1
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Xia Y, Lai Z, Do YY, Huang PL. Characterization of MicroRNAs and Gene Expression in ACC Oxidase RNA Interference-Based Transgenic Bananas. PLANTS (BASEL, SWITZERLAND) 2023; 12:3414. [PMID: 37836154 PMCID: PMC10574930 DOI: 10.3390/plants12193414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/17/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023]
Abstract
Banana (Musa acuminata, AAA group) is a typically respiratory climacteric fruit. Previously, genes encoding ACC oxidase, one of the key enzymes in ethylene biosynthesis, Mh-ACO1 and Mh-ACO2 in bananas were silenced individually using RNAi interference technology, and fruit ripening of transgenic bananas was postponed. Here, the differential expression of miRNAs and their targeted mRNAs were analyzed in the transcriptomes of fruits at the third ripening stage, peel color more green than yellow, from the untransformed and RNAi transgenic bananas. Five significantly differentially expressed miRNAs (mac-miR169a, mac-miR319c-3p, mac-miR171a, mac-miR156e-5p, and mac-miR164a-5p) were identified. The predicted miRNA target genes were mainly enriched in six KEGG pathways, including 'sulfur relay system', 'protein digestion and absorption', 'histidine metabolism', 'pathogenic E. coli infection', 'sulfur metabolism', and 'starch and sucrose metabolism'. After ethylene treatment, the expression of ACC oxidase silencing-associated miRNAs was down-regulated, and that of their target genes was up-regulated along with fruit ripening. The evolutionary clustering relationships of miRNA precursors among 12 gene families related to fruit ripening were analyzed. The corresponding expression patterns of mature bodies were mainly concentrated in flowers, fruits, and leaves. Our results indicated that ethylene biosynthesis is associated with miRNAs regulating the expression of sulfur metabolism-related genes in bananas.
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Affiliation(s)
- Yan Xia
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Yi-Yin Do
- Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei 10617, Taiwan
| | - Pung-Ling Huang
- Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei 10617, Taiwan
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2
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Teng C, Zhang C, Guo F, Song L, Fang Y. Advances in the Study of the Transcriptional Regulation Mechanism of Plant miRNAs. Life (Basel) 2023; 13:1917. [PMID: 37763320 PMCID: PMC10533097 DOI: 10.3390/life13091917] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/12/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
MicroRNAs (miRNA) are a class of endogenous, non-coding, small RNAs with about 22 nucleotides (nt), that are widespread in plants and are involved in various biological processes, such as development, flowering phase transition, hormone signal transduction, and stress response. The transcriptional regulation of miRNAs is an important process of miRNA gene regulation, and it is essential for miRNA biosynthesis and function. Like mRNAs, miRNAs are transcribed by RNA polymerase II, and these transcription processes are regulated by various transcription factors and other proteins. Consequently, the upstream genes regulating miRNA transcription, their specific expression, and the regulating mechanism were reviewed to provide more information for further research on the miRNA regulatory mechanism and help to further understand the regulatory networks of plant miRNAs.
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Affiliation(s)
| | | | | | | | - Yanni Fang
- College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China; (C.T.); (C.Z.); (F.G.)
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3
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Xu Y, Chen X. microRNA biogenesis and stabilization in plants. FUNDAMENTAL RESEARCH 2023; 3:707-717. [PMID: 38933298 PMCID: PMC11197542 DOI: 10.1016/j.fmre.2023.02.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 02/18/2023] [Accepted: 02/28/2023] [Indexed: 03/19/2023] Open
Abstract
MicroRNAs (miRNAs) are short endogenous non-coding RNAs that regulate gene expression at the post-transcriptional level in a broad range of eukaryotic species. In animals, it is estimated that more than 60% of mammalian genes are targets of miRNAs, with miRNAs regulating cellular processes such as differentiation and proliferation. In plants, miRNAs regulate gene expression and play essential roles in diverse biological processes, including growth, development, and stress responses. Arabidopsis mutants with defective miRNA biogenesis are embryo lethal, and abnormal expression of miRNAs can cause severe developmental phenotypes. It is therefore crucial that the homeostasis of miRNAs is tightly regulated. In this review, we summarize the key mechanisms of plant miRNA biogenesis and stabilization. We provide an update on nuclear proteins with functions in miRNA biogenesis and proteins linking miRNA biogenesis to environmental triggers.
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Affiliation(s)
- Ye Xu
- Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, United States
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, United States
| | - Xuemei Chen
- Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, United States
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, United States
- School of Life Sciences, Peking-Tsinghua Joint Center for Life Sciences, Peking University, Beijing 100871, China
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4
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Yadav VK, Sawant SV, Yadav A, Jalmi SK, Kerkar S. Genome-wide analysis of long non-coding RNAs under diel light exhibits role in floral development and the circadian clock in Arabidopsis thaliana. Int J Biol Macromol 2022; 223:1693-1704. [PMID: 36257367 DOI: 10.1016/j.ijbiomac.2022.09.295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 09/19/2022] [Accepted: 09/30/2022] [Indexed: 11/05/2022]
Abstract
The circadian clock is regulated by signaling networks that enhance a plant's ability to coordinate internal events with the external environment. In this study, we examine the rhythmic expression of long non-coding RNAs (lncRNAs) using multiple transcriptomes of Arabidopsis thaliana in the diel light cycle and integrated this information to have a better understanding of the functions of lncRNAs in regulating the circadian clock. We identified 968, 1050, and 998 lncRNAs at 8 h light, 16 h light and 8 h dark conditions, respectively. Among these, 423, 486, and 417 lncRNAs were uniquely present at 8 h light, 16 h light, and 8 h dark, respectively, whereas 334 lncRNAs were common under the three conditions. The specificity of identified lncRNAs under different light conditions was verified using qRT-PCR. The identified lncRNAs were less GC-rich and expressed at a significantly lower level than the mRNAs of protein-coding genes. In addition, we identified enriched motifs in lncRNA transcribing regions that were associated with light-responsive genes (SORLREP and SORLIP), flower development (AGAMOUS), and circadian clock (CCA1) under all three light conditions. We identified 10 and 12 different lncRNAs targeting different miRNAs with perfect and interrupted complementarity (endogenous target mimic). These predicted lncRNA-interacting miRNAs govern the function of a set of genes involved in the developmental process, reproductive structure development, gene silencing and transcription regulation. We demonstrated that the lncRNA transcribing regions were enriched for epigenetic marks such as H3.3, H3K4me2, H3K4me3, H4K16ac, H3K36ac, H3K56ac and depleted for heterochromatic (H3K9me2 and H3K27me1) and repressive (H3K27me3) histone modifications. Further, we found that hypermethylated genomic regions negatively correlated with lncRNA transcribing regions. Overall, our study showed that lncRNAs expressed corresponding to the diel light cycle are implicated in regulating the circadian rhythm and governing the developmental stage-specific growth.
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Affiliation(s)
- Vikash Kumar Yadav
- School of Biological Sciences and Biotechnology, Goa University, Goa 403206, India.
| | | | - Amrita Yadav
- CSIR-National Botanical Research Institute, Lucknow 226001, India
| | | | - Savita Kerkar
- School of Biological Sciences and Biotechnology, Goa University, Goa 403206, India
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5
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Luján-Soto E, Aguirre de la Cruz PI, Juárez-González VT, Reyes JL, Sanchez MDLP, Dinkova TD. Transcriptional Regulation of zma- MIR528a by Action of Nitrate and Auxin in Maize. Int J Mol Sci 2022; 23:15718. [PMID: 36555358 PMCID: PMC9779399 DOI: 10.3390/ijms232415718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/23/2022] [Accepted: 12/03/2022] [Indexed: 12/14/2022] Open
Abstract
In recent years, miR528, a monocot-specific miRNA, has been assigned multifaceted roles during development and stress response in several plant species. However, the transcription regulation and the molecular mechanisms controlling MIR528 expression in maize are still poorly explored. Here we analyzed the zma-MIR528a promoter region and found conserved transcription factor binding sites related to diverse signaling pathways, including the nitrate (TGA1/4) and auxin (AuxRE) response networks. Accumulation of both pre-miR528a and mature miR528 was up-regulated by exogenous nitrate and auxin treatments during imbibition, germination, and maize seedling establishment. Functional promoter analyses demonstrated that TGA1/4 and AuxRE sites are required for transcriptional induction by both stimuli. Overall, our findings of the nitrogen- and auxin-induced zma-MIR528a expression through cis-regulatory elements in its promoter contribute to the knowledge of miR528 regulome.
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Affiliation(s)
- Eduardo Luján-Soto
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de Méxcio 04510, Mexico
| | - Paola I. Aguirre de la Cruz
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de Méxcio 04510, Mexico
| | - Vasti T. Juárez-González
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de Méxcio 04510, Mexico
- Department of Plant Biology, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
| | - José L. Reyes
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de Mexico, Av. Universidad 2001, Cuernavaca 62210, Mexico
| | - María de la Paz Sanchez
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - Tzvetanka D. Dinkova
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de Méxcio 04510, Mexico
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6
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Bao C, Qin G, Cao F, He J, Shen X, Chen P, Niu C, Zhang D, Ren T, Zhi F, Ma L, Ma F, Guan Q. MdZAT5 regulates drought tolerance via mediating accumulation of drought-responsive miRNAs and mRNAs in apple. THE NEW PHYTOLOGIST 2022; 236:2131-2150. [PMID: 36161284 DOI: 10.1111/nph.18512] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 09/06/2022] [Indexed: 06/16/2023]
Abstract
Drought limits apple yield and fruit quality. However, the molecular mechanism of apple in response to drought is not well known. Here, we report a Cys2/His2 (C2H2)-type zinc-finger protein, MdZAT5, that positively regulates apple drought tolerance by regulating drought-responsive RNAs and microRNAs (miRNAs). DNA affinity purification and sequencing and yeast-one hybrid analysis identified the binding motifs of MdZAT5, T/ACACT/AC/A/G. Chromatin immunoprecipitation quantitative polymerase chain reaction (ChIP-qPCR) and electrophoretic mobility shift assays (EMSAs) showed that MdZAT5 directly binds to the promoters of the drought-responsive genes including MdRHA2a, MdLEA14, MdTPX1, and MdCAT3, and activates their expression under drought stress. MdZAT5 interacts with and directly targets HYPONASTIC LEAVES1 (MdHYL1). MdZAT5 may facilitate the interaction of MdHYL1 with pri-miRNAs or MdDCL1 by activating MdHYL1 expression, thereby regulating the biogenesis of drought-responsive miRNAs. Genetic dissection showed that MdHYL1 is essential for MdZAT5-mediated drought tolerance and miRNA biogenesis. In addition, ChIP-qPCR and EMSA revealed that MdZAT5 binds directly to the promoters of some MIR genes including Mdm-miR171i and Mdm-miR172c, and modulates their transcription. Taken together, our findings improve our understanding of the molecular mechanisms of drought response in apple and provide a candidate gene for the breeding of drought-tolerant cultivars.
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Affiliation(s)
- Chana Bao
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Gege Qin
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Fuguo Cao
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Jieqiang He
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xiaoxia Shen
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Pengxiang Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Chundong Niu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Dehui Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Tianyu Ren
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Fang Zhi
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Lei Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Qingmei Guan
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
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7
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Nair MM, Kumar SHK, Jyothsna S, Sundaram KT, Manjunatha C, Sivasamy M, Alagu M. Stem and leaf rust-induced miRNAome in bread wheat near-isogenic lines and their comparative analysis. Appl Microbiol Biotechnol 2022; 106:8211-8232. [PMID: 36385566 DOI: 10.1007/s00253-022-12268-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 10/13/2022] [Accepted: 10/24/2022] [Indexed: 11/18/2022]
Abstract
Wheat rusts remain a major threat to global wheat production and food security. The R-gene-mediated resistance has been employed as an efficient approach to develop rust-resistant varieties. However, evolution of new fungal races and infection strategies put forward the urgency of unravelling novel molecular players, including non-coding RNAs for plant response. This study identified microRNAs associated with Sr36 and Lr45 disease resistance genes in response to stem and leaf rust, respectively. Here, small RNA sequencing was performed on susceptible and resistant wheat near-isogenic lines inoculated with stem and leaf rust pathotypes. microRNA mining in stem rust-inoculated cultivars revealed a total of distinct 26 known and 7 novel miRNAs, and leaf rust libraries culminated with 22 known and 4 novel miRNAs. The comparative analysis between two disease sets provides a better understanding of altered miRNA profiles associated with respective R-genes and infections. Temporal differential expression pattern of miRNAs pinpoints their role during the progress of infection. Differential expression pattern of miRNAs among various treatments as well as time-course expression of miRNAs revealed stem and leaf rust-responsive miRNAs and their possible role in balancing disease resistance/susceptibility. Disclosure of guide strand, passenger strand and a variant of novel-Tae-miR02 from different subgenome origins might serve as a potential link between stem and leaf rust defence mechanisms downstream to respective R-genes. The outcome from the analysis of microRNA dynamics among two rust diseases and further characterization of identified microRNAs can contribute to significant novel insights on wheat-rust interactions and rust management. KEY POINTS: • Identification and comparative analysis of stem and leaf rust-responsive miRNAs. • Chromosomal location and functional prediction of miRNAs. • Time-course expression analysis of pathogen-responsive miRNAs.
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Affiliation(s)
- Minu M Nair
- Department of Genomic Science, Central University of Kerala, Kasaragod, 671316, Kerala, India
| | - S Hari Krishna Kumar
- Department of Genomic Science, Central University of Kerala, Kasaragod, 671316, Kerala, India
| | - S Jyothsna
- Department of Genomic Science, Central University of Kerala, Kasaragod, 671316, Kerala, India
| | - Krishna T Sundaram
- International Rice Research Institute (IRRI), South Asia Hub, Patancheru, 502324, Telangana, India
| | - C Manjunatha
- ICAR-National Bureau of Agricultural Insect Resources, Bengaluru, 560024, Karnataka, India
| | - M Sivasamy
- ICAR-Indian Agricultural, Research Institute, Regional Station, Wellington, 643231, Tamil Nadu, India
| | - Manickavelu Alagu
- Department of Genomic Science, Central University of Kerala, Kasaragod, 671316, Kerala, India.
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8
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Yu X, Hou Y, Cao L, Zhou T, Wang S, Hu K, Chen J, Qu S. MicroRNA candidate miRcand137 in apple is induced by Botryosphaeria dothidea for impairing host defense. PLANT PHYSIOLOGY 2022; 189:1814-1832. [PMID: 35512059 PMCID: PMC9237668 DOI: 10.1093/plphys/kiac171] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 03/15/2022] [Indexed: 06/14/2023]
Abstract
MicroRNA (miRNA)-mediated gene silencing is a master gene regulatory pathway in plant-pathogen interactions. The differential accumulation of miRNAs among plant varieties alters the expression of target genes, affecting plant defense responses and causing resistance differences among varieties. Botryosphaeria dothidea is an important phytopathogenic fungus of apple (Malus domestica). Malus hupehensis (Pamp.) Rehder, a wild apple species, is highly resistant, whereas the apple cultivar "Fuji" is highly susceptible. Here, we identified a 22-nt miRNA candidate named miRcand137 that compromises host resistance to B. dothidea infection and whose processing was affected by precursor sequence variation between M. hupehensis and "Fuji." miRcand137 guides the direct cleavage of and produced target-derived secondary siRNA against Ethylene response factor 14 (ERF14), a transcriptional activator of pathogenesis-related homologs that confers disease resistance to apple. We showed that miRcand137 acts as an inhibitor of apple immunity by compromising ERF14-mediated anti-fungal defense and revealed a negative association between miRcand137 expression and B. dothidea sensitivity in both resistant and susceptible apples. Furthermore, MIRCAND137 was transcriptionally activated by the invading fungi but not by the fungal elicitor, implying B. dothidea induced host miRcand137 as an infection strategy. We propose that the inefficient miRcand137 processing in M. hupehensis decreased pathogen-initiated miRcand137 accumulation, leading to higher resistance against B. dothidea.
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Affiliation(s)
- Xinyi Yu
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Yingjun Hou
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Lifang Cao
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Tingting Zhou
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Sanhong Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Kaixu Hu
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Jingrui Chen
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
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9
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Barczak-Brzyżek A, Brzyżek G, Koter M, Siedlecka E, Gawroński P, Filipecki M. Plastid retrograde regulation of miRNA expression in response to light stress. BMC PLANT BIOLOGY 2022; 22:150. [PMID: 35346032 PMCID: PMC8962581 DOI: 10.1186/s12870-022-03525-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 03/10/2022] [Indexed: 05/03/2023]
Abstract
BACKGROUND MicroRNAs (miRNAs) are a class of endogenous noncoding RNAs that play a pivotal role in the regulation of plant development and responses to the surrounding environment. Despite the efforts made to elucidate their function in the adaptation of plants to many abiotic and biotic stresses, their role in high light (HL) stress is still vague. HL stress often arises upon plant exposure to full sunlight. Subsequent changes in nuclear gene expression are triggered by chloroplast-derived retrograde signals. RESULTS In this study, we show that HL is involved in miRNA-dependent regulation in Arabidopsis thaliana rosettes. Microtranscriptomic screening revealed a limited number of miRNAs reacting to HL. To explain the miRNA regulation mechanisms at the different biogenesis stages, chemical and genetic approaches were applied. First, we tested the possible role of plastoquinone (PQ) redox changes using photosynthetic electron transport chain inhibitors. The results suggest that increased primary transcript abundance (pri-miRNAs) of HL-regulated miRNAs is dependent on signals upstream of PQ. This indicates that such signals may originate from photosystem II, which is the main singlet oxygen (1O2) source. Nevertheless, no changes in pri-miRNA expression upon a dark-light shift in the conditional fluorescent (flu) mutant producing 1O2 were observed when compared to wild-type plants. Thus, we explored the 1O2 signaling pathway, which is initiated independently in HL and is related to β-carotene oxidation and production of volatile derivatives, such as β-cyclocitral (β-CC). Pri-miRNA induction by β-CC, which is a component of this 1O2 pathway, as well as an altered response in the methylene blue sensitivity 1 (mbs1) mutant support the role of 1O2 signaling in miRNA regulation. CONCLUSIONS We show that light stress triggers changes in miRNA expression. This stress response may be regulated by reactive oxygen species (ROS)-related signaling. In conclusion, our results link ROS action to miRNA biogenesis, suggesting its contribution to inconsistent pri- and mature miRNA dynamics.
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Affiliation(s)
- Anna Barczak-Brzyżek
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences-SGGW, 02-776, Warsaw, Poland
| | - Grzegorz Brzyżek
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, 02-106, Warsaw, Poland
| | - Marek Koter
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences-SGGW, 02-776, Warsaw, Poland
| | - Ewa Siedlecka
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences-SGGW, 02-776, Warsaw, Poland
| | - Piotr Gawroński
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences-SGGW, 02-776, Warsaw, Poland
| | - Marcin Filipecki
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences-SGGW, 02-776, Warsaw, Poland.
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10
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Gelaw TA, Sanan-Mishra N. Non-Coding RNAs in Response to Drought Stress. Int J Mol Sci 2021; 22:12519. [PMID: 34830399 PMCID: PMC8621352 DOI: 10.3390/ijms222212519] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/11/2021] [Accepted: 11/15/2021] [Indexed: 02/06/2023] Open
Abstract
Drought stress causes changes in the morphological, physiological, biochemical and molecular characteristics of plants. The response to drought in different plants may vary from avoidance, tolerance and escape to recovery from stress. This response is genetically programmed and regulated in a very complex yet synchronized manner. The crucial genetic regulations mediated by non-coding RNAs (ncRNAs) have emerged as game-changers in modulating the plant responses to drought and other abiotic stresses. The ncRNAs interact with their targets to form potentially subtle regulatory networks that control multiple genes to determine the overall response of plants. Many long and small drought-responsive ncRNAs have been identified and characterized in different plant varieties. The miRNA-based research is better documented, while lncRNA and transposon-derived RNAs are relatively new, and their cellular role is beginning to be understood. In this review, we have compiled the information on the categorization of non-coding RNAs based on their biogenesis and function. We also discuss the available literature on the role of long and small non-coding RNAs in mitigating drought stress in plants.
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Affiliation(s)
- Temesgen Assefa Gelaw
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India;
- Department of Biotechnology, College of Natural and Computational Science, Debre Birhan University, Debre Birhan P.O. Box 445, Ethiopia
| | - Neeti Sanan-Mishra
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India;
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11
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Li T, Lian H, Li H, Xu Y, Zhang H. HY5 regulates light-responsive transcription of microRNA163 to promote primary root elongation in Arabidopsis seedlings. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:1437-1450. [PMID: 33860639 DOI: 10.1111/jipb.13099] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 04/12/2021] [Indexed: 05/25/2023]
Abstract
MicroRNAs (miRNAs) play key roles in the post-transcriptional regulation of gene expression in plants. Many miRNAs are responsive to environmental signals. Light is the first environmental signal perceived by plants after emergence from the soil. However, less is known about the roles and regulatory mechanism of miRNAs in response to light signal. Here, using small RNA sequencing, we determined that miR163 is significantly rapidly induced by light signaling in Arabidopsis thaliana seedlings. The light-inducible response of miR163 functions genetically downstream of LONG HYPOCOTYL 5 (HY5), a central positive regulator of photomorphogenesis. HY5 directly binds to the two G/C-hybrid elements in the miR163 promoter with unequal affinity; one of these elements, which is located next to the transcription start site, plays a major role in light-induced expression of miR163. Overexpression of miR163 rescued the defective primary root elongation of hy5 seedlings without affecting lateral root growth, whereas overexpressing of miR163 target PXMT1 inhibited primary root elongation. These findings provide insight into understanding the post-transcriptional regulation of root photomorphogenesis mediated by the HY5-miR163-PXMT1 network.
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Affiliation(s)
- Tao Li
- College of Life Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Hongmei Lian
- College of Life Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Haojie Li
- College of Life Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yufang Xu
- College of Life Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Huiyong Zhang
- College of Life Science, Henan Agricultural University, Zhengzhou, 450002, China
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12
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Ahn J, Lee H, Jung CH, Ha SY, Seo HD, Kim YI, Ha T. 6-Gingerol Ameliorates Hepatic Steatosis via HNF4α/miR-467b-3p/GPAT1 Cascade. Cell Mol Gastroenterol Hepatol 2021; 12:1201-1213. [PMID: 34139323 PMCID: PMC8445893 DOI: 10.1016/j.jcmgh.2021.06.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 06/10/2021] [Accepted: 06/10/2021] [Indexed: 12/25/2022]
Abstract
BACKGROUND & AIMS The development of nonalcoholic fatty liver disease (NAFLD) can be modulated by microRNAs (miRNA). Dietary polyphenols modulate the expression of miRNA such as miR-467b-3p in the liver. In addition, 6-gingerol (6-G), the functional polyphenol of ginger, has been reported to ameliorate hepatic steatosis; however, the exact mechanism involved and the role of miRNA remain elusive. In this study, we assessed the role of miR-467b-3p in the pathogenesis of hepatic steatosis and the regulation of miR-467b-3p by 6-G through the hepatocyte nuclear factor 4α (HNF4α). METHODS miR-467b-3p expression was measured in free fatty acid (FFA)-treated hepatocytes or liver from high-fat diet (HFD)-fed mice. Gain- or loss-of-function of miR-467b-3p was induced using miR-467b-3p-specific miRNA mimic or miRNA inhibitor, respectively. 6-G was exposed to FFA-treated cells and HFD-fed mice. The HNF4α/miR-467b-3p/GPAT1 axis was measured in mouse and human fatty liver tissues. RESULTS We found that miR-467b-3p was down-regulated in liver tissues from HFD-fed mice and in FFA-treated Hepa1-6 cells. Overexpression of miR-467b-3p decreased intracellular lipid accumulation in FFA-treated hepatocytes and mitigated hepatic steatosis in HFD-fed mice via negative regulation of glycerol-3-phosphate acyltransferase-1 (GPAT1). In addition, miR-467b-3p up-regulation by 6-G was observed. 6-G inhibited FFA-induced lipid accumulation and mitigated hepatic steatosis. Moreover, it increased the transcriptional activity of HNF4α, resulting in the increase of miR-467b-3p and subsequent decrease of GPAT1. HNF4α/miR-467b-3p/GPAT1 signaling also was observed in human samples with hepatic steatosis. CONCLUSIONS Our findings establish a novel mechanism by which 6-G improves NAFLD. This suggests that targeting of the HNF4α/miR-467b-3p/GPAT1 cascade may be used as a potential therapeutic strategy to control NAFLD.
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Affiliation(s)
- Jiyun Ahn
- Metabolism and Nutrition Research Group, Korea Food Research Institute, Wanju-gun, Korea,Division of Food Biotechnology, University of Science and Technology, Daejeon, Korea,Correspondence Address correspondence to: Jiyun Ahn, PhD, DVM, Metabolism and Nutrition Research Group, Korea Food Research Institute, 245, Nongsaengmyeong-ro, Iseo-myeon, Wanju-gun, Jeollabuk-do 55365, Korea.
| | - Hyunjung Lee
- Metabolism and Nutrition Research Group, Korea Food Research Institute, Wanju-gun, Korea
| | - Chang Hwa Jung
- Metabolism and Nutrition Research Group, Korea Food Research Institute, Wanju-gun, Korea,Division of Food Biotechnology, University of Science and Technology, Daejeon, Korea
| | - Seung Yeon Ha
- Department of Pathology, Gachon University of Medicine and Science, Incheon, Korea
| | - Hyo-Deok Seo
- Metabolism and Nutrition Research Group, Korea Food Research Institute, Wanju-gun, Korea
| | - Young In Kim
- Metabolism and Nutrition Research Group, Korea Food Research Institute, Wanju-gun, Korea,Department of Food Science and Technology, Jeonbuk National University, Jeonju-si, South Korea
| | - Taeyoul Ha
- Metabolism and Nutrition Research Group, Korea Food Research Institute, Wanju-gun, Korea,Division of Food Biotechnology, University of Science and Technology, Daejeon, Korea,Correspondence Address correspondence to: Jiyun Ahn, PhD, DVM, Metabolism and Nutrition Research Group, Korea Food Research Institute, 245, Nongsaengmyeong-ro, Iseo-myeon, Wanju-gun, Jeollabuk-do 55365, Korea.
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13
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Wang X, Miao X, Chen G, Cui Y, Sun F, Fan J, Gao Z, Meng C. Identification of microRNAs involved in astaxanthin accumulation responding to high light and high sodium acetate (NaAC) stresses in Haematococcus pluvialis. ALGAL RES 2021. [DOI: 10.1016/j.algal.2020.102179] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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14
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Abstract
MicroRNAs (miRNAs) are essential non-coding riboregulators of gene expression in plants and animals. In plants, miRNAs guide their effector protein named ARGONAUTE (AGO) to find target RNAs for gene silencing through target RNA cleavage or translational inhibition. miRNAs are derived from primary miRNA transcripts (pri-miRNAs), most of which are transcribed by the DNA-dependent RNA polymerase II. In plants, an RNase III enzyme DICER-LIKE1-containing complex processes pri-miRNAs in the nucleus into miRNAs. To ensure proper function of miRNAs, plants use multiple mechanisms to control miRNA accumulation. On one hand, pri-miRNA levels are controlled through transcription and stability. On the other hand, the activities of the DCL1 complex are regulated by many protein factors at transcriptional, post-transcriptional and post-translational levels. Notably, recent studies reveal that pri-miRNA structure/sequence features and modifications also play important roles in miRNA biogenesis. In this review, we summarize recent progresses on the mechanisms regulating miRNA biogenesis.
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Affiliation(s)
- Mu Li
- School of Biological Sciences & Center for Plant Science Innovation University of Nebraska-Lincoln, Lincoln, Nebraska USA
| | - Bin Yu
- School of Biological Sciences & Center for Plant Science Innovation University of Nebraska-Lincoln, Lincoln, Nebraska USA
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15
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Alves A, Cordeiro D, Correia S, Miguel C. Small Non-Coding RNAs at the Crossroads of Regulatory Pathways Controlling Somatic Embryogenesis in Seed Plants. PLANTS (BASEL, SWITZERLAND) 2021; 10:504. [PMID: 33803088 PMCID: PMC8001652 DOI: 10.3390/plants10030504] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 02/26/2021] [Accepted: 03/01/2021] [Indexed: 11/25/2022]
Abstract
Small non-coding RNAs (sncRNAs) are molecules with important regulatory functions during development and environmental responses across all groups of terrestrial plants. In seed plants, the development of a mature embryo from the zygote follows a synchronized cell division sequence, and growth and differentiation events regulated by highly regulated gene expression. However, given the distinct features of the initial stages of embryogenesis in gymnosperms and angiosperms, it is relevant to investigate to what extent such differences emerge from differential regulation mediated by sncRNAs. Within these, the microRNAs (miRNAs) are the best characterized class, and while many miRNAs are conserved and significantly represented across angiosperms and other seed plants during embryogenesis, some miRNA families are specific to some plant lineages. Being a model to study zygotic embryogenesis and a relevant biotechnological tool, we systematized the current knowledge on the presence and characterization of miRNAs in somatic embryogenesis (SE) of seed plants, pinpointing the miRNAs that have been reported to be associated with SE in angiosperm and gymnosperm species. We start by conducting an overview of sncRNA expression profiles in the embryonic tissues of seed plants. We then highlight the miRNAs described as being involved in the different stages of the SE process, from its induction to the full maturation of the somatic embryos, adding references to zygotic embryogenesis when relevant, as a contribution towards a better understanding of miRNA-mediated regulation of SE.
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Affiliation(s)
- Ana Alves
- BioISI—Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisboa, Portugal;
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal
| | - Daniela Cordeiro
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal; (D.C.); (S.C.)
| | - Sandra Correia
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal; (D.C.); (S.C.)
| | - Célia Miguel
- BioISI—Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisboa, Portugal;
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal
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16
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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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17
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Xie D, Yu Y, Dai Z, Sun J, Su J. Identification and characterization of miRNAs and target genes in developing flax seeds by multigroup analysis. BIOTECHNOL BIOTEC EQ 2021. [DOI: 10.1080/13102818.2021.1903337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
- Dongwei Xie
- Department of Biotechnology, School of Life Science, Nantong University, Jiangsu, Nantong, PR China
| | - Yue Yu
- Laboratory of Germplasm Resources and Utilization of Economic Crops in South China, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Hunan, Changsha, PR China
| | - Zhigang Dai
- Laboratory of Germplasm Resources and Utilization of Economic Crops in South China, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Hunan, Changsha, PR China
| | - Jian Sun
- Department of Biotechnology, School of Life Science, Nantong University, Jiangsu, Nantong, PR China
| | - Jianguang Su
- Laboratory of Germplasm Resources and Utilization of Economic Crops in South China, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Hunan, Changsha, PR China
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18
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Buch DU, Sharma OA, Pable AA, Barvkar VT. Characterization of microRNA genes from Pigeonpea (Cajanus cajan L.) and understanding their involvement in drought stress. J Biotechnol 2020; 321:23-34. [PMID: 32610182 DOI: 10.1016/j.jbiotec.2020.06.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 06/22/2020] [Accepted: 06/23/2020] [Indexed: 12/20/2022]
Abstract
MicroRNAs (miRNA) are non-coding 20-24 nucleotide long RNAs regulating gene expression. In this study, we have characterized and analysed expression of miRNAs in Pigeonpea by using bioinformatics and experimental tools. We identified 116 miRNAs belonging to 32 phylogenetic families. Further, transcription start sites of miRNA genes revealed abundance and unique arrangement of adenine at +1 and thymine at -1 position. Promoter analysis exhibited presence of 19 most prevalent motifs which comprises majorly of TATA box and MYC domains. In total, 252 miRNA-targets were identified and found to be involved in various developmental processes and stress responses. Moreover, genome-wide localization studies demonstrated clustering of cca-miRNA 395 and 169 genes. The tandem and segmental duplication events were observed suggesting miRNA genes have been originated parallelly with protein coding genes. The expression analysis revealed induction of cca-miR169a, 398a and 408 miRNAs under drought stress highlighting their involvement. Conversely, down-regulation of their putative targets (NFYA, SOD, and UCLA, respectively) confirmed regulatory role of miRNAs in their expression emphasising the negative relationship between these miRNAs and targets in Pigeonpea. This study reports vast repertoire of miRNA genes which further can be experimentally characterized to elucidate their functions in various biological processes and can be recommended for Pigeonpea improvement programs.
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Affiliation(s)
- Drushtant U Buch
- Department of Botany, Savitribai Phule Pune University, Pune, 411007, India.
| | - Oshin A Sharma
- Department of Botany, Savitribai Phule Pune University, Pune, 411007, India.
| | - Anupama A Pable
- Department of Microbiology, Savitribai Phule Pune University, Pune, 411007, India.
| | - Vitthal T Barvkar
- Department of Botany, Savitribai Phule Pune University, Pune, 411007, India.
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19
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Zhang B, You C, Zhang Y, Zeng L, Hu J, Zhao M, Chen X. Linking key steps of microRNA biogenesis by TREX-2 and the nuclear pore complex in Arabidopsis. NATURE PLANTS 2020; 6:957-969. [PMID: 32690891 PMCID: PMC7426256 DOI: 10.1038/s41477-020-0726-z] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 06/18/2020] [Indexed: 05/03/2023]
Abstract
Unlike in metazoans, the stepwise biogenesis of microRNAs (miRNAs) in plants occurs within the nucleus. Whether or how the major steps in miRNA biogenesis are coordinated is largely unknown. Here we show that the plant TREX-2 complex promotes multiple steps in miRNA biogenesis, including transcription, processing and nuclear export. THP1 and SAC3A-the core subunits of TREX-2-interact and colocalize with RNA polymerase II to promote the transcription of MIR genes in the nucleoplasm. TREX-2 interacts with the microprocessor component SERRATE and promotes the formation of dicing bodies in the nucleoplasm. THP1 also interacts and colocalizes with the nucleoporin protein NUP1 at the nuclear envelope. NUP1 and THP1 promote the nuclear export of miRNAs and ARGONAUTE1. These results suggest that TREX-2 coordinates the transcription, processing and export steps in miRNA biogenesis to ensure efficient miRNA production.
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Affiliation(s)
- Bailong Zhang
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Chenjiang You
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, USA
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Yong Zhang
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Liping Zeng
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Jun Hu
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, USA
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Minglei Zhao
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, USA
- College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, USA.
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20
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Chen QJ, Deng BH, Gao J, Zhao ZY, Chen ZL, Song SR, Wang L, Zhao LP, Xu WP, Zhang CX, Ma C, Wang SP. A miRNA-Encoded Small Peptide, vvi-miPEP171d1, Regulates Adventitious Root Formation. PLANT PHYSIOLOGY 2020; 183:656-670. [PMID: 32241877 PMCID: PMC7271809 DOI: 10.1104/pp.20.00197] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 03/17/2020] [Indexed: 05/07/2023]
Abstract
One of the biggest challenges in clonal propagation of grapevine (Vitis vinifera) is difficulty of rooting. Adventitious root initiation and development are the critical steps in the cutting and layering process of grapevine, but the molecular mechanism of these processes remains unclear. Previous reports have found that microRNA (miRNA)-encoded peptides (miPEPs) can regulate plant root development by increasing the transcription of their corresponding primary miRNA. Here, we report the role of a miPEP in increasing adventitious root formation in grapevine. In this study, we performed a global analysis of miPEPs in grapevine and characterized the function of vvi-miPEP171d1, a functional, small peptide encoded by primary-miR171d. There were three small open reading frames in the 500-bp upstream sequence of pre-miR171d. One of them encoded a small peptide, vvi-miPEP171d1, which could increase the transcription of vvi-MIR171d Exogenous application of vvi-miPEP171d1 to grape tissue culture plantlets promoted adventitious root development by activating the expression of vvi-MIR171d Interestingly, neither exogenous application of the vvi-miPEP171d1 peptide nor overexpression of the vvi-miPEP171d1 coding sequence resulted in phenotypic changes in Arabidopsis (Arabidopsis thaliana). Similarly, application of synthetic ath-miPEP171c, the small peptide encoded by the Arabidopsis ortholog of vvi-MIR171d, inhibited the growth of primary roots and induced the early initiation of lateral and adventitious roots in Arabidopsis, while it had no effect on grape root development. Our findings reveal that miPEP171d1 regulates root development by promoting vvi-MIR171d expression in a species-specific manner, further enriching the theoretical research into miPEPs.
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Affiliation(s)
- Qiu-Ju Chen
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Bo-Han Deng
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jie Gao
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhong-Yang Zhao
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zi-Li Chen
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shi-Ren Song
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lei Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Li-Ping Zhao
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Wen-Ping Xu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Cai-Xi Zhang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chao Ma
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shi-Ping Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
- Institute of Agro-food Science and Technology/Key Laboratory of Agro-products Processing Technology of Shandong, Shandong Academy of Agricultural Sciences, Jinan 250100, China
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21
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Kačar D, Schleissner C, Cañedo LM, Rodríguez P, de la Calle F, Galán B, García JL. Genome of Labrenzia sp. PHM005 Reveals a Complete and Active Trans-AT PKS Gene Cluster for the Biosynthesis of Labrenzin. Front Microbiol 2019; 10:2561. [PMID: 31787953 PMCID: PMC6855096 DOI: 10.3389/fmicb.2019.02561] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 10/23/2019] [Indexed: 11/28/2022] Open
Abstract
The complete genome of the strain Labrenzia sp. PHM005, a free-living producer of a pederin analog 18-O-demethyl pederin, hereinafter labrenzin, has been sequenced. This strain contains two replicons comprising a circular chromosome of 6,167,349 bp and a circular plasmid (named p1BIR) of 19,450 bp. A putative gene cluster responsible for the synthesis of labrenzin (lab cluster) has been identified showing that it encodes a trans-AT mixed type PKS/NRPS biosynthetic pathway that is responsible for the synthesis of pederin and possibly an onnamide analog. The putative boundaries of the lab gene cluster were determined by genetic comparisons with other related strains, suggesting that the cluster consists of a 79-kb region comprising 3 genes encoding multidomain hybrid polyketide synthase/non-ribosomal peptide synthetase (PKS/NRPS) proteins (PKS4, PKS/NRPS13, and PKS/NRPS15), and 16 auxiliary enzymes. Transcriptomic analyses suggest that all the genes of the cluster are expressed in our culture conditions (i.e., in minimal medium in the absence of any specific inducer) at detectable levels. We have developed genetic tools to facilitate the manipulation of this strain and the functional characterization of the cluster genes. We have created a site-directed mutant unable to produce pederin, demonstrating experimentally for the first time the role of the cluster in the synthesis of pederin. This work paves the way to unravel the clues of the biosynthesis of pederin family compounds and opens the door to modify and overproduce these anticancer drugs for industrial and pharmaceutical purposes.
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Affiliation(s)
- Dina Kačar
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas, Agencia Estatal Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | | | - Librada M Cañedo
- Research and Development Department, PharmaMar S.A., Madrid, Spain
| | - Pilar Rodríguez
- Research and Development Department, PharmaMar S.A., Madrid, Spain
| | | | - Beatriz Galán
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas, Agencia Estatal Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - José Luis García
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas, Agencia Estatal Consejo Superior de Investigaciones Científicas, Madrid, Spain
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22
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Song X, Li Y, Cao X, Qi Y. MicroRNAs and Their Regulatory Roles in Plant-Environment Interactions. ANNUAL REVIEW OF PLANT BIOLOGY 2019; 70:489-525. [PMID: 30848930 DOI: 10.1146/annurev-arplant-050718-100334] [Citation(s) in RCA: 366] [Impact Index Per Article: 73.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
MicroRNAs (miRNAs) are 20-24 nucleotide noncoding RNAs abundant in plants and animals. The biogenesis of plant miRNAs involves transcription of miRNA genes, processing of primary miRNA transcripts by DICER-LIKE proteins into mature miRNAs, and loading of mature miRNAs into ARGONAUTE proteins to form miRNA-induced silencing complex (miRISC). By targeting complementary sequences, miRISC negatively regulates gene expression, thereby coordinating plant development and plant-environment interactions. In this review, we present and discuss recent updates on the mechanisms and regulation of miRNA biogenesis, miRISC assembly and actions as well as the regulatory roles of miRNAs in plant developmental plasticity, abiotic/biotic responses, and symbiotic/parasitic interactions. Finally, we suggest future directions for plant miRNA research.
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Affiliation(s)
- Xianwei Song
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China;
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100039, China
| | - Yan Li
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China;
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China;
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100039, China
| | - Yijun Qi
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China;
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
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23
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Pegler JL, Oultram JMJ, Grof CPL, Eamens AL. Profiling the Abiotic Stress Responsive microRNA Landscape of Arabidopsis thaliana. PLANTS 2019; 8:plants8030058. [PMID: 30857364 PMCID: PMC6473545 DOI: 10.3390/plants8030058] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 03/01/2019] [Accepted: 03/06/2019] [Indexed: 12/20/2022]
Abstract
It is well established among interdisciplinary researchers that there is an urgent need to address the negative impacts that accompany climate change. One such negative impact is the increased prevalence of unfavorable environmental conditions that significantly contribute to reduced agricultural yield. Plant microRNAs (miRNAs) are key gene expression regulators that control development, defense against invading pathogens and adaptation to abiotic stress. Arabidopsis thaliana (Arabidopsis) can be readily molecularly manipulated, therefore offering an excellent experimental system to alter the profile of abiotic stress responsive miRNA/target gene expression modules to determine whether such modification enables Arabidopsis to express an altered abiotic stress response phenotype. Towards this goal, high throughput sequencing was used to profile the miRNA landscape of Arabidopsis whole seedlings exposed to heat, drought and salt stress, and identified 121, 123 and 118 miRNAs with a greater than 2-fold altered abundance, respectively. Quantitative reverse transcriptase polymerase chain reaction (RT-qPCR) was next employed to experimentally validate miRNA abundance fold changes, and to document reciprocal expression trends for the target genes of miRNAs determined abiotic stress responsive. RT-qPCR also demonstrated that each miRNA/target gene expression module determined to be abiotic stress responsive in Arabidopsis whole seedlings was reflective of altered miRNA/target gene abundance in Arabidopsis root and shoot tissues post salt stress exposure. Taken together, the data presented here offers an excellent starting platform to identify the miRNA/target gene expression modules for future molecular manipulation to generate plant lines that display an altered response phenotype to abiotic stress.
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Affiliation(s)
- Joseph L Pegler
- Centre for Plant Science, School of Environmental and Life Sciences, Faculty of Science, University of Newcastle, Callaghan 2308, Australia.
| | - Jackson M J Oultram
- Centre for Plant Science, School of Environmental and Life Sciences, Faculty of Science, University of Newcastle, Callaghan 2308, Australia.
| | - Christopher P L Grof
- Centre for Plant Science, School of Environmental and Life Sciences, Faculty of Science, University of Newcastle, Callaghan 2308, Australia.
| | - Andrew L Eamens
- Centre for Plant Science, School of Environmental and Life Sciences, Faculty of Science, University of Newcastle, Callaghan 2308, Australia.
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24
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Dastidar MG, Scarpa A, Mägele I, Ruiz‐Duarte P, von Born P, Bald L, Jouannet V, Maizel A. ARF5/MONOPTEROS directly regulates miR390 expression in the Arabidopsis thaliana primary root meristem. PLANT DIRECT 2019; 3:e00116. [PMID: 31245759 PMCID: PMC6508847 DOI: 10.1002/pld3.116] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 01/08/2019] [Accepted: 01/09/2019] [Indexed: 05/25/2023]
Abstract
The root meristem is organized around a quiescent center (QC) surrounded by stem cells that generate all cell types of the root. In the transit-amplifying compartment, progeny of stem cells further divides prior to differentiation. Auxin controls the size of this transit-amplifying compartment via auxin response factors (ARFs) that interact with auxin response elements (AuxREs) in the promoter of their targets. The microRNA miR390 regulates abundance of ARF2, ARF3, and ARF4 by triggering the production of trans-acting (ta)-siRNA from the TAS3 precursor. This miR390/TAS3/ARF regulatory module confers sensitivity and robustness to auxin responses in diverse developmental contexts and organisms. Here, we show that miR390 is expressed in the transit-amplifying compartment of the root meristem where it modulates response to exogenous auxin. We show that a single AuxRE located in miR390 promoter is necessary for miR390 expression in this compartment and identify that ARF5/MONOPTEROS (MP) binds miR390 promoter via the AuxRE. We show that interfering with ARF5/MP-dependent auxin signaling attenuates miR390 expression in the transit-amplifying compartment of the root meristem. Our results show that ARF5/MP regulates directly the expression of miR390 in the root meristem. We propose that ARF5, miR390, and the ta-siRNAs-regulated ARFs modulate the response of the transit-amplifying region of the meristem to exogenous auxin.
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Affiliation(s)
- Mouli Ghosh Dastidar
- Center for Organismal Studies (COS)University of HeidelbergHeidelbergGermany
- Present address:
PsiOxus TherapeuticsAbingdonUK
| | - Andrea Scarpa
- Center for Organismal Studies (COS)University of HeidelbergHeidelbergGermany
| | - Ira Mägele
- Center for Organismal Studies (COS)University of HeidelbergHeidelbergGermany
| | - Paola Ruiz‐Duarte
- Center for Organismal Studies (COS)University of HeidelbergHeidelbergGermany
| | - Patrick von Born
- Center for Organismal Studies (COS)University of HeidelbergHeidelbergGermany
- Present address:
Max Planck Institute for Plant Breeding ResearchCologneGermany
| | - Lotte Bald
- Center for Organismal Studies (COS)University of HeidelbergHeidelbergGermany
| | - Virginie Jouannet
- Center for Organismal Studies (COS)University of HeidelbergHeidelbergGermany
| | - Alexis Maizel
- Center for Organismal Studies (COS)University of HeidelbergHeidelbergGermany
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25
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Huang LH, Kuo HC, Pan CT, Lin YS, Huang YH, Li SC. Multiomics analyses identified epigenetic modulation of the S100A gene family in Kawasaki disease and their significant involvement in neutrophil transendothelial migration. Clin Epigenetics 2018; 10:135. [PMID: 30382880 PMCID: PMC6211403 DOI: 10.1186/s13148-018-0557-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 10/02/2018] [Indexed: 02/08/2023] Open
Abstract
Background Kawasaki disease (KD) is a prevalent pediatric disease worldwide and can cause coronary artery aneurysm as a severe complication. Typically, DNA methylation is thought to repress the expression of nearby genes. However, the cases in which DNA methylation promotes gene expression have been reported. In addition, globally, to what extent DNA methylation affects gene expression and how it contributes to the pathogenesis of KD are not yet well understood. Methods To address these important biological questions, we enrolled subjects, collected DNA and RNA samples from the subjects’ total white blood cells, and performed DNA methylation (M450K) and gene expression (HTA 2.0) microarray assays. Results By analyzing the variation ratios of CpG beta values (methylation percentage) and gene expression intensities, we first concluded that the CpG markers close (− 1500 bp to + 500 bp) to the transcription start sites had higher variation ratios, reflecting significant regulation capacities. Next, we observed that, globally speaking, gene expression was modestly negatively correlated (correlation rho ≈ − 0.2) with the DNA methylation status of both upstream and downstream CpG markers in the promoter region. Third, we found that specific CpG markers were hypo-methylated in disease samples compared with healthy samples and hyper-methylated in convalescent samples compared with disease samples, promoting and repressing S100A genes’ expressions, respectively. Finally, using an in vitro cell model, we demonstrated that S100A family proteins enhanced leukocyte transendothelial migration in KD. Conclusions This is the first study to integrate genome-wide DNA methylation with gene expression assays in KD and showed that the S100A family plays important roles in the pathogenesis of KD. Electronic supplementary material The online version of this article (10.1186/s13148-018-0557-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lien-Hung Huang
- Genomics and Proteomics Core Laboratory, Department of Medical Research, Kaohsiung Chang Gung Memorial Hospital, 12th Floor, Children's Hospital, No.123, Dapi Rd, Niaosong District, Kaohsiung, 83301, Taiwan
| | - Ho-Chang Kuo
- Department of Pediatrics, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Kawasaki Disease Center, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
| | - Cheng-Tsung Pan
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan
| | - Yeong-Shin Lin
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan.,Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan
| | - Ying-Hsien Huang
- Department of Pediatrics, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Kawasaki Disease Center, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
| | - Sung-Chou Li
- Genomics and Proteomics Core Laboratory, Department of Medical Research, Kaohsiung Chang Gung Memorial Hospital, 12th Floor, Children's Hospital, No.123, Dapi Rd, Niaosong District, Kaohsiung, 83301, Taiwan.
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26
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Wang Y, Zou W, Xiao Y, Cheng L, Liu Y, Gao S, Shi Z, Jiang Y, Qi M, Xu T, Li T. MicroRNA1917 targets CTR4 splice variants to regulate ethylene responses in tomato. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:1011-1025. [PMID: 29365162 DOI: 10.1093/jxb/erx469] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 12/07/2017] [Indexed: 05/18/2023]
Abstract
Ethylene perception is regulated by receptors, and the downstream protein CONSTITUTIVE TRIPLE RESPONSE1 is a key suppressor of ethylene signalling. The non-conserved tomato (Solanum lycopersicum) microRNA1917 (Sly-miR1917) mediates degradation of SlCTR4 splice variants (SlCTR4sv) but the molecular details of this pathway remain unknown. Sly-miR1917 and the targeted SlCTR4sv are ubiquitously expressed in all tomato organs. Overexpression of Sly-miR1917 enhances ethylene responses, including the triple response in etiolated seedlings, in the absence of ethylene, as well as epinastic petiole growth, accelerated pedicel abscission, and fruit ripening. Enhanced ethylene signalling in Sly-miR1917-overexpressing plants (1917-OE) is accompanied by up-regulation of ethylene biosynthesis and signalling genes, and increased ethylene emission. These phenotypes were recovered by repressing the positive ethylene regulator EIN2. Moreover, the Sly-miR1917-targeted SlCTR4 splice variant SlCTR4sv3, expressed specifically in the abscission zone, exhibited the opposite expression pattern to Sly-miR1917. Complementation of the Arabidopsis thaliana ctr-1 mutant and yeast two-hybrid and bimolecular fluorescence complementation assays suggested that SlCTR4sv3 functions in ethylene signalling. Co-expression of Sly-miR1917 and SlCTR4sv3 in Nicotiana benthamiana further suggested that Sly-miR1917 cleaves SlCTR4sv3 in vivo. Database homology searching revealed a Solanum tuberosum CTR-like splice variant containing a Sly-miR1917 binding sequence, and a homologue of mature Sly-miR1917 in potato, indicating a conserved function for miR1917 and the regulatory miRNA-mediated ethylene network in solanaceous species.
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Affiliation(s)
- Yanling Wang
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Protected Horticulture of Ministry of Education, Shenyang, China
| | - Wenxiong Zou
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Protected Horticulture of Ministry of Education, Shenyang, China
| | - Yan Xiao
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Protected Horticulture of Ministry of Education, Shenyang, China
| | - Lina Cheng
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Protected Horticulture of Ministry of Education, Shenyang, China
| | - Yudong Liu
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Protected Horticulture of Ministry of Education, Shenyang, China
| | - Song Gao
- Liaoning Cash Crop Institute, Liaoyang, China
| | - Zihang Shi
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Protected Horticulture of Ministry of Education, Shenyang, China
| | - Yun Jiang
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Protected Horticulture of Ministry of Education, Shenyang, China
| | - Mingfang Qi
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Protected Horticulture of Ministry of Education, Shenyang, China
| | - Tao Xu
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Protected Horticulture of Ministry of Education, Shenyang, China
| | - Tianlai Li
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Protected Horticulture of Ministry of Education, Shenyang, China
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27
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Bai Q, Wang X, Chen X, Shi G, Liu Z, Guo C, Xiao K. Wheat miRNA TaemiR408 Acts as an Essential Mediator in Plant Tolerance to Pi Deprivation and Salt Stress via Modulating Stress-Associated Physiological Processes. FRONTIERS IN PLANT SCIENCE 2018; 9:499. [PMID: 29720988 PMCID: PMC5916090 DOI: 10.3389/fpls.2018.00499] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 04/03/2018] [Indexed: 05/18/2023]
Abstract
MicroRNAs (miRNA) families act as critical regulators for plant growth, development, and responses to abiotic stresses. In this study, we characterized TaemiR408, a miRNA family member of wheat (Triticum aestivum), for the role in mediating plant responses to Pi starvation and salt stress. TaemiR408 targets six genes that encode proteins involving biochemical metabolism, microtubule organization, and signaling transduction. 5'- and 3'-RACE analyses confirmed the mRNA cleavage of target genes mediated by this wheat miRNA. TaemiR408 showed induced expression patterns upon Pi starvation and salt stress and whose upregulated expression was gradually repressed by the normal recovery treatments. The target genes of TaemiR408 exhibited reverse expression patterns to this miRNA, whose transcripts were downregulated under Pi starvation and salt stress and the reduced expression was recovered by the followed normal condition. These results suggest the regulation of the target genes under TaemiR408 through a cleavage mechanism. Tobacco lines with TaemiR408 overexpression exhibited enhanced stress tolerance, showing improved phenotype, biomass, and photosynthesis behavior compared with wild type under both Pi starvation and salt treatments, which closely associate increased P accumulation upon Pi deprivation and elevated osmolytes under salt stress, respectively. Phosphate transporter (PT) gene NtPT2 displays upregulated transcripts in the Pi-deprived TaemiR408 overexpressors; knockdown of this PT gene reduces Pi acquisition under low-Pi stress, confirming its role in improving plant Pi taken up. Likewise, NtPYL2 and NtSAPK3, genes encoding abscisic acid (ABA) receptor and SnRK2 protein, respectively, exhibited upregulated transcripts in salt-challenged TaemiR408 overexpressors; knockdown of them caused deteriorated growth and lowered osmolytes amounts of plants upon salt treatment. Thus, TaemiR408 is crucial for plant adaptations to Pi starvation and salt stress through regulating Pi acquisition under low-Pi stress and remodel ABA signaling pathway and osmoprotects biosynthesis under salt stress.
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Affiliation(s)
| | | | | | | | | | | | - Kai Xiao
- *Correspondence: Chengjin Guo, Kai Xiao,
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28
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Zhang X, Jayaweera D, Peters JL, Szecsi J, Bendahmane M, Roberts JA, González-Carranza ZH. The Arabidopsis thaliana F-box gene HAWAIIAN SKIRT is a new player in the microRNA pathway. PLoS One 2017; 12:e0189788. [PMID: 29244865 PMCID: PMC5731758 DOI: 10.1371/journal.pone.0189788] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 12/03/2017] [Indexed: 11/26/2022] Open
Abstract
In Arabidopsis, the F-box HAWAIIAN SKIRT (HWS) protein is important for organ growth. Loss of function of HWS exhibits pleiotropic phenotypes including sepal fusion. To dissect the HWS role, we EMS-mutagenized hws-1 seeds and screened for mutations that suppress hws-1 associated phenotypes. We identified shs-2 and shs-3 (suppressor of hws-2 and 3) mutants in which the sepal fusion phenotype of hws-1 was suppressed. shs-2 and shs-3 (renamed hst-23/hws-1 and hst-24/hws-1) carry transition mutations that result in premature terminations in the plant homolog of Exportin-5 HASTY (HST), known to be important in miRNA biogenesis, function and transport. Genetic crosses between hws-1 and mutant lines for genes in the miRNA pathway also suppress the phenotypes associated with HWS loss of function, corroborating epistatic relations between the miRNA pathway genes and HWS. In agreement with these data, accumulation of miRNA is modified in HWS loss or gain of function mutants. Our data propose HWS as a new player in the miRNA pathway, important for plant growth.
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Affiliation(s)
- Xuebin Zhang
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, United Kingdom
| | - Dasuni Jayaweera
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, United Kingdom
| | - Janny L. Peters
- Department of Molecular Plant Physiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Judit Szecsi
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, Université Claude Bernard Lyon 1, CNRS, INRA, Lyon, France
| | - Mohammed Bendahmane
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, Université Claude Bernard Lyon 1, CNRS, INRA, Lyon, France
| | - Jeremy A. Roberts
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, United Kingdom
| | - Zinnia H. González-Carranza
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, United Kingdom
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29
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Yu Y, Jia T, Chen X. The 'how' and 'where' of plant microRNAs. THE NEW PHYTOLOGIST 2017; 216:1002-1017. [PMID: 29048752 PMCID: PMC6040672 DOI: 10.1111/nph.14834] [Citation(s) in RCA: 261] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Accepted: 08/21/2017] [Indexed: 05/18/2023]
Abstract
Contents 1002 I. 1002 II. 1007 III. 1010 IV. 1013 1013 References 1013 SUMMARY: MicroRNAs (miRNAs) are small non-coding RNAs, of typically 20-24 nt, that regulate gene expression post-transcriptionally through sequence complementarity. Since the identification of the first miRNA, lin-4, in the nematode Caenorhabditis elegans in 1993, thousands of miRNAs have been discovered in animals and plants, and their regulatory roles in numerous biological processes have been uncovered. In plants, research efforts have established the major molecular framework of miRNA biogenesis and modes of action, and are beginning to elucidate the mechanisms of miRNA degradation. Studies have implicated restricted and surprising subcellular locations in which miRNA biogenesis or activity takes place. In this article, we summarize the current knowledge on how plant miRNAs are made and degraded, and how they repress target gene expression. We discuss not only the players involved in these processes, but also the subcellular sites in which these processes are known or implicated to take place. We hope to raise awareness that the cell biology of miRNAs holds the key to a full understanding of these enigmatic molecules.
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Affiliation(s)
- Yu Yu
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Tianran Jia
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
- Department of Botany and Plant Sciences, Howard Hughes Medical Institute, University of California, Riverside, CA 92521, USA
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30
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Mei Y, Chen H, Shen W, Shen W, Huang L. Hydrogen peroxide is involved in hydrogen sulfide-induced lateral root formation in tomato seedlings. BMC PLANT BIOLOGY 2017; 17:162. [PMID: 29029623 PMCID: PMC5640930 DOI: 10.1186/s12870-017-1110-7] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Accepted: 10/09/2017] [Indexed: 05/18/2023]
Abstract
BACKGROUND Both hydrogen sulfide (H2S) and hydrogen peroxide (H2O2) are separately regarded as a highly reactive molecule involved in root morphogenesis. In this report, corresponding causal link governing lateral root formation was investigated. METHODS By using pharmacological, anatomic, and molecular approaches, evidence presented here revealed the molecular mechanism underlying tomato lateral root development triggered by H2S. RESULTS A H2S donor sodium hydrosulfide (NaHS) triggered the accumulation of H2O2, the up-regulation of RBOH1 transcript, and thereafter tomato lateral root formation. Above responses were sensitive to the H2O2 scavenger (dimethylthiourea; DMTU) and the inhibitor of NADPH oxidase (diphenylene idonium; DPI), showing that the accumulations of H2O2 and increased RBOH1 transcript were respectively prevented. Lateral root primordial and lateral root formation were also impaired. Further molecular evidence revealed that H2S-modulated gene expression of cell cycle regulatory genes, including up-regulation of SlCYCA2;1, SlCYCA3;1, and SlCDKA1, and the down-regulation of SlKRP2, were prevented by the co-treatment with DMTU or DPI. Above mentioned inducing phenotypes were consistent with the changes of lateral root formation-related microRNA transcripts: up-regulation of miR390a and miR160, and with the opposite tendencies of their target genes (encoding auxin response factors). Contrasting tendencies were observed when DMTU or DPI was added together. The occurrence of H2S-mediated S-sulfhydration during above responses was preliminarily discovered. CONCLUSIONS Overall, these results suggested an important role of RBOH1-mediated H2O2 in H2S-elicited tomato lateral root development, and corresponding H2S-target proteins regulated at transcriptional and post-translational levels.
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Affiliation(s)
- Yudong Mei
- College of Life Sciences, Laboratory Center of Life Sciences, Nanjing Agricultural University, Nanjing, 210095 China
| | - Haotian Chen
- College of Sciences, Nanjing Agricultural University, Nanjing, 210095 China
| | - Wenbiao Shen
- College of Life Sciences, Laboratory Center of Life Sciences, Nanjing Agricultural University, Nanjing, 210095 China
| | - Wei Shen
- College of Sciences, Nanjing Agricultural University, Nanjing, 210095 China
| | - Liqin Huang
- College of Sciences, Nanjing Agricultural University, Nanjing, 210095 China
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31
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Li X, Xie X, Li J, Cui Y, Hou Y, Zhai L, Wang X, Fu Y, Liu R, Bian S. Conservation and diversification of the miR166 family in soybean and potential roles of newly identified miR166s. BMC PLANT BIOLOGY 2017; 17:32. [PMID: 28143404 PMCID: PMC5286673 DOI: 10.1186/s12870-017-0983-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 01/23/2017] [Indexed: 05/21/2023]
Abstract
BACKGROUND microRNA166 (miR166) is a highly conserved family of miRNAs implicated in a wide range of cellular and physiological processes in plants. miR166 family generally comprises multiple miR166 members in plants, which might exhibit functional redundancy and specificity. The soybean miR166 family consists of 21 members according to the miRBase database. However, the evolutionary conservation and functional diversification of miR166 family members in soybean remain poorly understood. RESULTS We identified five novel miR166s in soybean by data mining approach, thus enlarging the size of miR166 family from 21 to 26 members. Phylogenetic analyses of the 26 miR166s and their precursors indicated that soybean miR166 family exhibited both evolutionary conservation and diversification, and ten pairs of miR166 precursors with high sequence identity were individually grouped into a discrete clade in the phylogenetic tree. The analysis of genomic organization and evolution of MIR166 gene family revealed that eight segmental duplications and four tandem duplications might occur during evolution of the miR166 family in soybean. The cis-elements in promoters of MIR166 family genes and their putative targets pointed to their possible contributions to the functional conservation and diversification. The targets of soybean miR166s were predicted, and the cleavage of ATHB14-LIKE transcript was experimentally validated by RACE PCR. Further, the expression patterns of the five newly identified MIR166s and 12 target genes were examined during seed development and in response to abiotic stresses, which provided important clues for dissecting their functions and isoform specificity. CONCLUSION This study enlarged the size of soybean miR166 family from 21 to 26 members, and the 26 soybean miR166s exhibited evolutionary conservation and diversification. These findings have laid a foundation for elucidating functional conservation and diversification of miR166 family members, especially during seed development or under abiotic stresses.
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Affiliation(s)
- Xuyan Li
- College of Plant Science, Jilin University, Changchun, Jilin, China
| | - Xin Xie
- College of Plant Science, Jilin University, Changchun, Jilin, China
| | - Ji Li
- College of Plant Science, Jilin University, Changchun, Jilin, China
| | - Yuhai Cui
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, ON, Canada
- Department of Biology, Western University, London, ON, Canada
| | - Yanming Hou
- College of Plant Science, Jilin University, Changchun, Jilin, China
| | - Lulu Zhai
- College of Plant Science, Jilin University, Changchun, Jilin, China
| | - Xiao Wang
- College of Plant Science, Jilin University, Changchun, Jilin, China
| | - Yanli Fu
- College of Plant Science, Jilin University, Changchun, Jilin, China
| | - Ranran Liu
- College of Plant Science, Jilin University, Changchun, Jilin, China
| | - Shaomin Bian
- College of Plant Science, Jilin University, Changchun, Jilin, China.
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Szyrajew K, Bielewicz D, Dolata J, Wójcik AM, Nowak K, Szczygieł-Sommer A, Szweykowska-Kulinska Z, Jarmolowski A, Gaj MD. MicroRNAs Are Intensively Regulated during Induction of Somatic Embryogenesis in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2017; 8:18. [PMID: 28167951 PMCID: PMC5253390 DOI: 10.3389/fpls.2017.00018] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 01/04/2017] [Indexed: 05/06/2023]
Abstract
Several genes encoding transcription factors (TFs) were indicated to have a key role in the induction of somatic embryogenesis (SE), which is triggered in the somatic cells of plants. In order to further explore the genetic regulatory network that is involved in the embryogenic transition induced in plant somatic cells, micro-RNA (miRNAs) molecules, the products of MIRNA (MIR) genes and the common regulators of TF transcripts, were analyzed in an embryogenic culture of Arabidopsis thaliana. In total, the expression of 190 genes of the 114 MIRNA families was monitored during SE induction and the levels of the primary (pri-miRNAs) transcripts vs. the mature miRNAs were investigated. The results revealed that the majority (98%) of the MIR genes were active and that most of them (64%) were differentially expressed during SE. A distinct attribute of the MIR expression in SE was the strong repression of MIR transcripts at the early stage of SE followed by their significant up-regulation in the advanced stage of SE. Comparison of the mature miRNAs vs. pri-miRNAs suggested that the extensive post-transcriptional regulation of miRNA is associated with SE induction. Candidate miRNA molecules of the assumed function in the embryogenic response were identified among the mature miRNAs that had a differential expression in SE, including miR156, miR157, miR159, miR160, miR164, miR166, miR169, miR319, miR390, miR393, miR396, and miR398. Consistent with the central role of phytohormones and stress factors in SE induction, the functions of the candidate miRNAs were annotated to phytohormone and stress responses. To confirm the functions of the candidate miRNAs in SE, the expression patterns of the mature miRNAs and their presumed targets were compared and regulatory relation during SE was indicated for most of the analyzed miRNA-target pairs. The results of the study contribute to the refinement of the miRNA-controlled regulatory pathways that operate during embryogenic induction in plants and provide a valuable platform for the identification of the genes that are targeted by the candidate miRNAs in SE induction.
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Affiliation(s)
- Katarzyna Szyrajew
- Department of Genetics, Faculty of Biology and Environmental Protection, University of SilesiaKatowice, Poland
| | - Dawid Bielewicz
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz UniversityPoznan, Poland
| | - Jakub Dolata
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz UniversityPoznan, Poland
| | - Anna M. Wójcik
- Department of Genetics, Faculty of Biology and Environmental Protection, University of SilesiaKatowice, Poland
| | - Katarzyna Nowak
- Department of Genetics, Faculty of Biology and Environmental Protection, University of SilesiaKatowice, Poland
| | - Aleksandra Szczygieł-Sommer
- Department of Genetics, Faculty of Biology and Environmental Protection, University of SilesiaKatowice, Poland
| | - Zofia Szweykowska-Kulinska
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz UniversityPoznan, Poland
| | - Artur Jarmolowski
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz UniversityPoznan, Poland
| | - Małgorzata D. Gaj
- Department of Genetics, Faculty of Biology and Environmental Protection, University of SilesiaKatowice, Poland
- *Correspondence: Małgorzata D. Gaj
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33
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Stepien A, Knop K, Dolata J, Taube M, Bajczyk M, Barciszewska-Pacak M, Pacak A, Jarmolowski A, Szweykowska-Kulinska Z. Posttranscriptional coordination of splicing and miRNA biogenesis in plants. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 8. [DOI: 10.1002/wrna.1403] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 09/30/2016] [Accepted: 10/08/2016] [Indexed: 12/20/2022]
Affiliation(s)
- Agata Stepien
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology; Adam Mickiewicz University; Poznan Poland
| | - Katarzyna Knop
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology; Adam Mickiewicz University; Poznan Poland
| | - Jakub Dolata
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology; Adam Mickiewicz University; Poznan Poland
| | - Michal Taube
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology; Adam Mickiewicz University; Poznan Poland
| | - Mateusz Bajczyk
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology; Adam Mickiewicz University; Poznan Poland
| | - Maria Barciszewska-Pacak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology; Adam Mickiewicz University; Poznan Poland
| | - Andrzej Pacak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology; Adam Mickiewicz University; Poznan Poland
| | - Artur Jarmolowski
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology; Adam Mickiewicz University; Poznan Poland
| | - Zofia Szweykowska-Kulinska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology; Adam Mickiewicz University; Poznan Poland
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Couzigou JM, Combier JP. Plant microRNAs: key regulators of root architecture and biotic interactions. THE NEW PHYTOLOGIST 2016; 212:22-35. [PMID: 27292927 DOI: 10.1111/nph.14058] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 05/08/2016] [Indexed: 05/24/2023]
Abstract
Contents 22 I. 22 II. 24 III. 25 IV. 27 V. 29 VI. 10 31 References 32 SUMMARY: Plants have evolved a remarkable faculty of adaptation to deal with various and changing environmental conditions. In this context, the roots have taken over nutritional aspects and the root system architecture can be modulated in response to nutrient availability or biotic interactions with soil microorganisms. This adaptability requires a fine tuning of gene expression. Indeed, root specification and development are highly complex processes requiring gene regulatory networks involved in hormonal regulations and cell identity. Among the different molecular partners governing root development, microRNAs (miRNAs) are key players for the fast regulation of gene expression. miRNAs are small RNAs involved in most developmental processes and are required for the normal growth of organisms, by the negative regulation of key genes, such as transcription factors and hormone receptors. Here, we review the known roles of miRNAs in root specification and development, from the embryonic roots to the establishment of root symbioses, highlighting the major roles of miRNAs in these processes.
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Affiliation(s)
- Jean-Malo Couzigou
- UMR5546, Laboratoire de Recherche en Sciences Végétales, UPS, CNRS, Université de Toulouse, Castanet-Tolosan, 31326, France
| | - Jean-Philippe Combier
- UMR5546, Laboratoire de Recherche en Sciences Végétales, UPS, CNRS, Université de Toulouse, Castanet-Tolosan, 31326, France
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35
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Mermigka G, Verret F, Kalantidis K. RNA silencing movement in plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2016; 58:328-42. [PMID: 26297506 DOI: 10.1111/jipb.12423] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 08/20/2015] [Indexed: 05/21/2023]
Abstract
Multicellular organisms, like higher plants, need to coordinate their growth and development and to cope with environmental cues. To achieve this, various signal molecules are transported between neighboring cells and distant organs to control the fate of the recipient cells and organs. RNA silencing produces cell non-autonomous signal molecules that can move over short or long distances leading to the sequence specific silencing of a target gene in a well defined area of cells or throughout the entire plant, respectively. The nature of these signal molecules, the route of silencing spread, and the genes involved in their production, movement and reception are discussed in this review. Additionally, a short section on features of silencing spread in animal models is presented at the end of this review.
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Affiliation(s)
- Glykeria Mermigka
- Department of Biology, University of Crete, Heraklion, Crete, Greece
| | - Frédéric Verret
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Heraklion, Crete, Greece
| | - Kriton Kalantidis
- Department of Biology, University of Crete, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Heraklion, Crete, Greece
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36
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Niu J, Wang J, Hu H, Chen Y, An J, Cai J, Sun R, Sheng Z, Liu X, Lin S. Cross-talk between freezing response and signaling for regulatory transcriptions of MIR475b and its targets by miR475b promoter in Populus suaveolens. Sci Rep 2016; 6:20648. [PMID: 26853706 PMCID: PMC4745078 DOI: 10.1038/srep20648] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 01/07/2016] [Indexed: 01/20/2023] Open
Abstract
MicroRNAs (miRNAs) are small, non-coding RNAs that play important roles in post-transcriptional regulation of their target genes, yet the transcriptional regulation of plant miRNAs by promoter is poorly understood. Here, we firstly clone pri-miR475b cDNA and its native promoter from P. suaveolens, and characterize Psu-MIR475b as class-II gene transcribed by RNA polymerase II. By 5′ deletion analysis of Psu-miR475b promoter in a series of promoter-GUS chimeric vectors, we functionally identify three positive regulatory regions and multiple cis-acting elements responsible for Psu-miR475b promoter activity in response to freezing stress and exogenous hormone treatment. Moreover, the Psu-miR475b promoter activity displays a tissue-specific manner, negatively regulated by freezing stress and positively by MeJA, SA or GA treatment. Importantly, we comparatively analyze the time-course transcriptional profiles of Psu-miR475b and its targets in Psu-miR475b over-expression transgenic plants controlled by Psu-miR475b-specific promoter or CaMV 35S constitutive promoter, and explore the regulatory mechanism of Psu-miR475b promoter controlling transcriptional expressions of Psu-MIR475b and its targets in response to freezing stress and exogenous hormone treatment. Our results reveal that Psu-miR475b promoter-mediated transcriptions of Psu-MIR475b and its targets in response to freezing stress may be involved in a cross-talk between freezing response and stress signaling process.
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Affiliation(s)
- Jun Niu
- College of Biological Sciences and Biotechnology, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing 10083, China
| | - Jia Wang
- College of Biological Sciences and Biotechnology, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing 10083, China
| | - Huiwen Hu
- College of Biological Sciences and Biotechnology, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing 10083, China
| | - Yinlei Chen
- College of Biological Sciences and Biotechnology, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing 10083, China
| | - Jiyong An
- College of Biological Sciences and Biotechnology, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing 10083, China
| | - Jian Cai
- College of Biological Sciences and Biotechnology, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing 10083, China
| | - Runze Sun
- College of Biological Sciences and Biotechnology, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing 10083, China
| | - Zhongting Sheng
- College of Biological Sciences and Biotechnology, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing 10083, China
| | - Xieping Liu
- College of Biological Sciences and Biotechnology, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing 10083, China
| | - Shanzhi Lin
- College of Biological Sciences and Biotechnology, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing 10083, China
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37
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Plant miRNA function prediction based on functional similarity network and transductive multi-label classification algorithm. Neurocomputing 2016. [DOI: 10.1016/j.neucom.2015.12.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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38
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Lei KJ, Lin YM, Ren J, Bai L, Miao YC, An GY, Song CP. Modulation of the Phosphate-Deficient Responses by MicroRNA156 and its Targeted SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 3 in Arabidopsis. PLANT & CELL PHYSIOLOGY 2016; 57:192-203. [PMID: 26647245 DOI: 10.1093/pcp/pcv197] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 12/01/2015] [Indexed: 05/26/2023]
Abstract
The microRNA156 (miR156)-modulated SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) is involved in diverse biological processes that include growth, development and metabolism. Here, we report that the Arabidopsis miR156 and SPL3 as regulators play important roles in phosphate (Pi) deficiency response. MiR156 was induced during Pi starvation whereas SPL3 expression was repressed. Phenotypes of reduced rhizosphere acidification and decreased anthocyanin accumulation were observed in 35S:MIM156 (via target mimicry) transgenic plants under Pi deficiency. The content and uptake of Pi in 35S:MIM156 Arabidopsis plants were increased compared with wild-type (Col-0 ecotype) plants. 35S:rSPL3 seedlings showed similar anthocyanin accumulation and Pi content phenotypes to those of 35S:MIM156 plants. Chromatin immunoprecipitation and an electrophoretic mobility shift assay indicated that the SPL3 protein directly bound to GTAC motifs in the PLDZ2, Pht1;5 and miR399f promoters. The expression of several Pi starvation-induced genes was increased in 35S:MIM156 and 35S:rSPL3 plants, including high-affinity Pi transporters, Mt4/TPS1-like genes and phosphatases. Collectively, our results suggest that the miR156-SPL3-Pht1;5 (-PLDZ2 and -miR399f) pathways constitute a component of the Pi deficiency-induced regulatory mechanism of Arabidopsis.
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Affiliation(s)
- Kai-Jian Lei
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, Kaifeng 475001, China
| | - Ya-Ming Lin
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, Kaifeng 475001, China
| | - Jing Ren
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, Kaifeng 475001, China
| | - Ling Bai
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, Kaifeng 475001, China
| | - Yu-Chen Miao
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, Kaifeng 475001, China
| | - Guo-Yong An
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, Kaifeng 475001, China
| | - Chun-Peng Song
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, Kaifeng 475001, China
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39
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Usha S, Jyothi MN, Sharadamma N, Dixit R, Devaraj VR, Nagesh Babu R. Identification of microRNAs and their targets in Finger millet by high throughput sequencing. Gene 2015; 574:210-6. [PMID: 26255946 DOI: 10.1016/j.gene.2015.08.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 08/03/2015] [Accepted: 08/05/2015] [Indexed: 12/27/2022]
Abstract
MicroRNAs are short non-coding RNAs which play an important role in regulating gene expression by mRNA cleavage or by translational repression. The majority of identified miRNAs were evolutionarily conserved; however, others expressed in a species-specific manner. Finger millet is an important cereal crop; nonetheless, no practical information is available on microRNAs to date. In this study, we have identified 95 conserved microRNAs belonging to 39 families and 3 novel microRNAs by high throughput sequencing. For the identified conserved and novel miRNAs a total of 507 targets were predicted. 11 miRNAs were validated and tissue specificity was determined by stem loop RT-qPCR, Northern blot. GO analyses revealed targets of miRNA were involved in wide range of regulatory functions. This study implies large number of known and novel miRNAs found in Finger millet which may play important role in growth and development.
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Affiliation(s)
- S Usha
- Post Graduate Department of Biochemistry, Maharani's Science College for Women, Bangalore 560001, India; Centre for Bioinformatics, Faculty of Biological Engineering, Shobhit University, Meerut, 250110 India
| | - M N Jyothi
- Post Graduate Department of Biochemistry, Maharani's Science College for Women, Bangalore 560001, India; Centre for Bioinformatics, Faculty of Biological Engineering, Shobhit University, Meerut, 250110 India
| | - N Sharadamma
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012 India
| | - Rekha Dixit
- Centre for Bioinformatics, Faculty of Biological Engineering, Shobhit University, Meerut, 250110 India
| | - V R Devaraj
- Department of Biochemistry, Central College Campus, Bangalore University, Bangalore 560001 India
| | - R Nagesh Babu
- Post Graduate Department of Biochemistry, Maharani's Science College for Women, Bangalore 560001, India.
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40
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Sanei M, Chen X. Mechanisms of microRNA turnover. CURRENT OPINION IN PLANT BIOLOGY 2015; 27:199-206. [PMID: 26342825 PMCID: PMC4618239 DOI: 10.1016/j.pbi.2015.07.008] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 07/14/2015] [Accepted: 07/17/2015] [Indexed: 05/20/2023]
Abstract
MicroRNAs (miRNAs) are 20-24 nucleotide (nt) RNAs that regulate gene expression by guiding Argonaute (AGO) proteins to specific target RNAs to cause their degradation or translational repression. The abundance of miRNAs is strictly controlled at the transcriptional or post-transcriptional levels. miRNA turnover is presumably a necessary means to regulate miRNA levels in response to physiological, developmental, and environmental changes. miRNA 3' end methylation, 3' end nucleotide addition, AGO and complementary target transcripts are known or probable processes/factors that affect miRNA stability and turnover. Here we discuss the mechanisms that control miRNA turnover in plants and, where applicable, make references to similarities and differences in these mechanisms between plants and animals.
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Affiliation(s)
- Maryam Sanei
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, United States
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, United States; Howard Hughes Medical Institute, University of California, Riverside, CA, United States.
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41
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Ganie SA, Dey N, Mondal TK. Promoter methylation regulates the abundance of osa-miR393a in contrasting rice genotypes under salinity stress. Funct Integr Genomics 2015; 16:1-11. [PMID: 26319531 DOI: 10.1007/s10142-015-0460-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 07/28/2015] [Accepted: 08/02/2015] [Indexed: 01/03/2023]
Abstract
MicroRNAs (miRNAs) are important molecules that regulate gene expression under salinity stress. Despite their evolutionary conservation, these regulatory elements have been shown to behave differently in different plant species under a particular environmental stress. In this study, we investigated the behavior of salt responsive osa-miR393a and its target gene (TIR1, LOC_Os05g05800) in salt-tolerant (FL478) and salt-sensitive (IR29) rice genotypes. It was found that the mature and precursor sequences of osa-miR393a as well as its cleavage site in TIR1 were conserved among salt tolerant and sensitive genotypes. Promoters of different salt-responsive miRNAs were also found to be less variable between salt-tolerant and salt-susceptible genotypes. Analysis of gene expression, promoter methylation, and cis-element abundance showed that osa-miR393a behaves differently in FL478 and IR29. Salt stress altered the expression pattern of osa-miR393a-TIR1 module in a time-dependent manner in the roots and shoots of two genotypes. Promoter methylation of this regulatory module was also altered at different time points under salt stress. Expression analysis in two genotypes indicated the overall down-regulation of osa-miR393a and up-regulation of TIR1 in FL478 and their reciprocal regulation in IR29. The expression results were complemented by the differential promoter methylation and cis-element abundance of this regulatory module. Together, the results of transcript abundance and promoter methylation of osa-miR393a-TIR1 module signified the association between these two processes which is reported for the first time in plants to the best of our knowledge.
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Affiliation(s)
- Showkat Ahmad Ganie
- Division of Genomic Resources, National Bureau of Plant Genetic Resources, IARI Campus, New Delhi, 110012, India
| | - Narottam Dey
- Department of Biotechnology, Visva-Bharati, Santiniketan, 731 235, West Bengal, India
| | - Tapan Kumar Mondal
- Division of Genomic Resources, National Bureau of Plant Genetic Resources, IARI Campus, New Delhi, 110012, India.
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42
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Zhang S, Liu Y, Yu B. New insights into pri-miRNA processing and accumulation in plants. WILEY INTERDISCIPLINARY REVIEWS-RNA 2015; 6:533-45. [PMID: 26119101 DOI: 10.1002/wrna.1292] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Revised: 05/12/2015] [Accepted: 05/22/2015] [Indexed: 12/31/2022]
Abstract
MicroRNAs (miRNAs) regulate many biological processes such as development, metabolism, and others. They are processed from their primary transcripts called primary miRNA transcripts (pri-miRNAs) by the processor complex containing the RNAse III enzyme, DICER-LIKE1 (DCL1), in plants. Consequently, miRNA biogenesis is controlled through altering pri-miRNA accumulation and processing, which is crucial for plant development and adaptation to environmental changes. Plant pri-miRNAs are transcribed by DNA-dependent RNA polymerase II (Pol II) and their levels are determined through transcription and degradation, whereas pri-miRNA processing is affected by its structure, splicing, alternative splicing, loading to the processor and the processor activity, which involve in many accessory proteins. Here, we summarize recent progresses related to pri-miRNA transcription, stability, and processing in plants.
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Affiliation(s)
- Shuxin Zhang
- Center for Plant Science Innovation & School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA.,State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Yuhui Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences & Key Laboratory of Agricultural Genomics, Ministry of Agriculture, Beijing, China
| | - Bin Yu
- Center for Plant Science Innovation & School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
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43
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Gao J, Ge W, Zhang Y, Cheng Z, Li L, Hou D, Hou C. Identification and characterization of microRNAs at different flowering developmental stages in moso bamboo (Phyllostachys edulis) by high-throughput sequencing. Mol Genet Genomics 2015; 290:2335-53. [PMID: 26044981 DOI: 10.1007/s00438-015-1069-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 05/18/2015] [Indexed: 11/30/2022]
Abstract
Researching moso bamboo flowering has been difficult because of its unknown flowering interval and the rarity of florescent samples. To identify microRNAs (miRNAs) and study their expression patterns during the flower developmental process of moso bamboo, small RNAs from non-flowering leaves and four flower developmental periods were sequenced using Illumina technology. In total, 409 known miRNAs and 492 differentially expressed novel miRNAs were identified in moso bamboo. Of the known miRNAs that were differentially expressed between non-flowering and flowering samples, 64 were predicted to have a total of 308 targets. Among the miRNAs, seven known and five novel miRNAs were selected, as were four of their target genes, and their expression profiles were validated using qRT-PCR. The results indicated that the miRNA expression levels were negatively correlated with those of their targets. The research comprehensively revealed that the differentially expressed miRNAs and their targets participated in diverse biological pathways and played significant regulatory roles in moso bamboo flowering. The data provide a significant resource for understanding the molecular mechanisms in moso bamboo flowering and senescence, and serve as the primary foundation for further studies on metabolic regulatory networks that involve miRNAs.
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Affiliation(s)
- Jian Gao
- Key Laboratory of Bamboo and Rattan Science and Technology of the State Forestry Administration, International Centre for Bamboo and Rattan, No. 8 Futong Dongdajie, Wangjing, Chaoyang District, 100102, Beijing, People's Republic of China.
| | - Wei Ge
- Key Laboratory of Bamboo and Rattan Science and Technology of the State Forestry Administration, International Centre for Bamboo and Rattan, No. 8 Futong Dongdajie, Wangjing, Chaoyang District, 100102, Beijing, People's Republic of China
| | - Ying Zhang
- Key Laboratory of Bamboo and Rattan Science and Technology of the State Forestry Administration, International Centre for Bamboo and Rattan, No. 8 Futong Dongdajie, Wangjing, Chaoyang District, 100102, Beijing, People's Republic of China
| | - Zhanchao Cheng
- Key Laboratory of Bamboo and Rattan Science and Technology of the State Forestry Administration, International Centre for Bamboo and Rattan, No. 8 Futong Dongdajie, Wangjing, Chaoyang District, 100102, Beijing, People's Republic of China
| | - Long Li
- Key Laboratory of Bamboo and Rattan Science and Technology of the State Forestry Administration, International Centre for Bamboo and Rattan, No. 8 Futong Dongdajie, Wangjing, Chaoyang District, 100102, Beijing, People's Republic of China
| | - Dan Hou
- Key Laboratory of Bamboo and Rattan Science and Technology of the State Forestry Administration, International Centre for Bamboo and Rattan, No. 8 Futong Dongdajie, Wangjing, Chaoyang District, 100102, Beijing, People's Republic of China
| | - Chenglin Hou
- Capital Normal University School of Life Science, No. 105, The Third Ring Road, Haidian District, 100048, Beijing, People's Republic of China
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44
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Budak H, Kantar M, Bulut R, Akpinar BA. Stress responsive miRNAs and isomiRs in cereals. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 235:1-13. [PMID: 25900561 DOI: 10.1016/j.plantsci.2015.02.008] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2014] [Revised: 02/12/2015] [Accepted: 02/13/2015] [Indexed: 05/18/2023]
Abstract
Abiotic and biotic stress conditions are vital determinants in the production of cereals, the major caloric source in human nutrition. Small RNAs, miRNAs and isomiRs are central to post-transcriptional regulation of gene expression in a variety of cellular processes including development and stress responses. Several miRNAs have been identified using new technologies and have roles in stress responses in plants, including cereals. The overall knowledge about the cereal miRNA repertoire, as well as an understanding of complex miRNA mediated mechanisms of target regulation in response to stress conditions, is far from complete. Ongoing efforts that add to our understanding of complex miRNA machinery have implications in plant response to stress conditions. Additionally, sequence variants of miRNAs (isomiRNAs or isomiRs), regulation of their expression through dissection of upstream regulatory elements, the role of Processing-bodies (P-bodies) in miRNA exerted gene regulation and yet unveiled organellar plant miRNAs are newly emerging topics, which will contribute to the elucidation of the miRNA machinery and its role in cereal tolerance against abiotic and biotic stresses.
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Affiliation(s)
- Hikmet Budak
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, 34956 Istanbul, Turkey.
| | - Melda Kantar
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, 34956 Istanbul, Turkey
| | - Reyyan Bulut
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, 34956 Istanbul, Turkey
| | - Bala Ani Akpinar
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, 34956 Istanbul, Turkey
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45
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Barciszewska-Pacak M, Milanowska K, Knop K, Bielewicz D, Nuc P, Plewka P, Pacak AM, Vazquez F, Karlowski W, Jarmolowski A, Szweykowska-Kulinska Z. Arabidopsis microRNA expression regulation in a wide range of abiotic stress responses. FRONTIERS IN PLANT SCIENCE 2015; 6:410. [PMID: 26089831 PMCID: PMC4454879 DOI: 10.3389/fpls.2015.00410] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 05/21/2015] [Indexed: 05/19/2023]
Abstract
Arabidopsis microRNA expression regulation was studied in a wide array of abiotic stresses such as drought, heat, salinity, copper excess/deficiency, cadmium excess, and sulfur deficiency. A home-built RT-qPCR mirEX platform for the amplification of 289 Arabidopsis microRNA transcripts was used to study their response to abiotic stresses. Small RNA sequencing, Northern hybridization, and TaqMan® microRNA assays were performed to study the abundance of mature microRNAs. A broad response on the level of primary miRNAs (pri-miRNAs) was observed. However, stress response at the level of mature microRNAs was rather confined. The data presented show that in most instances, the level of a particular mature miRNA could not be predicted based on the level of its pri-miRNA. This points to an essential role of posttranscriptional regulation of microRNA expression. New Arabidopsis microRNAs responsive to abiotic stresses were discovered. Four microRNAs: miR319a/b, miR319b.2, and miR400 have been found to be responsive to several abiotic stresses and thus can be regarded as general stress-responsive microRNA species.
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Affiliation(s)
- Maria Barciszewska-Pacak
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz UniversityPoznan, Poland
- *Correspondence: Maria Barciszewska-Pacak and Zofia Szweykowska-Kulinska, Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614 Poznan, Poland ;
| | - Kaja Milanowska
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz UniversityPoznan, Poland
| | - Katarzyna Knop
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz UniversityPoznan, Poland
| | - Dawid Bielewicz
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz UniversityPoznan, Poland
| | - Przemyslaw Nuc
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz UniversityPoznan, Poland
| | - Patrycja Plewka
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz UniversityPoznan, Poland
| | - Andrzej M. Pacak
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz UniversityPoznan, Poland
| | - Franck Vazquez
- Zurich-Basel Plant Science Center, Swiss Plant Science Web, Botanical Institute, University of BaselBasel, Switzerland
| | - Wojciech Karlowski
- Department of Computational Biology, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz UniversityPoznan, Poland
| | - Artur Jarmolowski
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz UniversityPoznan, Poland
| | - Zofia Szweykowska-Kulinska
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz UniversityPoznan, Poland
- *Correspondence: Maria Barciszewska-Pacak and Zofia Szweykowska-Kulinska, Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614 Poznan, Poland ;
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46
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Kulcheski FR, Côrrea R, Gomes IA, de Lima JC, Margis R. NPK macronutrients and microRNA homeostasis. FRONTIERS IN PLANT SCIENCE 2015; 6:451. [PMID: 26136763 PMCID: PMC4468412 DOI: 10.3389/fpls.2015.00451] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 06/02/2015] [Indexed: 05/02/2023]
Abstract
Macronutrients are essential elements for plant growth and development. In natural, non-cultivated systems, the availability of macronutrients is not a limiting factor of growth, due to fast recycling mechanisms. However, their availability might be an issue in modern agricultural practices, since soil has been frequently over exploited. From a crop management perspective, the nitrogen (N), phosphorus (P), and potassium (K) are three important limiting factors and therefore frequently added as fertilizers. NPK are among the nutrients that have been reported to alter post-embryonic root developmental processes and consequently, impairs crop yield. To cope with nutrients scarcity, plants have evolved several mechanisms involved in metabolic, physiological, and developmental adaptations. In this scenario, microRNAs (miRNAs) have emerged as additional key regulators of nutrients uptake and assimilation. Some studies have demonstrated the intrinsic relation between miRNAs and their targets, and how they can modulate plants to deal with the NPK availability. In this review, we focus on miRNAs and their regulation of targets involved in NPK metabolism. In general, NPK starvation is related with miRNAs that are involved in root-architectural changes and uptake activity modulation. We further show that several miRNAs were discovered to be involved in plant-microbe symbiosis during N and P uptake, and in this way we present a global view of some studies that were conducted in the last years. The integration of current knowledge about miRNA-NPK signaling may help future studies to focus in good candidates genes for the development of important tools for plant nutritional breeding.
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Affiliation(s)
- Franceli R. Kulcheski
- Departamento de Biofísica, Laboratório de Genomas e Populações de Plantas, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto AlegreBrazil
| | - Régis Côrrea
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de JaneiroBrazil
| | - Igor A. Gomes
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de JaneiroBrazil
| | - Júlio C. de Lima
- Laboratório de Genética Molecular, Instituto de Ciências Biológicas, Universidade de Passo Fundo, Passo FundoBrazil
| | - Rogerio Margis
- Departamento de Biofísica, Laboratório de Genomas e Populações de Plantas, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto AlegreBrazil
- *Correspondence: Rogerio Margis, Departamento de Biofísica, Laboratório de Genomas e Populações de Plantas, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves 9500, Setor IV, Prédio 43431, Sala 213, Porto Alegre, RS, CEP, Brazil
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Lin Y, Lai Z, Tian Q, Lin L, Lai R, Yang M, Zhang D, Chen Y, Zhang Z. Endogenous target mimics down-regulate miR160 mediation of ARF10, -16, and -17 cleavage during somatic embryogenesis in Dimocarpus longan Lour. FRONTIERS IN PLANT SCIENCE 2015; 6:956. [PMID: 26594219 PMCID: PMC4633511 DOI: 10.3389/fpls.2015.00956] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 10/20/2015] [Indexed: 05/20/2023]
Abstract
MicroRNA160 plays a critical role in plant development by negatively regulating the auxin response factors ARF10, -16, and -17. However, the ways in which miR160 expression is regulated at the transcriptional level, and how miR160 interacts with its targets during plant embryo development, remain unknown. Here, we studied the regulatory relationships among endogenous target mimics (eTMs), and miR160 and its targets, and their involvement in hormone signaling and somatic embryogenesis (SE) in Dimocarpus longan. We identified miR160 family members and isolated the miR160 precursor, primary transcript, and promoter. The promoter contained cis-acting elements responsive to stimuli such as light, abscisic acid, salicylic acid (SA) and heat stress. The pri-miR160 was down-regulated in response to SA but up-regulated by gibberellic acid, ethylene, and methyl jasmonate treatment, suggesting that pri-miR160 was associated with hormone transduction. Dlo-miR160a, -a(∗) and -d(∗) reached expression peaks in torpedo-shaped embryos, globular embryos and cotyledonary embryos, respectively, but were barely detectable in friable-embryogenic callus. This suggests that they have expression-related and functional diversity, especially during the middle and later developmental stages of SE. Four potential eTMs for miR160 were identified. Two of them, glucan endo-1,3-beta- glucosidase-like protein 2-like and calpain-type cysteine protease DEK1, were confirmed to control the corresponding dlo-miR160a(∗) expression level. This suggests that they may function to abolish the binding between dlo-miR160a(∗) and its targets. These two eTMs also participated in 2,4-D and ABA signal transduction. DlARF10, -16, and -17 targeting by dlo-miR160a was confirmed; their expression levels were higher in friable-embryogenic callus and incomplete compact pro-embryogenic cultures and responded to 2,4-D, suggesting they may play a major role in the early stages of longan SE dependent on 2,4-D. The eTMs, miR160, and ARF10, -16, and -17 exhibited tissue specificity in 'Sijimi' longan vegetative and reproductive organs, but were not significant negatively correlated. These results provide insights into the possible role of the eTM-miR160-ARF10-16-17 pathway in longan somatic embryo development.
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48
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Xie M, Zhang S, Yu B. microRNA biogenesis, degradation and activity in plants. Cell Mol Life Sci 2015; 72:87-99. [PMID: 25209320 PMCID: PMC11113746 DOI: 10.1007/s00018-014-1728-7] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 08/13/2014] [Accepted: 09/04/2014] [Indexed: 12/11/2022]
Abstract
microRNAs (miRNAs) are important regulators of gene expression. After excised from primary miRNA transcript by dicer-like1 (DCL1, an RNAse III enzyme), miRNAs bind and guide their effector protein named argonaute 1 (AGO1) to silence the expression of target RNAs containing their complementary sequences in plants. miRNA levels and activities are tightly controlled to ensure their functions in various biological processes such as development, metabolism and responses to abiotic and biotic stresses. Studies have identified many factors that involve in miRNA accumulation and activities. Characterization of these factors in turn greatly improves our understanding of the processes related to miRNAs. Here, we review recent progress of mechanisms underlying miRNA expression and functions in plants.
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Affiliation(s)
- Meng Xie
- Center for Plant Science Innovation and School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588–0660 USA
| | - Shuxin Zhang
- Center for Plant Science Innovation and School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588–0660 USA
| | - Bin Yu
- Center for Plant Science Innovation and School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588–0660 USA
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Lin Y, Lai Z, Tian Q, Lin L, Lai R, Yang M, Zhang D, Chen Y, Zhang Z. Endogenous target mimics down-regulate miR160 mediation of ARF10, -16, and -17 cleavage during somatic embryogenesis in Dimocarpus longan Lour. FRONTIERS IN PLANT SCIENCE 2015. [PMID: 26594219 DOI: 10.1007/s11032-015-0420-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
MicroRNA160 plays a critical role in plant development by negatively regulating the auxin response factors ARF10, -16, and -17. However, the ways in which miR160 expression is regulated at the transcriptional level, and how miR160 interacts with its targets during plant embryo development, remain unknown. Here, we studied the regulatory relationships among endogenous target mimics (eTMs), and miR160 and its targets, and their involvement in hormone signaling and somatic embryogenesis (SE) in Dimocarpus longan. We identified miR160 family members and isolated the miR160 precursor, primary transcript, and promoter. The promoter contained cis-acting elements responsive to stimuli such as light, abscisic acid, salicylic acid (SA) and heat stress. The pri-miR160 was down-regulated in response to SA but up-regulated by gibberellic acid, ethylene, and methyl jasmonate treatment, suggesting that pri-miR160 was associated with hormone transduction. Dlo-miR160a, -a(∗) and -d(∗) reached expression peaks in torpedo-shaped embryos, globular embryos and cotyledonary embryos, respectively, but were barely detectable in friable-embryogenic callus. This suggests that they have expression-related and functional diversity, especially during the middle and later developmental stages of SE. Four potential eTMs for miR160 were identified. Two of them, glucan endo-1,3-beta- glucosidase-like protein 2-like and calpain-type cysteine protease DEK1, were confirmed to control the corresponding dlo-miR160a(∗) expression level. This suggests that they may function to abolish the binding between dlo-miR160a(∗) and its targets. These two eTMs also participated in 2,4-D and ABA signal transduction. DlARF10, -16, and -17 targeting by dlo-miR160a was confirmed; their expression levels were higher in friable-embryogenic callus and incomplete compact pro-embryogenic cultures and responded to 2,4-D, suggesting they may play a major role in the early stages of longan SE dependent on 2,4-D. The eTMs, miR160, and ARF10, -16, and -17 exhibited tissue specificity in 'Sijimi' longan vegetative and reproductive organs, but were not significant negatively correlated. These results provide insights into the possible role of the eTM-miR160-ARF10-16-17 pathway in longan somatic embryo development.
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Affiliation(s)
- Yuling Lin
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University Fuzhou, China
| | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University Fuzhou, China
| | - Qilin Tian
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University Fuzhou, China
| | - Lixia Lin
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University Fuzhou, China
| | - Ruilian Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University Fuzhou, China
| | - Manman Yang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University Fuzhou, China
| | - Dongmin Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University Fuzhou, China
| | - Yukun Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University Fuzhou, China
| | - Zihao Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University Fuzhou, China
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Baldrich P, Kakar K, Siré C, Moreno AB, Berger A, García-Chapa M, López-Moya JJ, Riechmann JL, San Segundo B. Small RNA profiling reveals regulation of Arabidopsis miR168 and heterochromatic siRNA415 in response to fungal elicitors. BMC Genomics 2014; 15:1083. [PMID: 25491154 PMCID: PMC4299684 DOI: 10.1186/1471-2164-15-1083] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2014] [Accepted: 11/27/2014] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Small RNAs (sRNAs), including small interfering RNAs (siRNAs) and microRNAs (miRNAs), have emerged as important regulators of eukaryotic gene expression. In plants, miRNAs play critical roles in development, nutrient homeostasis and abiotic stress responses. Accumulating evidence also reveals that sRNAs are involved in plant immunity. Most studies on pathogen-regulated sRNAs have been conducted in Arabidopsis plants infected with the bacterial pathogen Pseudomonas syringae, or treated with the flagelin-derived elicitor peptide flg22 from P. syringae. This work investigates sRNAs that are regulated by elicitors from the fungus Fusarium oxysporum in Arabidopsis. RESULTS Microarray analysis revealed alterations on the accumulation of a set of sRNAs in response to elicitor treatment, including miRNAs and small RNA sequences derived from massively parallel signature sequencing. Among the elicitor-regulated miRNAs was miR168 which regulates ARGONAUTE1, the core component of the RNA-induced silencing complex involved in miRNA functioning. Promoter analysis in transgenic Arabidopsis plants revealed transcriptional activation of MIR168 by fungal elicitors. Furthermore, transgenic plants expressing a GFP-miR168 sensor gene confirmed that the elicitor-induced miR168 is active. MiR823, targeting Chromomethylase3 (CMT3) involved in RNA-directed DNA methylation (RdDM) was also found to be regulated by fungal elicitors. In addition to known miRNAs, microarray analysis allowed the identification of an elicitor-inducible small RNA that was incorrectly annotated as a miRNA. Studies on Arabidopsis mutants impaired in small RNA biogenesis demonstrated that this sRNA, is a heterochromatic-siRNA (hc-siRNA) named as siRNA415. Hc-siRNAs are known to be involved in RNA-directed DNA methylation (RdDM). SiRNA415 is detected in several plant species. CONCLUSION Results here presented support a transcriptional regulatory mechanism underlying MIR168 expression. This finding highlights the importance of miRNA functioning in adaptive processes of Arabidopsis plants to fungal infection. The results of this study also lay a foundation for the involvement of RdDM processes through the activity of siRNA415 and miR823 in mediating regulation of immune responses in Arabidopsis plants.
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Affiliation(s)
- Patricia Baldrich
- />Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Bellaterra (Cerdanyola del Vallés), Campus UAB, 08193 Barcelona, Spain
| | - Klementina Kakar
- />Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Bellaterra (Cerdanyola del Vallés), Campus UAB, 08193 Barcelona, Spain
| | - Christelle Siré
- />Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Bellaterra (Cerdanyola del Vallés), Campus UAB, 08193 Barcelona, Spain
| | - Ana Beatriz Moreno
- />Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Bellaterra (Cerdanyola del Vallés), Campus UAB, 08193 Barcelona, Spain
| | - Angélique Berger
- />Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Bellaterra (Cerdanyola del Vallés), Campus UAB, 08193 Barcelona, Spain
| | - Meritxell García-Chapa
- />Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Bellaterra (Cerdanyola del Vallés), Campus UAB, 08193 Barcelona, Spain
| | - Juan José López-Moya
- />Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Bellaterra (Cerdanyola del Vallés), Campus UAB, 08193 Barcelona, Spain
| | - José Luis Riechmann
- />Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Bellaterra (Cerdanyola del Vallés), Campus UAB, 08193 Barcelona, Spain
- />Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Blanca San Segundo
- />Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Bellaterra (Cerdanyola del Vallés), Campus UAB, 08193 Barcelona, Spain
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