondary growth and increased xylem production. Conversely, during the transition from primary to secondary vascular development, plants with downregulated PtoTCP20expression (PtoTCP20-SRDX), downregulated miR396 expression (35S:STTM396), and PtoGRF15 overexpression (35S:PtoGRF15) showed delayed secondary growth. Novel regulatory modules were identified by integrated analysis of the miRNA and mRNA transcriptome, and the regulatory role of the PtoTCP20-miR396d-PtoGRF15 signaling cascade in secondary vascular development was validated in Populus, providing information to support improvements in forest cultivation and wood properties.
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Affiliation(s)
- Lingyan Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Jie Hou
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Huimin Xu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yufei Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Runzhou Huang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Donghui Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xin-Qiang He
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China.
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MicroRNAs Mediated Plant Responses to Salt Stress. Cells 2022; 11:cells11182806. [PMID: 36139379 PMCID: PMC9496875 DOI: 10.3390/cells11182806] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/26/2022] [Accepted: 08/27/2022] [Indexed: 12/17/2022] Open
Abstract
One of the most damaging issues to cultivatable land is soil salinity. While salt stress influences plant growth and yields at low to moderate levels, severe salt stress is harmful to plant growth. Mineral shortages and toxicities frequently exacerbate the problem of salinity. The growth of many plants is quantitatively reduced by various levels of salt stress depending on the stage of development and duration of stress. Plants have developed various mechanisms to withstand salt stress. One of the key strategies is the utilization of microRNAs (miRNAs) that can influence gene regulation at the post-transcriptional stage under different environmental conditions, including salinity. Here, we have reviewed the miRNA-mediated adaptations of various plant species to salt stress and other abiotic variables. Moreover, salt responsive (SR)-miRNAs, their targets, and corresponding pathways have also been discussed. The review article concludes by suggesting that the utilization of miRNAs may be a vital strategy to generate salt tolerant crops ensuring food security in the future.
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Lakatos L, Groma G, Silhavy D, Nagy F. In Arabidopsis thaliana, RNA-Induced Silencing Complex-Loading of MicroRNAs Plays a Minor Regulatory Role During Photomorphogenesis Except for miR163. FRONTIERS IN PLANT SCIENCE 2022; 13:854869. [PMID: 35909792 PMCID: PMC9326452 DOI: 10.3389/fpls.2022.854869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
The shift of dark-grown seedlings to the light leads to substantial reprogramming of gene expression, which results in dramatic developmental changes (referred to as de-etiolation or photomorphogenesis). MicroRNAs (miRNAs) regulate most steps of plant development, thus miRNAs might play important role in transcriptional reprogramming during de-etiolation. Indeed, miRNA biogenesis mutants show aberrant de-etiolation. Previous works showed that the total miRNA expression pattern (total miRNAome) is only moderately altered during photomorphogenesis. However, a recent study has shown that plant miRNAs are present in two pools, biologically active miRNAs loaded to RISC (RNA-induced silencing complex-loaded) form while inactive miRNAs accumulate in duplex form upon organ formation. To test if RISC-loading efficiency is changed during photomorphogenesis. we compared the total miRNAome and the RISC-loaded miRNAome of dark-grown and de-etiolated Arabidopsis thaliana seedlings. miRNA sequencing has revealed that although regulated RISC-loading is involved in the control of active miRNAome formation during de-etiolation, this effect is moderate. The total miRNAomes and the RISC-loaded miRNAomes of dark-grown and de-etiolated plants are similar indicating that most miRNAs are loaded onto RISC with similar efficiency in dark and light. Few miRNAs were loaded onto RISC with different efficiency and one miRNA, miR163, was RISC-loaded much more effectively in light than in dark. Thus, our results suggest that although RISC-loading contributes significantly to the control of the formation of organ-specific active miRNA pools, it plays a limited role in the regulation of active miRNA pool formation during de-etiolation. Regulated RISC-loading strongly modifies the expression of miRNA163, could play a role in the fine-tuning of a few other miRNAs, and do not modify the expression of most miRNAs.
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Affiliation(s)
- Lóránt Lakatos
- Laboratory of Photo and Chronobiology, Biological Research Centre, Institute of Plant Biology, Eötvös Loránd Research Network, Szeged, Hungary
| | - Gergely Groma
- Dermatological Research Group, University of Szeged, Szeged, Hungary
| | - Daniel Silhavy
- Laboratory of Photo and Chronobiology, Biological Research Centre, Institute of Plant Biology, Eötvös Loránd Research Network, Szeged, Hungary
| | - Ferenc Nagy
- Laboratory of Photo and Chronobiology, Biological Research Centre, Institute of Plant Biology, Eötvös Loránd Research Network, Szeged, Hungary
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Dong Q, Hu B, Zhang C. microRNAs and Their Roles in Plant Development. FRONTIERS IN PLANT SCIENCE 2022; 13:824240. [PMID: 35251094 PMCID: PMC8895298 DOI: 10.3389/fpls.2022.824240] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 01/27/2022] [Indexed: 05/26/2023]
Abstract
Small RNAs are short non-coding RNAs with a length ranging between 20 and 24 nucleotides. Of these, microRNAs (miRNAs) play a distinct role in plant development. miRNAs control target gene expression at the post-transcriptional level, either through direct cleavage or inhibition of translation. miRNAs participate in nearly all the developmental processes in plants, such as juvenile-to-adult transition, shoot apical meristem development, leaf morphogenesis, floral organ formation, and flowering time determination. This review summarizes the research progress in miRNA-mediated gene regulation and its role in plant development, to provide the basis for further in-depth exploration regarding the function of miRNAs and the elucidation of the molecular mechanism underlying the interaction of miRNAs and other pathways.
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Affiliation(s)
- Qingkun Dong
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Binbin Hu
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Cui Zhang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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Kumar S, Abass Ahanger M, Alshaya H, Latief Jan B, Yerramilli V. Salicylic acid mitigates salt induced toxicity through the modifications of biochemical attributes and some key antioxidants in capsicum annuum. Saudi J Biol Sci 2022. [DOI: 10.1016/j.sjbs.2022.01.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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7
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Deng W, Pan M, Zhu S, Chao R, Wang L. Emerging roles of microRNAs in acute lymphoblastic leukemia and their clinical prospects. Expert Rev Hematol 2021; 14:987-992. [PMID: 34784832 DOI: 10.1080/17474086.2021.2007763] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
INTRODUCTION Targeted therapy with microRNAs (miRNAs) has been a significant challenge in recent years. Studying the role and mechanism through which miRNAs regulate various cancer processes is very critical in cancer treatment, including acute lymphoblastic leukemia (ALL). AREAS COVERED This review summarizes the diverse roles of miRNAs in ALL and provides new perspectives in miRNA-based therapeutic strategies. EXPERT OPINION MiRNAs belong to a kind of endogenous non-coding small RNA with the length of 19 ~ 25 nucleotides. They inhibit the expression of target genes and participate in almost all essential physiological processes such as cell proliferation, apoptosis, differentiation, and inflammatory responses. Many miRNAs are abnormally expressed in tumor cells, suggesting that they might be related to the occurrence and development of tumor. ALL is a common hematological malignancy in children. Its clinical manifestation, morphology, immunophenotype, and genetic characteristics are highly heterogeneous. A number of miRNAs have been found to be abnormally expressed in ALL and related to the biological characteristics, clinical features, diagnosis, and treatment in ALL patients. The understanding of miRNAs could help reveal ALL pathogenesis and identify accurate molecular markers for ALL diagnosis, prognosis, and therapeutic targets.
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Affiliation(s)
- Wei Deng
- Department of Pediatric General Internal Medicine, Gansu Provincial Maternity and Child-care Hospital, Lanzhou, Gansu, China
| | - Ming Pan
- Department of Hematology, Wuwei People's Hospital, Wuwei, Gansu, China
| | - Shengdong Zhu
- Department of Pediatric General Internal Medicine, Gansu Provincial Maternity and Child-care Hospital, Lanzhou, Gansu, China
| | - Rong Chao
- Department of Pediatric General Internal Medicine, Gansu Provincial Maternity and Child-care Hospital, Lanzhou, Gansu, China
| | - Li Wang
- Department of Pediatric General Internal Medicine, Gansu Provincial Maternity and Child-care Hospital, Lanzhou, Gansu, China
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John S, Olas JJ, Mueller-Roeber B. Regulation of alternative splicing in response to temperature variation in plants. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:6150-6163. [PMID: 34028544 PMCID: PMC8483784 DOI: 10.1093/jxb/erab232] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 05/21/2021] [Indexed: 05/08/2023]
Abstract
Plants have evolved numerous molecular strategies to cope with perturbations in environmental temperature, and to adjust growth and physiology to limit the negative effects of extreme temperature. One of the strategies involves alternative splicing of primary transcripts to encode alternative protein products or transcript variants destined for degradation by nonsense-mediated decay. Here, we review how changes in environmental temperature-cold, heat, and moderate alterations in temperature-affect alternative splicing in plants, including crops. We present examples of the mode of action of various temperature-induced splice variants and discuss how these alternative splicing events enable favourable plant responses to altered temperatures. Finally, we point out unanswered questions that should be addressed to fully utilize the endogenous mechanisms in plants to adjust their growth to environmental temperature. We also indicate how this knowledge might be used to enhance crop productivity in the future.
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Affiliation(s)
- Sheeba John
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Straße, Haus, Potsdam, Germany
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg, Potsdam, Germany
| | - Justyna Jadwiga Olas
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Straße, Haus, Potsdam, Germany
- Correspondence: or
| | - Bernd Mueller-Roeber
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Straße, Haus, Potsdam, Germany
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg, Potsdam, Germany
- Center of Plant Systems Biology and Biotechnology (CPSBB), Plovdiv, Bulgaria
- Correspondence: or
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Lin Y, Chen Y, Zeng Y, Zhang S, Zhang Z, Chen Y, Gong J, Lai Z. Molecular characterization of miRNA genes and their expression in Dimocarpus longan Lour. PLANTA 2021; 253:41. [PMID: 33475870 DOI: 10.1007/s00425-021-03564-w] [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: 07/30/2020] [Accepted: 01/02/2021] [Indexed: 06/12/2023]
Abstract
A genome-wide analysis of longan miRNA genes was conducted, and full-length pri-miRNA transcripts were cloned. Bioinformatics and expression analyses contributed to the functional characterization of longan miRNA genes. MicroRNAs are important for the post-transcriptional regulation of target genes. However, little is known about the transcription and regulation of miRNA genes in longan (Dimocarpus longan Lour.). In this study, 80 miRNA precursors (pre-miRNA) were predicted, and their secondary structure, size, conservation, and diversity were analyzed. Furthermore, the full-length cDNA sequences of 13 longan primary miRNAs (pri-miRNAs) were amplified by RLM-RACE and SMART-RACE and analyzed, which revealed that longan pri-miRNA transcripts have multiple transcription start sites (TSSs) and the downstream pre-miRNAs are polymorphic. Accordingly, the longan pri-miRNAs and protein-encoding genes may have similar transcriptional specificities. An analysis of the longan miRNA gene promoter elements indicated that the three most abundant cis-acting elements were light-responsive, stress-responsive, and hormone-responsive elements. A quantitative real-time PCR assay elucidated the potential spatial and temporal expression patterns of longan pre-miRNAs during the early stages of somatic embryogenesis (SE) and in different longan organs/tissues. This is the first report regarding the molecular characterization of miRNA genes and their expression profiles in longan. The generated data may serve as a foundation for future research aimed at clarifying the longan miRNA gene functions.
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Affiliation(s)
- Yuling Lin
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Yan Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Youjing Zeng
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Shuting Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Zihao Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - YuKun Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Jiawei Gong
- Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
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Mohanty P, Ayachit G, Mohanty JN, Pandya H, Mankad AU, Das J. Documentation of conserved and novel miRNAs participated in plant secondary metabolic pathways of sanctified Aegle marmelos. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Namgyal D, Chandan K, Sultan A, Aftab M, Ali S, Mehta R, El-Serehy HA, Al-Misned FA, Sarwat M. Dim Light at Night Induced Neurodegeneration and Ameliorative Effect of Curcumin. Cells 2020; 9:cells9092093. [PMID: 32933226 PMCID: PMC7565558 DOI: 10.3390/cells9092093] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 08/28/2020] [Accepted: 09/05/2020] [Indexed: 12/16/2022] Open
Abstract
It is a well-known fact that following a proper routine light/dark or diurnal rhythm controls almost all biological processes. With the introduction of modern lighting and artificial illumination systems, continuous exposure to light at night may lead to the disruption of diurnal rhythm. However, the effect of light during the night on brain anatomy, physiology, and human body functions is less explored and poorly understood. In this study, we have evaluated the effect of exposure to dim light (5 lux) at night (dLAN) on Swiss Albino mice over a duration of three consecutive weeks. Results have revealed that exposure to dLAN led to an impairment of cognitive and non-cognitive behaviour, oxidative stress–mediated elevation of lipid peroxidation, and reduction of superoxide dismutase and catalase activity. It also led to the downregulation of hippocampal proteins (BDNF, Synapsin II and DCX) at both protein and mRNA level. Additionally, there was downregulation of CREB and SIRT1 mRNAs and neurodegeneration-associated miRNA21a-5p and miRNA34a-5p. The pyramidal and cortical neurons started showing pyknotic and chromatolysis characteristics. However, a dose of curcumin administered to the mice positively modulated these parameters in our experimental animals. We proposed the modulatory role of curcumin in addressing the deleterious effects of dLAN.
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Affiliation(s)
- Dhondup Namgyal
- Amity Institute of Neuropsychology and Neuroscience, Amity University, Noida UP 201303, India; (D.N.); (R.M.)
- Amity Institute of Pharmacy, Amity University, Noida UP 201303, India;
| | - Kumari Chandan
- Amity Institute of Pharmacy, Amity University, Noida UP 201303, India;
| | - Armiya Sultan
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India;
| | - Mehreen Aftab
- Amity Institute of Molecular Medicine and Stem Cell Research, Amity University, Noida UP 201303, India;
| | - Sher Ali
- School of Basic Sciences and Research, Department of Life Sciences, Sharda University, Greater Noida, Uttar Pradesh 201310, India;
| | - Rachna Mehta
- Amity Institute of Neuropsychology and Neuroscience, Amity University, Noida UP 201303, India; (D.N.); (R.M.)
| | - Hamed A. El-Serehy
- Department of Zoology, College of Science, King Saud University, Riyadh l1451, Saudi Arabia; (H.A.E.-S.); (F.A.A.-M.)
| | - Fahad A. Al-Misned
- Department of Zoology, College of Science, King Saud University, Riyadh l1451, Saudi Arabia; (H.A.E.-S.); (F.A.A.-M.)
| | - Maryam Sarwat
- Amity Institute of Pharmacy, Amity University, Noida UP 201303, India;
- Correspondence: Correspondence: ; Tel.: +91-12-0439-2472
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Zhang Y, Yin S, Tu Y, Mei H, Yang Y. A novel microRNA, SlymiR208, promotes leaf senescence via regulating cytokinin biosynthesis in tomato. PHYSIOLOGIA PLANTARUM 2020; 169:143-155. [PMID: 31985059 DOI: 10.1111/ppl.13068] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 01/13/2020] [Accepted: 01/20/2020] [Indexed: 06/10/2023]
Abstract
Leaf senescence is a highly-programmed developmental process during the plant life cycle. Cytokinin (CK) has been widely acknowledged as a negative regulator to delay leaf senescence. MiRNAs play key roles in a variety of developmental and physiological processes through negatively regulating their target gene expression. However, to date, the roles of microRNAs (miRNAs) in CK biosynthesis remain unclear, and the knowledge on miRNA regulation of leaf senescence is still very limited. Isopentenyltransferases (IPTs) catalyze the initial and rate-limiting step of CK biosynthesis in higher plants. Our previous work uncovered that silencing of SlIPT4 expression in tomato resulted in premature leaf senescence. Here, we identified a novel tomato miRNA, SlymiR208, which regulates the expression of SlIPT2 and SlIPT4 at the post-transcriptional level. SlymiR208 expression is ubiquitous in tomato and exhibits an opposite transition to its target transcripts in aged leaf. SlymiR208 overexpression in tomato sharply reduced the transcript levels of SlIPT2 and SlIPT4, and the concentrations of endogenous CKs in leaves. The early leaf senescence caused by SlymiR208 overexpression was consistent with the phenotype of SlIPT4-silenced lines. The data demonstrated that SlymiR208 is a positive regulator in leaf senescence through negatively regulating CK biosynthesis via targeting SlIPT2 and SlIPT4 in tomato. This study indicated that post-transcriptional regulation via miRNA is a control point of CK biosynthesis and added a new layer to the understanding of the regulation of CK biosynthesis in tomato and a new factual proof to support that miRNAs are involved in leaf senescence.
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Affiliation(s)
- Yong Zhang
- Bioengineering College, Chongqing University, Chongqing, 400044, China
| | - Shuangqin Yin
- Bioengineering College, Chongqing University, Chongqing, 400044, China
| | - Yun Tu
- Bioengineering College, Chongqing University, Chongqing, 400044, China
| | - Hu Mei
- Bioengineering College, Chongqing University, Chongqing, 400044, China
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Chongqing University, Chongqing, 400044, China
| | - Yingwu Yang
- Bioengineering College, Chongqing University, Chongqing, 400044, China
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Chongqing University, Chongqing, 400044, China
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Leclercq J, Wu S, Farinas B, Pointet S, Favreau B, Vignes H, Kuswanhadi K, Ortega-Abboud E, Dufayard JF, Gao S, Droc G, Hu S, Tang C, Montoro P. Post-transcriptional regulation of several biological processes involved in latex production in Hevea brasiliensis. PeerJ 2020; 8:e8932. [PMID: 32391199 PMCID: PMC7195832 DOI: 10.7717/peerj.8932] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 03/17/2020] [Indexed: 11/20/2022] Open
Abstract
Background Small RNAs modulate plant gene expression at both the transcriptional and post-transcriptional level, mostly through the induction of either targeted DNA methylation or transcript cleavage, respectively. Small RNA networks are involved in specific plant developmental processes, in signaling pathways triggered by various abiotic stresses and in interactions between the plant and viral and non-viral pathogens. They are also involved in silencing maintenance of transposable elements and endogenous viral elements. Alteration in small RNA production in response to various environmental stresses can affect all the above-mentioned processes. In rubber trees, changes observed in small RNA populations in response to trees affected by tapping panel dryness, in comparison to healthy ones, suggest a shift from a transcriptional to a post-transcriptional regulatory pathway. This is the first attempt to characterise small RNAs involved in post-transcriptional silencing and their target transcripts in Hevea. Methods Genes producing microRNAs (MIR genes) and loci producing trans-activated small interfering RNA (ta-siRNA) were identified in the clone PB 260 re-sequenced genome. Degradome libraries were constructed with a pool of total RNA from six different Hevea tissues in stressed and non-stressed plants. The analysis of cleaved RNA data, associated with genomics and transcriptomics data, led to the identification of transcripts that are affected by 20–22 nt small RNA-mediated post-transcriptional regulation. A detailed analysis was carried out on gene families related to latex production and in response to growth regulators. Results Compared to other tissues, latex cells had a higher proportion of transcript cleavage activity mediated by miRNAs and ta-siRNAs. Post-transcriptional regulation was also observed at each step of the natural rubber biosynthesis pathway. Among the genes involved in the miRNA biogenesis pathway, our analyses showed that all of them are expressed in latex. Using phylogenetic analyses, we show that both the Argonaute and Dicer-like gene families recently underwent expansion. Overall, our study underlines the fact that important biological pathways, including hormonal signalling and rubber biosynthesis, are subject to post-transcriptional silencing in laticifers.
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Affiliation(s)
- Julie Leclercq
- CIRAD, UMR AGAP, Montpellier, France.,AGAP, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Shuangyang Wu
- University of Chinese Academy of Sciences, CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Benoît Farinas
- CIRAD, UMR AGAP, Montpellier, France.,AGAP, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Stéphanie Pointet
- CIRAD, UMR AGAP, Montpellier, France.,AGAP, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Bénédicte Favreau
- CIRAD, UMR AGAP, Montpellier, France.,AGAP, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Hélène Vignes
- CIRAD, UMR AGAP, Montpellier, France.,AGAP, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | | | - Enrique Ortega-Abboud
- CIRAD, UMR AGAP, Montpellier, France.,AGAP, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Jean-François Dufayard
- CIRAD, UMR AGAP, Montpellier, France.,AGAP, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Shenghan Gao
- University of Chinese Academy of Sciences, CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Gaëtan Droc
- CIRAD, UMR AGAP, Montpellier, France.,AGAP, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Songnian Hu
- University of Chinese Academy of Sciences, CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Chaorong Tang
- Hainan University, College of Tropical Crops, Haikou, China
| | - Pascal Montoro
- CIRAD, UMR AGAP, Montpellier, France.,AGAP, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
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14
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Chandan K, Gupta M, Sarwat M. Role of Host and Pathogen-Derived MicroRNAs in Immune Regulation During Infectious and Inflammatory Diseases. Front Immunol 2020; 10:3081. [PMID: 32038627 PMCID: PMC6992578 DOI: 10.3389/fimmu.2019.03081] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 12/17/2019] [Indexed: 12/11/2022] Open
Abstract
MicroRNAs (miRNAs, miRs) are short, endogenously initiated, non-coding RNAs that bind to target mRNAs, leading to the degradation or translational suppression of respective mRNAs. They have been reported as key players in physiological processes like differentiation, cellular proliferation, development, and apoptosis. They have gained importance as gene expression regulators in the immune system. They control antibody production and release various inflammatory mediators. Abnormal expression and functioning of miRNA in the immune system is linked to various diseases like inflammatory disorders, allergic diseases, cancers etc. As compared to the average human genome, miRNA targets the genes of immune system quite differently. miRNA appeared to regulate the responses related to both acquired and innate immunity of the humans. Several miRNAs importantly regulate the transcription and even, dysregulation of inflammation-related mediators. Many miRNAs are either upregulated or downregulated in various inflammatory and infectious diseases. Hence, modifying or targeting the expression of miRNAs might serve as a novel strategy for the diagnosis, prevention, and treatment of various inflammatory and infectious conditions.
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Affiliation(s)
| | | | - Maryam Sarwat
- Amity Institute of Pharmacy, Amity University, Noida, India
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15
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Mishra R, Mohapatra R, Mahanty B, Joshi RK. Analysis of microRNAs and their targets from onion (Allium cepa) using genome survey sequences (GSS) and expressed sequence tags (ESTs). Bioinformation 2019; 15:907-917. [PMID: 32256010 PMCID: PMC7088424 DOI: 10.6026/97320630015907] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 12/30/2019] [Accepted: 12/31/2019] [Indexed: 01/31/2023] Open
Abstract
MicroRNAs are small non-coding RNAs of 21-24 nucleotides in length that acts as important modulators of gene expression related to numerous biological processes including development and defense response in eukaryotes. However, only a limited report on onion (Allium cepa) miRNAs is available and their associated role in growth and development of onion is not yet clear. Therefore, it is of interest to identify miRNAs and their targets in Allium cepa using the genome survey sequences (GSSs) and expressed sequence tags (ESTs) and deduce the functions of the target genes using gene ontology (GO) terms. We report 14 potential miRNAs belonging to 13 different families (miR162, miR168, miR172c, miR172e, miR398, miR400, miR414, miR1134, miR1223, miR6219, miR7725, miR8570, miR8703 and miR8752). BLAST analysis using psRNATarget server predicted 39 potential targets for the identified miRNAs majority of which were transcription factors implicated in plant growth, development, hormone signaling and stress responses. These data forms the basis for further analysis and verification towards understanding the miRNA mediated regulatory mechanism in Allium cepa.
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Affiliation(s)
- Rukmini Mishra
- School of Applied Sciences, Centurion University of Technology and Management, Odisha, India
| | - Rupesh Mohapatra
- Centre for Biotechnology, Siksha O Anusandhan University, Bhubaneswar-751030, Odisha, India
| | - Bijayalaxmi Mahanty
- Dept. of Biotechnology, Rama Devi Women's University, Vidya Vihar, Bhubaneswar-751022, Odisha, India
| | - Raj Kumar Joshi
- Dept. of Biotechnology, Rama Devi Women's University, Vidya Vihar, Bhubaneswar-751022, Odisha, India
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16
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Ye W, Jiang J, Lin Y, Yeh KW, Lai Z, Xu X, Oelmüller R. Colonisation of Oncidium orchid roots by the endophyte Piriformospora indica restricts Erwinia chrysanthemi infection, stimulates accumulation of NBS-LRR resistance gene transcripts and represses their targeting micro-RNAs in leaves. BMC PLANT BIOLOGY 2019; 19:601. [PMID: 31888486 PMCID: PMC6937650 DOI: 10.1186/s12870-019-2105-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 10/28/2019] [Indexed: 05/30/2023]
Abstract
BACKGROUND Erwinia chrysanthemi (Ec) is a destructive pathogen which causes soft-rot diseases in diverse plant species including orchids. We investigated whether colonization of Oncidium roots by the endophytic fungus Piriformospora indica (Pi) restricts Ec-induced disease development in leaves, and whether this might be related to the regulation of nucleotide binding site-leucine rich repeat (NBS-LRR) Resistance (R) genes. RESULTS Root colonization of Oncidium stackings by Pi restricts progression of Ec-induced disease development in the leaves. Since Pi does not inhibit Ec growth on agar plates, we tested whether NBS-LRR R gene transcripts and the levels of their potential target miRNAs in Oncidium leaves might be regulated by Pi. Using bioinformatic tools, we first identified NBS-LRR R gene sequences from Oncidium, which are predicted to be targets of miRNAs. Among them, the expression of two R genes was repressed and the accumulation of several regulatory miRNA stimulated by Ec in the leaves of Oncidium plants. This correlated with the progression of disease development, jasmonic and salicylic acid accumulation, ethylene synthesis and H2O2 production after Ec infection of Oncidium leaves. Interestingly, root colonization by Pi restricted disease development in the leaves, and this was accompanied by higher expression levels of several defense-related R genes and lower expression level of their target miRNA. CONCLUSION Based on these data we propose that Pi controls the levels of NBS-LRR R mRNAs and their target miRNAs in leaves. This regulatory circuit correlates with the protection of Oncidium plants against Ec infection, and molecular and biochemical investigations will demonstrate in the future whether, and if so, to what extent these two observations are related to each other.
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Affiliation(s)
- Wei Ye
- Sanming Academy of Agricultural Sciences, Sanming, Fujian China
| | - Jinlan Jiang
- Sanming Academy of Agricultural Sciences, Sanming, Fujian China
| | - Yuling Lin
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian China
| | - Kai-Wun Yeh
- Matthias-Schleiden-Institute, Plant Physiology, Friedrich Schiller University Jena, Jena, Germany
| | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian China
| | - Xuming Xu
- Sanming Academy of Agricultural Sciences, Sanming, Fujian China
| | - Ralf Oelmüller
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian China
- Matthias-Schleiden-Institute, Plant Physiology, Friedrich Schiller University Jena, Jena, Germany
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17
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Liu T, Tang J, Chen L, Zeng J, Wen J, Yi B, Ma C, Tu J, Fu T, Shen J. Differential expression of miRNAs and their targets in wax-deficient rapeseed. Sci Rep 2019; 9:12201. [PMID: 31434948 PMCID: PMC6704058 DOI: 10.1038/s41598-019-48439-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 08/02/2019] [Indexed: 11/25/2022] Open
Abstract
The cuticle of a plant, composed of cutin and wax, is the outermost hydrophobic layer covering the epidermis of all its aerial organs, protecting it from many abiotic and biotic stresses. The biosynthesis and regulation pathways of wax components have been well studied, whereas there are fewer reports on the small RNA-involved post-transcriptional regulation of wax biosynthesis in plants, particularly in Brassica napus. Previously, we conducted a study on a glossy mutant of rapeseed, and we assumed that there was a dominant repressor to inhibit the expression of wax-related genes. To verify this hypothesis and investigate the function of small RNAs in wax biosynthesis in B. napus, we constructed four small RNA libraries from the stem epidermis of wax-deficient mutant and wild-type plants for sequencing. Subsequently, 43,840,451 clean reads were generated and 24 nt sequences represented the dominant percentage. In total, 300 unique known miRNAs were identified and eight of them showed differential expression. In addition, the expression levels of six novel miRNAs were altered. Surprisingly, we found that four up-regulated miRNAs in the wax-deficient plants, bna-miR408b-5p, bna-miR165b-5p, bna-miR160a-3p, and bna-miR398-5p, were all complementary strands of their corresponding mature strands. Stem-loop qRT-PCR verified that the expression of bna-miR165a-5p was increased in the mutant stems, while its putative target, BnaA06g40560D (CYP96A2), was down-regulated. In addition, the expression of bna-miR827a was detected to be down-regulated in glossy mutant. 5' RACE experimental data showed that bna-miR827a cleaves three NITROGEN LIMITATION ADAPTATION (NLA) genes (BnaC08g45940D, BnaA10g01450D and BnaC05g01480D). The down-regulation of bna-miR827a resulted in decreased cleavage on its targets, and led to the up-regulation of its targets, especially BnaA10g01450D gene. These results showed that bna-miR165a-5p might participate in wax biosynthesis process by regulating its putative target BnaA06g40560D (CYP96A2). The expression levels of a phosphate (Pi)-related miRNA, bna-miR827a, and its target genes were affected in wax-deficient rapeseeds. These results will promote the study of post-transcriptional regulation mechanisms of wax biosynthesis in B. napus and provide new directions for further research.
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Affiliation(s)
- Tingting Liu
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jingquan Tang
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Li Chen
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jiayue Zeng
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jing Wen
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Chaozhi Ma
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, Hubei, China.
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18
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Li T, Wang YH, Liu JX, Feng K, Xu ZS, Xiong AS. Advances in genomic, transcriptomic, proteomic, and metabolomic approaches to study biotic stress in fruit crops. Crit Rev Biotechnol 2019; 39:680-692. [DOI: 10.1080/07388551.2019.1608153] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Tong Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Ya-Hui Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Jie-Xia Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Kai Feng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Zhi-Sheng Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Ai-Sheng Xiong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, China
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19
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Abstract
MicroRNAs (miRNAs) are important regulators of gene expression that bind complementary target mRNAs and repress their expression. Precursor miRNA molecules undergo nuclear and cytoplasmic processing events, carried out by the endoribonucleases DROSHA and DICER, respectively, to produce mature miRNAs that are loaded onto the RISC (RNA-induced silencing complex) to exert their biological function. Regulation of mature miRNA levels is critical in development, differentiation, and disease, as demonstrated by multiple levels of control during their biogenesis cascade. Here, we will focus on post-transcriptional mechanisms and will discuss the impact of cis-acting sequences in precursor miRNAs, as well as trans-acting factors that bind to these precursors and influence their processing. In particular, we will highlight the role of general RNA-binding proteins (RBPs) as factors that control the processing of specific miRNAs, revealing a complex layer of regulation in miRNA production and function.
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Affiliation(s)
- Gracjan Michlewski
- Division of Infection and Pathway Medicine, University of Edinburgh, Edinburgh EH16 4SB, United Kingdom
- Zhejiang University-University of Edinburgh Institute, Zhejiang University, Zhejiang 314400, P.R. China
| | - Javier F Cáceres
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, United Kingdom
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20
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Identification and characterization of known and novel microRNAs in strawberry fruits induced by Botrytis cinerea. Sci Rep 2018; 8:10921. [PMID: 30026481 PMCID: PMC6053406 DOI: 10.1038/s41598-018-29289-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 07/09/2018] [Indexed: 12/22/2022] Open
Abstract
MicroRNAs are endogenous small non-coding RNAs that negatively regulate mRNAs, mainly at the post-transcriptional level, and play an important role in resistance response of plants. To date, there are few reports on resistance response of strawberry miRNAs to pathogens. In this study, using high-throughput sequencing, 134 conserved and 35 novel miRNAs were identified in six libraries within the treatment of Botrytis cinerea. A total 497 potential target genes were predicted using Fragaria vesca genome. Most of the differential expressed miRNAs in strawberry fruits were up-regulated in early libraries and down-regulated in late libraries. PIRL, the target gene of miR5290a, showed the opposite expressed trend compared with miR5290 from T1 to T3 libraries, and functional analysis of the PIRL gene shows that it has obvious resistance to B. cinerea in the strawberry fruits with overexpressed PIRL gene. We speculate that miR5290a negatively regulates its target gene PIRL to increase resistance to pathogen infection, and further analysis of PIRL function is meaningful for studying the plant-pathogen relationship and improving strawberry fruit quality and yield.
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21
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Mishra R, Mohanty JN, Chand SK, Joshi RK. Can-miRn37a mediated suppression of ethylene response factors enhances the resistance of chilli against anthracnose pathogen Colletotrichum truncatum L. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 267:135-147. [PMID: 29362092 DOI: 10.1016/j.plantsci.2017.12.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 11/30/2017] [Accepted: 12/01/2017] [Indexed: 05/17/2023]
Abstract
Pepper anthracnose, caused by Colletotrichum species complex is the most destructive disease of chilli (Capsicum annuum L.). miRNAs are key modulators of transcriptional and post- transcriptional expression of genes during defense responses. In the present study, we performed a comparative miRNA profiling of susceptible (Arka Lohit-AL) and resistant (Punjab Lal-PL) chilli cultivars to identify 35 differentially expressed miRNAs that could be classified as positive, negative or basal regulators of defense against C. truncatum, the most potent anthracnose pathogen. Interestingly, a novel microRNA can-miRn37a was significantly induced in PL but largely repressed in AL genotype post pathogen attack. Subsequent over-expression of can-miRn37a in AL showed enhanced resistance to anthracnose, as evidenced by decreased fungal growth and induced expression of defense-related genes. Consequently, the expression of its three target genes encoding the ethylene response factors (ERFs) was down-regulated in PL as well as in the over-expression lines of AL genotypes. The ability of these targets to be regulated by can-miRn37a was further confirmed by transient co-expression in Nicotiana benthamiana. Additionally, the virus-induced silencing of the three targets in the susceptible AL cultivar revealed their role in fungal colonization and induction of C. truncatum pathogenicity in chilli. Taken together, our study suggests that can-miRn37a provides a potential miRNA mediated approach of engineering anthracnose resistance in chilli by repressing ERFs and preventing fungal colonization.
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Affiliation(s)
- Rukmini Mishra
- Functional Genomics Laboratory, Centre for Biotechnology, Siksha O Anusandhan University, Bhubaneswar, Odisha, India
| | - Jatindra Nath Mohanty
- Functional Genomics Laboratory, Centre for Biotechnology, Siksha O Anusandhan University, Bhubaneswar, Odisha, India
| | - Subodh Kumar Chand
- Functional Genomics Laboratory, Centre for Biotechnology, Siksha O Anusandhan University, Bhubaneswar, Odisha, India
| | - Raj Kumar Joshi
- Functional Genomics Laboratory, Centre for Biotechnology, Siksha O Anusandhan University, Bhubaneswar, Odisha, India.
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22
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Shapulatov U, van Hoogdalem M, Schreuder M, Bouwmeester H, Abdurakhmonov IY, van der Krol AR. Functional intron-derived miRNAs and host-gene expression in plants. PLANT METHODS 2018; 14:83. [PMID: 30258486 PMCID: PMC6151947 DOI: 10.1186/s13007-018-0351-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 09/18/2018] [Indexed: 02/08/2023]
Abstract
BACKGROUND Recently, putative pre-miRNAs locations have been identified in the introns of plant genes, raising the question whether such genes can show a dual functionality by having both correct maturation of the host gene pre-mRNA and maturation of the miRNAs from the intron. Here, we demonstrated that such dual functionality is indeed possible, using as host gene the firefly luciferase gene with intron (ffgLUC), and different artificial intronic miRNAs (aimiRNA) placed within the intron of ffgLUC. RESULTS The miRNAs were based on the structure of the natural miR319a. Luciferase (LUC) activity in planta was used to evaluate a correct splicing of the ffgLUC mRNA. Different target sequences were inserted into the aimiRNA to monitor efficiency of silencing of different target mRNAs. After adjusting the insertion cloning strategy, the ffgLUCaimiR-319a gene showed dual functionality with correct splicing of ffgLUC and efficient silencing of TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR1 transcription factor genes targeted in-trans by aimiR-319a or targeting the transgene ffLUC in-cis by an aimiR-LUC. Silencing of endogenous target genes by aimiRNA or amiRNA is efficient both in transient assays and stable transformants. A behave as strong phenotype the PHYTOCHROME B (PHYB) gene was also targeted by ffgLUCaimiR-PHYB. The lack of silencing of the PHYB target was most likely due to an insensitive target site within the PHYB mRNA which can potentially form a double stranded stem structure. CONCLUSION The combination of an overexpression construct with an artificial intronic microRNA allows for a simultaneous dual function in plants. The concept therefore adds new options to engineering of plant traits that require multiple gene manipulations.
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Affiliation(s)
- Umidjon Shapulatov
- 0000 0001 0791 5666grid.4818.5Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PD Wageningen, The Netherlands
- 0000 0001 2110 259Xgrid.419209.7Center of Genomics and Bioinformatics, Academy of Sciences of Uzbekistan, University Street-2, Qibray Region, Tashkent, Uzbekistan 111215
| | - Mark van Hoogdalem
- 0000 0001 0791 5666grid.4818.5Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PD Wageningen, The Netherlands
| | - Marielle Schreuder
- 0000 0001 0791 5666grid.4818.5Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PD Wageningen, The Netherlands
| | - Harro Bouwmeester
- 0000 0001 0791 5666grid.4818.5Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PD Wageningen, The Netherlands
| | - Ibrokhim Y. Abdurakhmonov
- 0000 0001 2110 259Xgrid.419209.7Center of Genomics and Bioinformatics, Academy of Sciences of Uzbekistan, University Street-2, Qibray Region, Tashkent, Uzbekistan 111215
| | - Alexander R. van der Krol
- 0000 0001 0791 5666grid.4818.5Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PD Wageningen, The Netherlands
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23
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Alptekin B, Langridge P, Budak H. Abiotic stress miRNomes in the Triticeae. Funct Integr Genomics 2017; 17:145-170. [PMID: 27665284 PMCID: PMC5383695 DOI: 10.1007/s10142-016-0525-9] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 09/02/2016] [Accepted: 09/09/2016] [Indexed: 12/14/2022]
Abstract
The continued growth in world population necessitates increases in both the quantity and quality of agricultural production. Triticeae members, particularly wheat and barley, make an important contribution to world food reserves by providing rich sources of carbohydrate and protein. These crops are grown over diverse production environments that are characterized by a range of environmental or abiotic stresses. Abiotic stresses such as drought, heat, salinity, or nutrient deficiencies and toxicities cause large yield losses resulting in economic and environmental damage. The negative effects of abiotic stresses have increased at an alarming rate in recent years and are predicted to further deteriorate due to climate change, land degradation, and declining water supply. New technologies have provided an important tool with great potential for improving crop tolerance to the abiotic stresses: microRNAs (miRNAs). miRNAs are small regulators of gene expression that act on many different molecular and biochemical processes such as development, environmental adaptation, and stress tolerance. miRNAs can act at both the transcriptional and post-transcriptional levels, although post-transcriptional regulation is the most common in plants where miRNAs can inhibit the translation of their mRNA targets via complementary binding and cleavage. To date, expression of several miRNA families such as miR156, miR159, and miR398 has been detected as responsive to environmental conditions to regulate stress-associated molecular mechanisms individually and/or together with their various miRNA partners. Manipulation of these miRNAs and their targets may pave the way to improve crop performance under several abiotic stresses. Here, we summarize the current status of our knowledge on abiotic stress-associated miRNAs in members of the Triticeae tribe, specifically in wheat and barley, and the miRNA-based regulatory mechanisms triggered by stress conditions. Exploration of further miRNA families together with their functions under stress will improve our knowledge and provide opportunities to enhance plant performance to help us meet global food demand.
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Affiliation(s)
- Burcu Alptekin
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, USA
| | - Peter Langridge
- School of Agriculture, Food and Wine, University of Adelaide, Adelaide, Australia
| | - Hikmet Budak
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, USA.
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24
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Chand SK, Nanda S, Mishra R, Joshi RK. Multiple garlic (Allium sativum L.) microRNAs regulate the immunity against the basal rot fungus Fusarium oxysporum f. sp. Cepae. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 257:9-21. [PMID: 28224922 DOI: 10.1016/j.plantsci.2017.01.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 12/21/2016] [Accepted: 01/16/2017] [Indexed: 05/07/2023]
Abstract
The basal plate rot fungus, Fusarium oxysporum f. sp. cepae (FOC), is the most devastating pathogen posing a serious threat to garlic (Allium sativum L.) production worldwide. MicroRNAs (miRNAs) are key modulators of gene expression related to development and defense responses in eukaryotes. However, the miRNA species associated with garlic immunity against FOC are yet to be explored. In the present study, a small RNA library developed from FOC infected resistant garlic line was sequenced to identify immune responsive miRNAs. Forty-five miRNAs representing 39 conserved and six novel sequences responsive to FOC were detected. qRT-PCR analyses further classified them into three classes based on their expression patterns in susceptible line CBT-As11 and in the resistant line CBT-As153. North-blot analyses of six selective miRNAs confirmed the qRT-PCR results. Expression studies on a selective set of target genes revealed a negative correlation with the complementary miRNAs. Furthermore, transgenic garlic plant overexpresing miR164a, miR168a and miR393 showed enhanced resistance to FOC, as revealed by decreased fungal growth and up-regulated expression of defense-responsive genes. These results indicate that multiple miRNAs are involved in garlic immunity against FOC and that the overexpression of miR164a, miR168a and miR393 can augment garlic resistance to Fusarium basal rot infection.
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Affiliation(s)
- Subodh Kumar Chand
- Functional Genomics Laboratory, Centre of Biotechnology, Siksha O Anusandhan University, Bhubaneswar, Odisha, India
| | - Satyabrata Nanda
- Functional Genomics Laboratory, Centre of Biotechnology, Siksha O Anusandhan University, Bhubaneswar, Odisha, India
| | - Rukmini Mishra
- Functional Genomics Laboratory, Centre of Biotechnology, Siksha O Anusandhan University, Bhubaneswar, Odisha, India
| | - Raj Kumar Joshi
- Functional Genomics Laboratory, Centre of Biotechnology, Siksha O Anusandhan University, Bhubaneswar, Odisha, India.
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Xu J, Li Y, Wang Y, Liu X, Zhu XG. Altered expression profiles of microRNA families during de-etiolation of maize and rice leaves. BMC Res Notes 2017; 10:108. [PMID: 28235420 PMCID: PMC5324284 DOI: 10.1186/s13104-016-2367-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 12/28/2016] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) are highly conserved small non-coding RNAs that play important regulatory roles in plants. Although many miRNA families are sequentially and functionally conserved across plant kingdoms (Dezulian et al. in Genome Biol 13, 2005), they still differ in many aspects such as family size, average length, genomic loci etc. (Unver et al. in Int J Plant Genomics, 2009). RESULTS In this study, we investigated changes of miRNA expression profiles during greening process of etiolated seedlings of Oryza sativa (C3) and Zea mays (C4) to explore conserved and species-specific characteristics of miRNAs between these two species. Futhermore, we predicted 47 and 42 candidate novel miRNAs using parameterized monocot specific miRDeep2 pipeline in maize and rice respectively. Potential targets of miRNAs comprising both mRNA and long non-coding RNA (lncRNA) were examined to clarify potential regulation of photosynthesis. Based on our result, two putative positive Kranz regulators reported by Wang et al. (2010) were predicted as potential targets of miR156. A few photosynthesis related genes such as sulfate adenylytransferase (APS3), chlorophyll a/b binding family protein etc. were suggested to be regulated by miRNAs. However, no C4 shuttle genes were predicted to be direct targets of either known or candidate novel miRNAs. CONCLUSIONS This study provided the comprehensive list of miRNA that showed altered expression during the de-etiolation process and a number of candidate miRNAs that might play regulatory roles in C3 and C4 photosynthesis.
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Affiliation(s)
- Jiajia Xu
- Key Laboratory of Computational Biology and Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai, China
| | - Yuanyuan Li
- Key Laboratory of Computational Biology and Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai, China
| | - Yaling Wang
- Key Laboratory of Computational Biology and Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai, China
| | - Xinyu Liu
- Key Laboratory of Computational Biology and Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai, China
| | - Xin-Guang Zhu
- Key Laboratory of Computational Biology and Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai, China
- State Key Laboratory of Hybrid Rice Research, Shanghai Institute of Biological Sciences, Chinese Academy of Sciences, Shanghai, China
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Frick KM, Kamphuis LG, Siddique KHM, Singh KB, Foley RC. Quinolizidine Alkaloid Biosynthesis in Lupins and Prospects for Grain Quality Improvement. FRONTIERS IN PLANT SCIENCE 2017; 8:87. [PMID: 28197163 PMCID: PMC5281559 DOI: 10.3389/fpls.2017.00087] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 01/16/2017] [Indexed: 05/21/2023]
Abstract
Quinolizidine alkaloids (QAs) are toxic secondary metabolites found within the genus Lupinus, some species of which are commercially important grain legume crops including Lupinus angustifolius (narrow-leafed lupin, NLL), L. luteus (yellow lupin), L. albus (white lupin), and L. mutabilis (pearl lupin), with NLL grain being the most largely produced of the four species in Australia and worldwide. While QAs offer the plants protection against insect pests, the accumulation of QAs in lupin grain complicates its use for food purposes as QA levels must remain below the industry threshold (0.02%), which is often exceeded. It is not well understood what factors cause grain QA levels to exceed this threshold. Much of the early work on QA biosynthesis began in the 1970-1980s, with many QA chemical structures well-characterized and lupin cell cultures and enzyme assays employed to identify some biosynthetic enzymes and pathway intermediates. More recently, two genes associated with these enzymes have been characterized, however, the QA biosynthetic pathway remains only partially elucidated. Here, we review the research accomplished thus far concerning QAs in lupin and consider some possibilities for further elucidation and manipulation of the QA pathway in lupin crops, drawing on examples from model alkaloid species. One breeding strategy for lupin is to produce plants with high QAs in vegetative tissues while low in the grain in order to confer insect resistance to plants while keeping grain QA levels within industry regulations. With the knowledge achieved on alkaloid biosynthesis in other plant species in recent years, and the recent development of genomic and transcriptomic resources for NLL, there is considerable scope to facilitate advances in our knowledge of QAs, leading to the production of improved lupin crops.
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Affiliation(s)
- Karen M. Frick
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Commonwealth Scientific and Industrial Research OrganisationFloreat, WA, Australia
- School of Plant Biology, The University of Western AustraliaCrawley, WA, Australia
- The UWA Institute of Agriculture, The University of Western AustraliaPerth, WA, Australia
| | - Lars G. Kamphuis
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Commonwealth Scientific and Industrial Research OrganisationFloreat, WA, Australia
- The UWA Institute of Agriculture, The University of Western AustraliaPerth, WA, Australia
| | | | - Karam B. Singh
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Commonwealth Scientific and Industrial Research OrganisationFloreat, WA, Australia
- The UWA Institute of Agriculture, The University of Western AustraliaPerth, WA, Australia
| | - Rhonda C. Foley
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Commonwealth Scientific and Industrial Research OrganisationFloreat, WA, Australia
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Habachi-Houimli Y, Khalfallah Y, Makni H, Makni M, Bouktila D. Large-scale bioinformatic analysis of the regulation of the disease resistance NBS gene family by microRNAs in Poaceae. C R Biol 2016; 339:347-56. [PMID: 27349470 DOI: 10.1016/j.crvi.2016.05.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 05/23/2016] [Accepted: 05/24/2016] [Indexed: 01/06/2023]
Abstract
In the present study, we have screened 71, 713, 525, 119 and 241 mature miRNA variants from Hordeum vulgare, Oryza sativa, Brachypodium distachyon, Triticum aestivum, and Sorghum bicolor, respectively, and classified them with respect to their conservation status and expression levels. These Poaceae non-redundant miRNA species (1,669) were distributed over a total of 625 MIR families, among which only 54 were conserved across two or more plant species, confirming the relatively recent evolutionary differentiation of miRNAs in grasses. On the other hand, we have used 257 H. vulgare, 286T. aestivum, 119 B. distachyon, 269 O. sativa, and 139 S. bicolor NBS domains, which were either mined directly from the annotated proteomes, or predicted from whole genome sequence assemblies. The hybridization potential between miRNAs and their putative NBS genes targets was analyzed, revealing that at least 454 NBS genes from all five Poaceae were potentially regulated by 265 distinct miRNA species, most of them expressed in leaves and predominantly co-expressed in additional tissues. Based on gene ontology, we could assign these probable miRNA target genes to 16 functional groups, among which three conferring resistance to bacteria (Rpm1, Xa1 and Rps2), and 13 groups of resistance to fungi (Rpp8,13, Rp3, Tsn1, Lr10, Rps1-k-1, Pm3, Rpg5, and MLA1,6,10,12,13). The results of the present analysis provide a large-scale platform for a better understanding of biological control strategies of disease resistance genes in Poaceae, and will serve as an important starting point for enhancing crop disease resistance improvement by means of transgenic lines with artificial miRNAs.
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Affiliation(s)
- Yosra Habachi-Houimli
- Unité de recherche UR11ES10, Génomique des insectes ravageurs des cultures d'intérêt agronomique (GIRC), faculté des sciences de Tunis, université de Tunis El Manar, 2092 El Manar, Tunis, Tunisia
| | - Yosra Khalfallah
- Unité de recherche UR11ES10, Génomique des insectes ravageurs des cultures d'intérêt agronomique (GIRC), faculté des sciences de Tunis, université de Tunis El Manar, 2092 El Manar, Tunis, Tunisia
| | - Hanem Makni
- Unité de recherche UR11ES10, Génomique des insectes ravageurs des cultures d'intérêt agronomique (GIRC), faculté des sciences de Tunis, université de Tunis El Manar, 2092 El Manar, Tunis, Tunisia; Institut supérieur de l'animation pour la jeunesse et la culture (ISAJC), université de Tunis, 2055 Bir El Bey, Tunisia
| | - Mohamed Makni
- Unité de recherche UR11ES10, Génomique des insectes ravageurs des cultures d'intérêt agronomique (GIRC), faculté des sciences de Tunis, université de Tunis El Manar, 2092 El Manar, Tunis, Tunisia
| | - Dhia Bouktila
- Unité de recherche UR11ES10, Génomique des insectes ravageurs des cultures d'intérêt agronomique (GIRC), faculté des sciences de Tunis, université de Tunis El Manar, 2092 El Manar, Tunis, Tunisia; Institut supérieur de biotechnologie de Béja (ISBB), université de Jendouba, 9000 Béja, Tunisia.
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Khaldun ABM, Huang W, Lv H, Liao S, Zeng S, Wang Y. Comparative Profiling of miRNAs and Target Gene Identification in Distant-Grafting between Tomato and Lycium (Goji Berry). FRONTIERS IN PLANT SCIENCE 2016; 7:1475. [PMID: 27803702 PMCID: PMC5067468 DOI: 10.3389/fpls.2016.01475] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 09/16/2016] [Indexed: 05/10/2023]
Abstract
Local translocation of small RNAs between cells is proved. Long distance translocation between rootstock and scion is also well documented in the homo-grafting system, but the process in distant-grafting is widely unexplored where rootstock and scion belonging to different genera. Micro RNAs are a class of small, endogenous, noncoding, gene silencing RNAs that regulate target genes of a wide range of important biological pathways in plants. In this study, tomato was grafted onto goji (Lycium chinense Mill.) to reveal the insight of miRNAs regulation and expression patterns within a distant-grafting system. Goji is an important traditional Chinese medicinal plant with enriched phytochemicals. Illumina sequencing technology has identified 68 evolutionary known miRNAs of 37 miRNA families. Moreover, 168 putative novel miRNAs were also identified. Compared with control tomato, 43 (11 known and 32 novels) and 163 (33 known and 130 novels) miRNAs were expressed significantly different in shoot and fruit of grafted tomato, respectively. The fruiting stage was identified as the most responsive in the distant-grafting approach and 123 miRNAs were found as up-regulating in the grafted fruit which is remarkably higher compare to the grafted shoot tip (28). Potential targets of differentially expressed miRNAs were found to be involved in diverse metabolic and regulatory pathways. ADP binding activities, molybdopterin synthase complex and RNA helicase activity were found as enriched terms in GO (Gene Ontology) analysis. Additionally, "metabolic pathways" was revealed as the most significant pathway in KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis. The information of the small RNA transcriptomes that are obtained from this study might be the first miRNAs elucidation for a distant-grafting system, particularly between goji and tomato. The results from this study will provide the insights into the molecular aspects of miRNA-mediated regulation in the medicinal plant goji, and in grafted tomato. Noteworthy, it would provide a basis how miRNA signals could exchange between rootstock and scion, and the relevance to diverse biological processes.
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Affiliation(s)
- A. B. M. Khaldun
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden (CAS)Wuhan, China
- University of the Chinese Academy of SciencesBeijing, China
- Oilseed Research Center, Bangladesh Agricultural Research Institute (BARI)Joydebpur, Gazipur, Bangladesh
| | - Wenjun Huang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden (CAS)Wuhan, China
| | - Haiyan Lv
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden (CAS)Wuhan, China
| | - Sihong Liao
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden (CAS)Wuhan, China
- University of the Chinese Academy of SciencesBeijing, China
| | - Shaohua Zeng
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden (CAS)Guangzhou, China
| | - Ying Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden (CAS)Wuhan, China
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden (CAS)Guangzhou, China
- Northwest Center for Agrobiotechnology (Ningxia), CASBeijing, China
- *Correspondence: Ying Wang
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Alptekin B, Akpinar BA, Budak H. A Comprehensive Prescription for Plant miRNA Identification. FRONTIERS IN PLANT SCIENCE 2016; 7:2058. [PMID: 28174574 PMCID: PMC5258749 DOI: 10.3389/fpls.2016.02058] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 12/23/2016] [Indexed: 05/15/2023]
Abstract
microRNAs (miRNAs) are tiny ribo-regulatory molecules involved in various essential pathways for persistence of cellular life, such as development, environmental adaptation, and stress response. In recent years, miRNAs have become a major focus in molecular biology because of their functional and diagnostic importance. This interest in miRNA research has resulted in the development of many specific software and pipelines for the identification of miRNAs and their specific targets, which is the key for the elucidation of miRNA-modulated gene expression. While the well-recognized importance of miRNAs in clinical research pushed the emergence of many useful computational identification approaches in animals, available software and pipelines are fewer for plants. Additionally, existing approaches suffers from mis-identification and annotation of plant miRNAs since the miRNA mining process for plants is highly prone to false-positives, particularly in cereals which have a highly repetitive genome. Our group developed a homology-based in silico miRNA identification approach for plants, which utilizes two Perl scripts "SUmirFind" and "SUmirFold" and since then, this method helped identify many miRNAs particularly from crop species such as Triticum or Aegliops. Herein, we describe a comprehensive updated guideline by the implementation of two new scripts, "SUmirPredictor" and "SUmirLocator," and refinements to our previous method in order to identify genuine miRNAs with increased sensitivity in consideration of miRNA identification problems in plants. Recent updates enable our method to provide more reliable and precise results in an automated fashion in addition to solutions for elimination of most false-positive predictions, miRNA naming and miRNA mis-annotation. It also provides a comprehensive view to genome/transcriptome-wide location of miRNA precursors as well as their association with transposable elements. The "SUmirPredictor" and "SUmirLocator" scripts are freely available together with a reference high-confidence plant miRNA list.
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Affiliation(s)
- Burcu Alptekin
- Cereal Genomics Lab, Department of Plant Sciences and Plant Pathology, Montana State UniversityBozeman, MT, USA
| | - Bala A. Akpinar
- Sabanci University Nanotechnology Research and Application Centre, Sabanci UniversityIstanbul, Turkey
| | - Hikmet Budak
- Cereal Genomics Lab, Department of Plant Sciences and Plant Pathology, Montana State UniversityBozeman, MT, USA
- *Correspondence: Hikmet Budak
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Tripathi A, Goswami K, Sanan-Mishra N. Role of bioinformatics in establishing microRNAs as modulators of abiotic stress responses: the new revolution. Front Physiol 2015; 6:286. [PMID: 26578966 PMCID: PMC4620411 DOI: 10.3389/fphys.2015.00286] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 09/28/2015] [Indexed: 12/15/2022] Open
Abstract
microRNAs (miRs) are a class of 21-24 nucleotide long non-coding RNAs responsible for regulating the expression of associated genes mainly by cleavage or translational inhibition of the target transcripts. With this characteristic of silencing, miRs act as an important component in regulation of plant responses in various stress conditions. In recent years, with drastic change in environmental and soil conditions different type of stresses have emerged as a major challenge for plants growth and productivity. The identification and profiling of miRs has itself been a challenge for research workers given their small size and large number of many probable sequences in the genome. Application of computational approaches has expedited the process of identification of miRs and their expression profiling in different conditions. The development of High-Throughput Sequencing (HTS) techniques has facilitated to gain access to the global profiles of the miRs for understanding their mode of action in plants. Introduction of various bioinformatics databases and tools have revolutionized the study of miRs and other small RNAs. This review focuses the role of bioinformatics approaches in the identification and study of the regulatory roles of plant miRs in the adaptive response to stresses.
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Affiliation(s)
- Anita Tripathi
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology New Delhi, India
| | - Kavita Goswami
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology New Delhi, India
| | - Neeti Sanan-Mishra
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology New Delhi, India
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31
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Huang Y, Ren HT, Zou Q, Wang YQ, Zhang JL, Yu XL. Computational identification and characterization of miRNAs and their target genes from five cyprinidae fishes. Saudi J Biol Sci 2015; 24:1126-1135. [PMID: 28855803 PMCID: PMC5562384 DOI: 10.1016/j.sjbs.2015.05.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2014] [Revised: 05/02/2015] [Accepted: 05/06/2015] [Indexed: 12/24/2022] Open
Abstract
MicroRNAs (miRNAs) are a kind of small single-strand RNA molecules with lengths of 18–25 nt, which do not encode any proteins. They play an essential role in gene expression regulation by binding to their target genes, leading to translational repression or transcript degradation. In this study, 23 miRNAs were predicted from five cyprinidae fishes by using a bioinformatics-based gene search based on blasting ESTs and GSS in NCBI, of which 21 miRNA genes have not been previously reported. To prove their validity, five of the computationally predicted miRNAs were verified by RTPCR, their transcripts were successfully detected, and, 46 potential target genes for these miRNAs were predicted, most target genes encode transcription factors, they are involved in signal transduction, metabolism and development processes.
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Affiliation(s)
- Yong Huang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Hong-Tao Ren
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Quan Zou
- School of Computer Science and Technology, Tianjin University, Tianjin, China
| | - Yu-Qin Wang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Ji-Liang Zhang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Xue-Li Yu
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
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Trumbo JL, Zhang B, Stewart CN. Manipulating microRNAs for improved biomass and biofuels from plant feedstocks. PLANT BIOTECHNOLOGY JOURNAL 2015; 13:337-54. [PMID: 25707745 DOI: 10.1111/pbi.12319] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 11/25/2014] [Accepted: 11/29/2014] [Indexed: 05/22/2023]
Abstract
Petroleum-based fuels are nonrenewable and unsustainable. Renewable sources of energy, such as lignocellulosic biofuels and plant metabolite-based drop-in fuels, can offset fossil fuel use and reverse environmental degradation through carbon sequestration. Despite these benefits, the lignocellulosic biofuels industry still faces many challenges, including the availability of economically viable crop plants. Cell wall recalcitrance is a major economic barrier for lignocellulosic biofuels production from biomass crops. Sustainability and biomass yield are two additional, yet interrelated, foci for biomass crop improvement. Many scientists are searching for solutions to these problems within biomass crop genomes. MicroRNAs (miRNAs) are involved in almost all biological and metabolic process in plants including plant development, cell wall biosynthesis and plant stress responses. Because of the broad functions of their targets (e.g. auxin response factors), the alteration of plant miRNA expression often results in pleiotropic effects. A specific miRNA usually regulates a biologically relevant bioenergy trait. For example, relatively low miR156 overexpression leads to a transgenic feedstock with enhanced biomass and decreased recalcitrance. miRNAs have been overexpressed in dedicated bioenergy feedstocks such as poplar and switchgrass yielding promising results for lignin reduction, increased plant biomass, the timing of flowering and response to harsh environments. In this review, we present the status of miRNA-related research in several major biofuel crops and relevant model plants. We critically assess published research and suggest next steps for miRNA manipulation in feedstocks for increased biomass and sustainability for biofuels and bioproducts.
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Affiliation(s)
- Jennifer Lynn Trumbo
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN, USA; Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA
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Gentile A, Dias LI, Mattos RS, Ferreira TH, Menossi M. MicroRNAs and drought responses in sugarcane. FRONTIERS IN PLANT SCIENCE 2015; 6:58. [PMID: 25755657 PMCID: PMC4337329 DOI: 10.3389/fpls.2015.00058] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 01/22/2015] [Indexed: 05/03/2023]
Abstract
There is a growing demand for renewable energy, and sugarcane is a promising bioenergy crop. In Brazil, the largest sugarcane producer in the world, sugarcane plantations are expanding into areas where severe droughts are common. Recent evidence has highlighted the role of miRNAs in regulating drought responses in several species, including sugarcane. This review summarizes the data from miRNA expression profiles observed in a wide array of experimental conditions using different sugarcane cultivars that differ in their tolerance to drought. We uncovered a complex regulation of sugarcane miRNAs in response to drought and discussed these data with the miRNA profiles observed in other plant species. The predicted miRNA targets revealed different transcription factors, proteins involved in tolerance to oxidative stress, cell modification, as well as hormone signaling. Some of these proteins might regulate sugarcane responses to drought, such as reduction of internode growth and shoot branching and increased leaf senescence. A better understanding on the regulatory network from miRNAs and their targets under drought stress has a great potential to contribute to sugarcane improvement, either as molecular markers as well as by using biotechnological approaches.
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Affiliation(s)
| | | | | | | | - Marcelo Menossi
- Laboratório de Genoma Funcional, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de CampinasCampinas, São Paulo, Brazil
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Shen D, Suhrkamp I, Wang Y, Liu S, Menkhaus J, Verreet JA, Fan L, Cai D. Identification and characterization of microRNAs in oilseed rape (Brassica napus) responsive to infection with the pathogenic fungus Verticillium longisporum using Brassica AA (Brassica rapa) and CC (Brassica oleracea) as reference genomes. THE NEW PHYTOLOGIST 2014; 204:577-594. [PMID: 25132374 DOI: 10.1111/nph.12934] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 06/05/2014] [Indexed: 05/22/2023]
Abstract
Verticillium longisporum, a soil-borne pathogenic fungus, causes vascular disease in oilseed rape (Brassica napus). We proposed that plant microRNAs (miRNAs) are involved in the plant-V. longisporum interaction. To identify oilseed rape miRNAs, we deep-sequenced two small RNA libraries made from V. longisporum infected/noninfected roots and employed Brassica rapa and Brassica oleracea genomes as references for miRNA prediction and characterization. We identified 893 B. napus miRNAs representing 360 conserved and 533 novel miRNAs, and mapped 429 and 464 miRNAs to the AA and CC genomes, respectively. Microsynteny analysis with the conserved miRNAs and their flanking protein coding sequences revealed 137 AA-CC genome syntenic miRNA pairs and 61 AA and 42 CC genome-unique miRNAs. Sixty-two miRNAs were responsive to the V. longisporum infection. We present data for specific interactions and simultaneously reciprocal changes in the expression levels of the miRNAs and their targets in the infected roots. We demonstrate that miRNAs are involved in the plant-fungus interaction and that miRNA168-Argonaute 1 (AGO1) expression modulation might act as a key regulatory module in a compatible plant-V. longisporum interaction. Our results suggest that V. longisporum may have evolved a virulence mechanism by interference with plant miRNAs to reprogram plant gene expression and achieve infection.
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Affiliation(s)
- Dan Shen
- Department of Molecular Phytopathology and Biotechnology, Institute of Phytopathology, Christian Albrechts University of Kiel, Hermann Rodewald Str. 9, D-24118, Kiel, Germany
| | - Ina Suhrkamp
- Department of Molecular Phytopathology and Biotechnology, Institute of Phytopathology, Christian Albrechts University of Kiel, Hermann Rodewald Str. 9, D-24118, Kiel, Germany
| | - Yu Wang
- Department of Agronomy, James D. Watson Institute of Genome Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China
| | - Shenyi Liu
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Jan Menkhaus
- Department of Molecular Phytopathology and Biotechnology, Institute of Phytopathology, Christian Albrechts University of Kiel, Hermann Rodewald Str. 9, D-24118, Kiel, Germany
| | - Joseph-Alexander Verreet
- Department of Molecular Phytopathology and Biotechnology, Institute of Phytopathology, Christian Albrechts University of Kiel, Hermann Rodewald Str. 9, D-24118, Kiel, Germany
| | - Longjiang Fan
- Department of Agronomy, James D. Watson Institute of Genome Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China
| | - Daguang Cai
- Department of Molecular Phytopathology and Biotechnology, Institute of Phytopathology, Christian Albrechts University of Kiel, Hermann Rodewald Str. 9, D-24118, Kiel, Germany
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Hofferek V, Mendrinna A, Gaude N, Krajinski F, Devers EA. MiR171h restricts root symbioses and shows like its target NSP2 a complex transcriptional regulation in Medicago truncatula. BMC PLANT BIOLOGY 2014; 14:199. [PMID: 25928247 PMCID: PMC4115173 DOI: 10.1186/s12870-014-0199-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 07/15/2014] [Indexed: 05/18/2023]
Abstract
BACKGROUND Legumes have the unique capability to undergo root nodule and arbuscular mycorrhizal symbiosis. Both types of root endosymbiosis are regulated by NSP2, which is a target of microRNA171h (miR171h). Although, recent data implies that miR171h specifically restricts arbuscular mycorrhizal symbiosis in the root elongation zone of Medicago truncatula roots, there is limited knowledge available about the spatio-temporal regulation of miR171h expression at different physiological and symbiotic conditions. RESULTS We show that miR171h is functionally expressed from an unusual long primary transcript, previously predicted to encode two identical miR171h strands. Both miR171h and NSP2 transcripts display a complex regulation pattern, which involves the symbiotic status and the fertilization regime of the plant. Quantitative Real-time PCR revealed that miR171h and NSP2 transcript levels show a clear anti-correlation in all tested conditions except in mycorrhizal roots, where NSP2 transcript levels were induced despite of an increased miR171h expression. This was also supported by a clear correlation of transcript levels of NSP2 and MtPt4, a phosphate transporter specifically expressed in a functional AM symbiosis. MiR171h is strongly induced in plants growing in sufficient phosphate conditions, which we demonstrate to be independent of the CRE1 signaling pathway and which is also not required for transcriptional induction of NSP2 in mycorrhizal roots. In situ hybridization and promoter activity analysis of both genes confirmed the complex regulation involving the symbiotic status, P and N nutrition, where both genes show a mainly mutual exclusive expression pattern. Overexpression of miR171h in M. truncatula roots led to a reduction in mycorrhizal colonization and to a reduced nodulation by Sinorhizobium meliloti. CONCLUSION The spatio-temporal expression of miR171h and NSP2 is tightly linked to the nutritional status of the plant and, together with the results from the overexpression analysis, points to an important function of miR171h to integrate the nutrient homeostasis in order to safeguard the expression domain of NSP2 during both, arbuscular mycorrhizal and root nodule symbiosis.
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Affiliation(s)
- Vinzenz Hofferek
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, (OT) Golm, Germany.
| | - Amelie Mendrinna
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, (OT) Golm, Germany.
| | - Nicole Gaude
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, (OT) Golm, Germany.
| | - Franziska Krajinski
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, (OT) Golm, Germany.
| | - Emanuel A Devers
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, (OT) Golm, Germany.
- Present address: Department of Biology, Swiss Federal Institute of Technology Zurich, Zürich, Switzerland.
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36
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Abstract
MicroRNAs are 20-24-nucleotide-long noncoding RNAs that bind to the 3' UTR (untranslated region) of target mRNAs. Since their discovery, microRNAs have been gaining attention for their ability to contribute to gene expression regulation under various physiological conditions. Consequently, deregulated expression of microRNAs has been linked to different disease states. Here, a brief overview of the canonical and alternative microRNA biogenesis pathways and microRNA functions in biological systems is given based on recent developments. In addition, newly emerging regulatory mechanisms, such as alternative polyadenylation, in connection with microRNA-dependent gene expression regulation are discussed.
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37
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Huang Y, Zou Q, Sun XH, Zhao LP. Computational identification of microRNAs and their targets in perennial Ryegrass (Lolium perenne). Appl Biochem Biotechnol 2014; 173:1011-22. [PMID: 24752936 DOI: 10.1007/s12010-014-0891-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Accepted: 03/24/2014] [Indexed: 10/25/2022]
Abstract
MicroRNAs (miRNAs) are small non-coding RNA molecules of 22 nucleotides in length that have been characterized as regulators of messenger RNA (mRNA) regulating a number of developmental processes in plants and animals by silencing genes using multiple mechanisms. miRNAs have been extensively studied in various plant species; however, few information are available about miRNAs in perennial ryegrass, animal feed, and industrial raw materials. In this study, the 12 potential perennial ryegrass miRNAs were identified for the first time by computational approach. Using the newly identified miRNA sequences, the perennial ryegrass mRNA database was further used for BLAST search and detected 33 potential targets of miRNAs. Prediction of potential miRNA target genes revealed their functions involved in various important plant biological processes. Our result should be useful for further investigation into the biological functions of miRNAs in perennial ryegrass. The selected miRNAs representing four families were verified by RT-PCR experiment, indicating that the prediction method that we used to identify the miRNAs was effective.
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Affiliation(s)
- Yong Huang
- Animal Science and Technology College, Henan University of Science and Technology, Luoyang City, 471003, Henan Province, People's Republic of China,
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38
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Taylor RS, Tarver JE, Hiscock SJ, Donoghue PCJ. Evolutionary history of plant microRNAs. TRENDS IN PLANT SCIENCE 2014; 19:175-82. [PMID: 24405820 DOI: 10.1016/j.tplants.2013.11.008] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 11/18/2013] [Accepted: 11/28/2013] [Indexed: 05/11/2023]
Abstract
microRNAs (miRNAs) are short noncoding regulatory genes that perform important roles in plant development and physiology. With the increasing power of next generation sequencing technologies and the development of bioinformatic tools, there has been a dramatic increase in the number of studies surveying the miRNAomes of plant species, which has led to an explosion in the number of described miRNAs. Unfortunately, very many of these new discoveries have been incompletely annotated and thus fail to discriminate genuine miRNAs from small interfering RNAs (siRNAs), fragments of longer RNAs, and random sequence. We review the published repertoire of plant miRNAs, discriminating those that have been correctly annotated. We use these data to explore prevailing hypotheses on the tempo and mode of miRNA evolution within the plant kingdom.
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Affiliation(s)
- Richard S Taylor
- School of Earth Sciences, University of Bristol, Wills Memorial Building, Queen's Road, Bristol BS8 1RJ, UK
| | - James E Tarver
- School of Earth Sciences, University of Bristol, Wills Memorial Building, Queen's Road, Bristol BS8 1RJ, UK; Genome Evolution Laboratory, Department of Biology, National University of Ireland Maynooth, Maynooth, Co. Kildare, Ireland
| | - Simon J Hiscock
- School of Biological Sciences, University of Bristol, Woodland Road, Bristol BS8 1UG, UK
| | - Philip C J Donoghue
- School of Earth Sciences, University of Bristol, Wills Memorial Building, Queen's Road, Bristol BS8 1RJ, UK.
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39
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Yamasaki T, Voshall A, Kim EJ, Moriyama E, Cerutti H, Ohama T. Complementarity to an miRNA seed region is sufficient to induce moderate repression of a target transcript in the unicellular green alga Chlamydomonas reinhardtii. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 76:1045-56. [PMID: 24127635 DOI: 10.1111/tpj.12354] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Revised: 10/02/2013] [Accepted: 10/09/2013] [Indexed: 05/12/2023]
Abstract
MicroRNAs (miRNAs) are 20-24 nt non-coding RNAs that play important regulatory roles in a broad range of eukaryotes by pairing with mRNAs to direct post-transcriptional repression. The mechanistic details of miRNA-mediated post-transcriptional regulation have been well documented in multicellular model organisms. However, this process remains poorly studied in algae such as Chlamydomonas reinhardtii, and specific features of miRNA biogenesis, target mRNA recognition and subsequent silencing are not well understood. In this study, we report on the characterization of a Chlamydomonas miRNA, cre-miR1174.2, which is processed from a near-perfect hairpin RNA. Using Gaussia luciferase (gluc) reporter genes, we have demonstrated that cre-miR1174.2 is functional in Chlamydomonas and capable of triggering site-specific cleavage at the center of a perfectly complementary target sequence. A mismatch tolerance test assay, based on pools of transgenic strains, revealed that target hybridization to nucleotides of the seed region, at the 5' end of an miRNA, was sufficient to induce moderate repression of expression. In contrast, pairing to the 3' region of the miRNA was not critical for silencing. Our results suggest that the base-pairing requirements for small RNA-mediated repression in C. reinhardtii are more similar to those of metazoans compared with the extensive complementarity that is typical of land plants. Individual Chlamydomonas miRNAs may potentially modulate the expression of numerous endogenous targets as a result of these relaxed base-pairing requirements.
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Affiliation(s)
- Tomohito Yamasaki
- Department of Environmental Systems Engineering, Kochi University of Technology, 185 Miyanokuchi, Tosayamada, Kami, Kochi, 782-8502, Japan
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40
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Luo X, Gao Z, Shi T, Cheng Z, Zhang Z, Ni Z. Identification of miRNAs and their target genes in peach (Prunus persica L.) using high-throughput sequencing and degradome analysis. PLoS One 2013; 8:e79090. [PMID: 24236092 PMCID: PMC3827290 DOI: 10.1371/journal.pone.0079090] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Accepted: 09/18/2013] [Indexed: 12/05/2022] Open
Abstract
MicroRNAs play critical roles in various biological and metabolic processes. The function of miRNAs has been widely studied in model plants such as Arabidopsis and rice. However, the number of identified miRNAs and related miRNA targets in peach (Prunus persica) is limited. To understand further the relationship between miRNAs and their target genes during tissue development in peach, a small RNA library and three degradome libraries were constructed from three tissues for deep sequencing. We identified 117 conserved miRNAs and 186 novel miRNA candidates in peach by deep sequencing and 19 conserved miRNAs and 13 novel miRNAs were further evaluated for their expression by RT-qPCR. The number of gene targets that were identified for 26 conserved miRNA families and 38 novel miRNA candidates, were 172 and 87, respectively. Some of the identified miRNA targets were abundantly represented as conserved miRNA targets in plant. However, some of them were first identified and showed important roles in peach development. Our study provides information concerning the regulatory network of miRNAs in peach and advances our understanding of miRNA functions during tissue development.
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Affiliation(s)
- Xiaoyan Luo
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, People’s Republic of China
| | - Zhihong Gao
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, People’s Republic of China
- * E-mail:
| | - Ting Shi
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, People’s Republic of China
| | - Zongming Cheng
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, People’s Republic of China
| | - Zhen Zhang
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, People’s Republic of China
| | - Zhaojun Ni
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, People’s Republic of China
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41
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Gébelin V, Leclercq J, Argout X, Chaidamsari T, Hu S, Tang C, Sarah G, Yang M, Montoro P. The small RNA profile in latex from Hevea brasiliensis trees is affected by tapping panel dryness. TREE PHYSIOLOGY 2013; 33:1084-98. [PMID: 24218245 DOI: 10.1093/treephys/tpt076] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Natural rubber is harvested by tapping Hevea brasiliensis (Willd. ex A. Juss.) Müll. Arg. Harvesting stress can lead to tapping panel dryness (TPD). MicroRNAs (miRNAs) are induced by abiotic stress and regulate gene expression by targeting the cleavage or translational inhibition of target messenger RNAs. This study set out to sequence miRNAs expressed in latex cells and to identify TPD-related putative targets. Deep sequencing of small RNAs was carried out on latex from trees affected by TPD using Solexa technology. The most abundant small RNA class size was 21 nucleotides for TPD trees compared with 24 nucleotides in healthy trees. By combining the LeARN pipeline, data from the Plant MicroRNA database and Hevea EST sequences, we identified 19 additional conserved and four putative species-specific miRNA families not found in previous studies on rubber. The relative transcript abundance of the Hbpre-MIR159b gene increased with TPD. This study revealed a small RNA-specific signature of TPD-affected trees. Both RNA degradation and a shift in miRNA biogenesis are suggested to explain the general decline in small RNAs and, particularly, in miRNAs.
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42
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Gébelin V, Leclercq J, Hu S, Tang C, Montoro P. Regulation of MIR genes in response to abiotic stress in Hevea brasiliensis. Int J Mol Sci 2013; 14:19587-604. [PMID: 24084713 PMCID: PMC3821574 DOI: 10.3390/ijms141019587] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 09/06/2013] [Accepted: 09/16/2013] [Indexed: 12/31/2022] Open
Abstract
Increasing demand for natural rubber (NR) calls for an increase in latex yield and also an extension of rubber plantations in marginal zones. Both harvesting and abiotic stresses lead to tapping panel dryness through the production of reactive oxygen species. Many microRNAs regulated during abiotic stress modulate growth and development. The objective of this paper was to study the regulation of microRNAs in response to different types of abiotic stress and hormone treatments in Hevea. Regulation of MIR genes differs depending on the tissue and abiotic stress applied. A negative co-regulation between HbMIR398b with its chloroplastic HbCuZnSOD target messenger is observed in response to salinity. The involvement of MIR gene regulation during latex harvesting and tapping panel dryness (TPD) occurrence is further discussed.
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Affiliation(s)
- Virginie Gébelin
- Centre de Coopération Internationale en Recherche Agronomique Pour le Développement, Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, Avenue Agropolis, Montpellier F-34398, France; E-Mails: (V.G.); (J.L.)
| | - Julie Leclercq
- Centre de Coopération Internationale en Recherche Agronomique Pour le Développement, Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, Avenue Agropolis, Montpellier F-34398, France; E-Mails: (V.G.); (J.L.)
| | - Songnian Hu
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China; E-Mail:
| | - Chaorong Tang
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou 531737, China; E-Mail:
| | - Pascal Montoro
- Centre de Coopération Internationale en Recherche Agronomique Pour le Développement, Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, Avenue Agropolis, Montpellier F-34398, France; E-Mails: (V.G.); (J.L.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +33-0-467-61-5682; Fax: +33-0-467-61-5605
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43
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Seo PJ, Park MJ, Park CM. Alternative splicing of transcription factors in plant responses to low temperature stress: mechanisms and functions. PLANTA 2013; 237:1415-24. [PMID: 23624977 PMCID: PMC3664756 DOI: 10.1007/s00425-013-1882-4] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Accepted: 04/08/2013] [Indexed: 05/19/2023]
Abstract
Transcription factors play a central role in the gene regulatory networks that mediate various aspects of plant developmental processes and responses to environmental changes. Therefore, their activities are elaborately regulated at multiple steps. In particular, accumulating evidence illustrates that post-transcriptional control of mRNA metabolism is a key molecular scheme that modulates the transcription factor activities in plant responses to temperature fluctuations. Transcription factors have a modular structure consisting of distinct protein domains essential for DNA binding, dimerization, and transcriptional regulation. Alternative splicing produces multiple proteins having different structural domain compositions from a single transcription factor gene. Recent studies have shown that alternative splicing of some transcription factor genes generates small interfering peptides (siPEPs) that negatively regulate the target transcription factors via peptide interference (PEPi), constituting self-regulatory circuits in plant cold stress response. A number of splicing factors, which are involved in RNA binding, splice site selection, and spliceosome assembly, are also affected by temperature fluctuations, supporting the close association of alternative splicing of transcription factors with plant responses to low temperatures. In this review, we summarize recent progress on the temperature-responsive alternative splicing of transcription factors in plants with emphasis on the siPEP-mediated PEPi mechanism.
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Affiliation(s)
- Pil Joon Seo
- Department of Chemistry, Chonbuk National University, Jeonju, 561-756 Korea
| | - Mi-Jeong Park
- Department of Chemistry, Seoul National University, Seoul, 151-742 Korea
| | - Chung-Mo Park
- Department of Chemistry, Seoul National University, Seoul, 151-742 Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, 151-742 Korea
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44
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Asgari S. MicroRNA functions in insects. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2013; 43:388-97. [PMID: 23103375 DOI: 10.1016/j.ibmb.2012.10.005] [Citation(s) in RCA: 184] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Revised: 10/11/2012] [Accepted: 10/16/2012] [Indexed: 05/14/2023]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that are generated in all eukaryotes and viruses. Their role as master regulators of gene expression in various biological processes has only been fully appreciated over the last decade. Accumulating evidence suggests that alterations in the expression of miRNAs may lead to disorders, including developmental defects, diseases and cancer. Here, I review what is currently known about miRNA functions in insects to provide an insight into their diverse roles in insect biology.
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Affiliation(s)
- Sassan Asgari
- School of Biological Sciences, The University of Queensland, Brisbane, St Lucia, QLD 4072, Australia.
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45
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Sarwat M, Naqvi AR, Ahmad P, Ashraf M, Akram NA. Phytohormones and microRNAs as sensors and regulators of leaf senescence: assigning macro roles to small molecules. Biotechnol Adv 2013; 31:1153-71. [PMID: 23453916 DOI: 10.1016/j.biotechadv.2013.02.003] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Revised: 01/26/2013] [Accepted: 02/02/2013] [Indexed: 10/27/2022]
Abstract
Ageing or senescence is an intricate and highly synchronized developmental phase in the life of plant parts including leaf. Senescence not only means death of a plant part, but during this process, different macromolecules undergo degradation and the resulting components are transported to other parts of the plant. During the period from when a leaf is young and green to the stage when it senesces, a multitude of factors such as hormones, environmental factors and senescence associated genes (SAGs) are involved. Plant hormones including salicylic acid, abscisic acid, jasmonic acid and ethylene advance leaf senescence, whereas others like cytokinins, gibberellins, and auxins delay this process. The environmental factors which generally affect plant development and growth, can hasten senescence, the examples being nutrient dearth, water stress, pathogen attack, radiations, high temperature and light intensity, waterlogging, and air, water or soil contamination. Other important influences include carbohydrate accumulation and high carbon/nitrogen level. To date, although several genes involved in this complex process have been identified, still not much information exists in the literature on the signalling mechanism of leaf senescence. Now, the Arabidopsis mutants have paved our way and opened new vistas to elucidate the signalling mechanism of leaf senescence for which various mutants are being utilized. Recent studies demonstrating the role of microRNAs in leaf senescence have reinforced our knowledge of this intricate process. This review provides a comprehensive and critical analysis of the information gained particularly on the roles of several plant growth regulators and microRNAs in regulation of leaf senescence.
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Affiliation(s)
- Maryam Sarwat
- Pharmaceutical Biotechnology, Amity Institute of Pharmacy, Amity University, Uttar Pradesh (AUUP), NOIDA, India.
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