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Gao C, Zhao B, Zhang J, Du X, Wang J, Guo Y, He Y, Feng H, Huang L. Adaptive regulation of miRNAs/milRNAs in tissue-specific interaction between apple and Valsa mali. HORTICULTURE RESEARCH 2024; 11:uhae094. [PMID: 38799130 PMCID: PMC11116833 DOI: 10.1093/hr/uhae094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 03/25/2024] [Indexed: 05/29/2024]
Abstract
In plant-pathogen interactions, pathogens display tissue specificity, infecting and causing disease in particular tissues. However, the involvement of microRNAs/microRNA-like RNAs (miRNAs/milRNAs) in tissue-specific regulation during plant-pathogen interactions remains largely unexplored. This study investigates the differential expression of miRNAs/milRNAs, as well as their corresponding target genes, in interactions between Valsa mali (Vm) and different apple tissues. The results demonstrated that both apple miRNAs and Vm milRNAs exhibited distinct expression profiles when Vm infected bark and leaves, with functionally diverse corresponding target genes. Furthermore, one apple miRNA (Mdo-miR482a) and one Vm milRNA (Vm-milR57) were identified as exhibiting tissue-specific expression in interactions between Vm and apple bark or leaves. Mdo-miR482a was exclusively up-regulated in response to Vm infection in bark and target a nucleotide-binding leucine-rich repeat (NLR) gene of apple. When Mdo-miR482a was transiently over-expressed or silenced, the resistance was significantly reduced or improved. Similarly, transient expression of the NLR gene also showed an increase in resistance. Vm-milR57 could target two essential pathogenicity-related genes of Vm. During Vm infection in bark, the expression of Vm-milR57 was down-regulated to enhance the expression of the corresponding target gene to improve the pathogenicity. The study is the first to reveal tissue-specific characteristics of apple miRNAs and Vm milRNAs in interactions between Vm and different apple tissues, providing new insights into adaptive regulation in tissue-specific interactions between plants and fungi.
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Affiliation(s)
- Chengyu Gao
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Binsen Zhao
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jian Zhang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xuan Du
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jie Wang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yan Guo
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yanting He
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Hao Feng
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Lili Huang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
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Land ES, Sheppard J, Doherty CJ, Perera IY. Conserved plant transcriptional responses to microgravity from two consecutive spaceflight experiments. FRONTIERS IN PLANT SCIENCE 2024; 14:1308713. [PMID: 38259952 PMCID: PMC10800490 DOI: 10.3389/fpls.2023.1308713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 12/12/2023] [Indexed: 01/24/2024]
Abstract
Introduction Understanding how plants adapt to the space environment is essential, as plants will be a valuable component of long duration space missions. Several spaceflight experiments have focused on transcriptional profiling as a means of understanding plant adaptation to microgravity. However, there is limited overlap between results from different experiments. Differences in experimental conditions and hardware make it difficult to find a consistent response across experiments and to distinguish the primary effects of microgravity from other spaceflight effects. Methods Plant Signaling (PS) and Plant RNA Regulation (PRR) were two separate spaceflight experiments conducted on the International Space Station utilizing the European Modular Cultivation System (EMCS). The EMCS provided a lighted environment for plant growth with centrifugal capabilities providing an onboard 1 g control. Results and discussion An RNA-Seq analysis of shoot samples from PS and PRR revealed a significant overlap of genes differentially expressed in microgravity between the two experiments. Relative to onboard 1 g controls, genes involved in transcriptional regulation, shoot development, and response to auxin and light were upregulated in microgravity in both experiments. Conversely, genes involved in defense response, abiotic stress, Ca++ signaling, and cell wall modification were commonly downregulated in both datasets. The downregulation of stress responses in microgravity in these two experiments is interesting as these pathways have been previously observed as upregulated in spaceflight compared to ground controls. Similarly, we have observed many stress response genes to be upregulated in the 1 g onboard control compared to ground reference controls; however these genes were specifically downregulated in microgravity. In addition, we analyzed the sRNA landscape of the 1 g and microgravity (μ g) shoot samples from PRR. We identified three miRNAs (miR319c, miR398b, and miR8683) which were upregulated in microgravity, while several of their corresponding target genes were found to be downregulated in microgravity. Interestingly, the downregulated target genes are enriched in those encoding chloroplast-localized enzymes and proteins. These results uncover microgravity unique transcriptional changes and highlight the validity and importance of an onboard 1 g control.
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Affiliation(s)
- Eric S. Land
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - James Sheppard
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, United States
| | - Colleen J. Doherty
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, United States
| | - Imara Y. Perera
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
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Mehdi SMM, Krishnamoorthy S, Szczesniak MW, Ludwików A. Identification of Novel miRNAs and Their Target Genes in the Response to Abscisic Acid in Arabidopsis. Int J Mol Sci 2021; 22:7153. [PMID: 34281207 PMCID: PMC8268864 DOI: 10.3390/ijms22137153] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 06/23/2021] [Accepted: 06/28/2021] [Indexed: 12/12/2022] Open
Abstract
miRNAs are involved in various biological processes, including adaptive responses to abiotic stress. To understand the role of miRNAs in the response to ABA, ABA-responsive miRNAs were identified by small RNA sequencing in wild-type Arabidopsis, as well as in abi1td, mkkk17, and mkkk18 mutants. We identified 10 novel miRNAs in WT after ABA treatment, while in abi1td, mkkk17, and mkkk18 mutants, three, seven, and nine known miRNAs, respectively, were differentially expressed after ABA treatment. One novel miRNA (miRn-8) was differentially expressed in the mkkk17 mutant. Potential target genes of the miRNA panel were identified using psRNATarget. Sequencing results were validated by quantitative RT-PCR of several known and novel miRNAs in all genotypes. Of the predicted targets of novel miRNAs, seven target genes of six novel miRNAs were further validated by 5' RLM-RACE. Gene ontology analyses showed the potential target genes of ABA-responsive known and novel miRNAs to be involved in diverse cellular processes in plants, including development and stomatal movement. These outcomes suggest that a number of the identified miRNAs have crucial roles in plant responses to environmental stress, as well as in plant development, and might have common regulatory roles in the core ABA signaling pathway.
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Affiliation(s)
- Syed Muhammad Muntazir Mehdi
- Laboratory of Biotechnology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland; (S.M.M.M.); (S.K.)
| | - Sivakumar Krishnamoorthy
- Laboratory of Biotechnology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland; (S.M.M.M.); (S.K.)
| | - Michal Wojciech Szczesniak
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University in Poznan, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland;
| | - Agnieszka Ludwików
- Laboratory of Biotechnology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland; (S.M.M.M.); (S.K.)
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Roshan NM, Ashouri M, Sadeghi SM. Identification, evolution, expression analysis of phospholipase D (PLD) gene family in tea ( Camellia sinensis). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:1219-1232. [PMID: 34177145 PMCID: PMC8212259 DOI: 10.1007/s12298-021-01007-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 05/05/2021] [Accepted: 05/18/2021] [Indexed: 05/16/2023]
Abstract
UNLABELLED Phospholipase D (PLD) (EC 3.1.4.4) plays important roles in plants growth, development, and response to environmental stresses. Tea plant (Camellia sinensis) is the most important non-alcoholic beverage in the world with health benefits, but tea production decreases in response to environmental stresses such as cold and drought. Therefore, a genome-wide analysis of the C. sinensis PLD gene family (CsPLDs) was carried out. In the current study, identification, evolutionary relationship, duplication, selection pressure, gene structure, promoter analysis, transcript-targeted miRNA, and simple sequence repeat markers prediction, RNA-seq data analysis, and three-dimensional structure of the CsPLDs have been investigated using bioinformatics tools. 15 PLDs were identified from the tea genome which belongs to five groups, including CsPLDα, CsPLDβ, CsPLDδ, CsPLDε, and CsPLDζ. Both segmental and tandem duplications have occurred in the CsPLD gene family. Ka/Ks ratio for the most duplicated pair genes was less than 1 which implies negative selection to conserve their function during the tea evolution. 68 cis-elements have been found in CsPLDs indicating the contribution of these genes in response to environmental stresses. Likewise, 72 SSR loci and 96 miRNA molecules in 14 and 15 CsPLDs have been detected. According to RNA-seq data, the highest expression in all tissues under various abiotic stresses was related to CsPLDα1. Besides, a three-dimensional structure of the CsPLDα1 was evaluated to better understand its biological activity. This research provides comprehensive information that could be useful in future studies to develop stress-tolerant tea. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01007-0.
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Affiliation(s)
| | - Majid Ashouri
- Department of Agronomy and Plant Breeding, Lahijan Branch, Islamic Azad University, Lahijan, Iran
| | - Seyyed Mostafa Sadeghi
- Department of Agronomy and Plant Breeding, Lahijan Branch, Islamic Azad University, Lahijan, Iran
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Habermann K, Tiwari B, Krantz M, Adler SO, Klipp E, Arif MA, Frank W. Identification of small non-coding RNAs responsive to GUN1 and GUN5 related retrograde signals in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:138-155. [PMID: 32639635 DOI: 10.1111/tpj.14912] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 06/10/2020] [Accepted: 06/17/2020] [Indexed: 05/03/2023]
Abstract
Chloroplast perturbations activate retrograde signalling pathways, causing dynamic changes of gene expression. Besides transcriptional control of gene expression, different classes of small non-coding RNAs (sRNAs) act in gene expression control, but comprehensive analyses regarding their role in retrograde signalling are lacking. We performed sRNA profiling in response to norflurazon (NF), which provokes retrograde signals, in Arabidopsis thaliana wild type (WT) and the two retrograde signalling mutants gun1 and gun5. The RNA samples were also used for mRNA and long non-coding RNA profiling to link altered sRNA levels to changes in the expression of their cognate target RNAs. We identified 122 sRNAs from all known sRNA classes that were responsive to NF in the WT. Strikingly, 142 and 213 sRNAs were found to be differentially regulated in both mutants, indicating a retrograde control of these sRNAs. Concomitant with the changes in sRNA expression, we detected about 1500 differentially expressed mRNAs in the NF-treated WT and around 900 and 1400 mRNAs that were differentially regulated in the gun1 and gun5 mutants, with a high proportion (~30%) of genes encoding plastid proteins. Furthermore, around 20% of predicted miRNA targets code for plastid-localised proteins. Among the sRNA-target pairs, we identified pairs with an anticorrelated expression as well pairs showing other expressional relations, pointing to a role of sRNAs in balancing transcriptional changes upon retrograde signals. Based on the comprehensive changes in sRNA expression, we assume a considerable impact of sRNAs in retrograde-dependent transcriptional changes to adjust plastidic and nuclear gene expression.
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Affiliation(s)
- Kristin Habermann
- Plant Molecular Cell Biology, Department Biology I, Ludwig-Maximilians-Universität München, LMU Biocenter, Planegg-Martinsried, 82152, Germany
| | - Bhavika Tiwari
- Plant Molecular Cell Biology, Department Biology I, Ludwig-Maximilians-Universität München, LMU Biocenter, Planegg-Martinsried, 82152, Germany
| | - Maria Krantz
- Department Biologie, Bereich Theoretische Biophysik, Humboldt-Universität Berlin, Berlin, 10115, Germany
| | - Stephan O Adler
- Department Biologie, Bereich Theoretische Biophysik, Humboldt-Universität Berlin, Berlin, 10115, Germany
| | - Edda Klipp
- Department Biologie, Bereich Theoretische Biophysik, Humboldt-Universität Berlin, Berlin, 10115, Germany
| | - M Asif Arif
- Plant Molecular Cell Biology, Department Biology I, Ludwig-Maximilians-Universität München, LMU Biocenter, Planegg-Martinsried, 82152, Germany
| | - Wolfgang Frank
- Plant Molecular Cell Biology, Department Biology I, Ludwig-Maximilians-Universität München, LMU Biocenter, Planegg-Martinsried, 82152, Germany
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Liu XX, Luo XF, Luo KX, Liu YL, Pan T, Li ZZ, Duns GJ, He FL, Qin ZD. Small RNA sequencing reveals dynamic microRNA expression of important nutrient metabolism during development of Camellia oleifera fruit. Int J Biol Sci 2019; 15:416-429. [PMID: 30745831 PMCID: PMC6367553 DOI: 10.7150/ijbs.26884] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 11/10/2018] [Indexed: 12/13/2022] Open
Abstract
To obtain insight into the function of miRNAs in the synthesis and storage of important nutrients during the development of Camellia oleifera fruit, Illumina sequencing of flower and fruit small-RNA was conducted. The results revealed that 797 miRNAs were significantly differentially expressed between flower and fruit samples of Camellia oleifera. Through integrated GO and KEGG function annotations, it was determined that the miRNA target genes were mainly involved in metabolic pathways, plant hormone signal transduction, fruit development, mitosis and regulation of biosynthetic processes. Carbohydrate accumulation genes were differentially regulated by miR156, miR390 and miR395 in the fruit growth and development process. MiR477 is the key miRNA functioning in regulation of genes and involved in fatty acid synthesis. Additionally, miR156 also has the function of regulating glycolysis and nutrient transformation genes.
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Affiliation(s)
- Xiao-Xia Liu
- Key Laboratory of Comprehensive Utilization of Advantage Plants Resources in Hunan South, Hunan Provincial Engineering Research Center for Ginkgo biloba, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou 425100, China
| | - Xiao-Fang Luo
- Key Laboratory of Comprehensive Utilization of Advantage Plants Resources in Hunan South, Hunan Provincial Engineering Research Center for Ginkgo biloba, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou 425100, China
| | - Ke-Xin Luo
- Key Laboratory of Comprehensive Utilization of Advantage Plants Resources in Hunan South, Hunan Provincial Engineering Research Center for Ginkgo biloba, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou 425100, China
| | - Ya-Lin Liu
- Key Laboratory of Comprehensive Utilization of Advantage Plants Resources in Hunan South, Hunan Provincial Engineering Research Center for Ginkgo biloba, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou 425100, China
| | - Ting Pan
- Key Laboratory of Comprehensive Utilization of Advantage Plants Resources in Hunan South, Hunan Provincial Engineering Research Center for Ginkgo biloba, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou 425100, China
| | - Zhi-Zhang Li
- Key Laboratory of Comprehensive Utilization of Advantage Plants Resources in Hunan South, Hunan Provincial Engineering Research Center for Ginkgo biloba, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou 425100, China
| | - Gregory J Duns
- Key Laboratory of Comprehensive Utilization of Advantage Plants Resources in Hunan South, Hunan Provincial Engineering Research Center for Ginkgo biloba, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou 425100, China
| | - Fu-Lin He
- Key Laboratory of Comprehensive Utilization of Advantage Plants Resources in Hunan South, Hunan Provincial Engineering Research Center for Ginkgo biloba, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou 425100, China
| | - Zuo-Dong Qin
- Key Laboratory of Comprehensive Utilization of Advantage Plants Resources in Hunan South, Hunan Provincial Engineering Research Center for Ginkgo biloba, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou 425100, China
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Genome-wide exploration of metal tolerance protein (MTP) genes in common wheat (Triticum aestivum): insights into metal homeostasis and biofortification. Biometals 2017; 30:217-235. [PMID: 28150142 DOI: 10.1007/s10534-017-9997-x] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 01/21/2017] [Indexed: 10/20/2022]
Abstract
Metal transport process in plants is a determinant of quality and quantity of the harvest. Although it is among the most important of staple crops, knowledge about genes that encode for membrane-bound metal transporters is scarce in wheat. Metal tolerance proteins (MTPs) are involved in trace metal homeostasis at the sub-cellular level, usually by providing metal efflux out of the cytosol. Here, by using various bioinformatics approaches, genes that encode for MTPs in the hexaploid wheat genome (Triticum aestivum, abbreviated as Ta) were identified and characterized. Based on the comparison with known rice MTPs, the wheat genome contained 20 MTP sequences; named as TaMTP1-8A, B and D. All TaMTPs contained a cation diffusion facilitator (CDF) family domain and most members harbored a zinc transporter dimerization domain. Based on motif, phylogeny and alignment analysis, A, B and D genomes of TaMTP3-7 sequences demonstrated higher homology compared to TaMTP1, 2 and 8. With reference to their rice orthologs, TaMTP1s and TaMTP8s belonged to Zn-CDFs, TaMTP2s to Fe/Zn-CDFs and TaMTP3-7s to Mn-CDFs. Upstream regions of TaMTP genes included diverse cis-regulatory motifs, indicating regulation by developmental stage, tissue type and stresses. A scan of the coding sequences of 20 TaMTPs against published miRNAs predicted a total of 14 potential miRNAs, mainly targeting the members of most diverged groups. Expression analysis showed that several TaMTPs were temporally and spatially regulated during the developmental time-course. In grains, MTPs were preferentially expressed in the aleurone layer, which is known as a reservoir for high concentrations of iron and zinc. The work identified and characterized metal tolerance proteins in common wheat and revealed a potential involvement of MTPs in providing a sink for trace element storage in wheat grains.
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Liu WW, Meng J, Cui J, Luan YS. Characterization and Function of MicroRNA ∗s in Plants. FRONTIERS IN PLANT SCIENCE 2017; 8:2200. [PMID: 29312425 PMCID: PMC5744440 DOI: 10.3389/fpls.2017.02200] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 12/14/2017] [Indexed: 05/20/2023]
Abstract
MicroRNAs, a group of non-coding RNA molecules, play essential roles in a wide range of cellular processes in different molecules, cells, and organisms. In plants, microRNAs are a class of 20- to 24-nucleotides endogenous small RNAs that repress gene expression. The microRNA guide strand (miRNA) and its complementary strand (miRNA∗) both originate from the miRNA/miRNA∗ duplex. Generally, the guide strands act as post-transcriptional regulators that suppress gene expression by cleaving their target mRNA transcripts, whereas the complementary strands were thought to be degraded as 'passenger strands.' However, the complementary strand has been confirmed to possess significant biological functionality in recent reports. In this review, we summarized the binding characteristics of the miRNA∗ strands with ARGONAUTE proteins, their tissue-specific accumulations and their biological functions, illustrating the essential roles of miRNA∗s in biological processes and therefore providing directions for further exploration.
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Affiliation(s)
- Wei-wei Liu
- School of Life Sciences and Biotechnology, Dalian University of Technology, Dalian, China
| | - Jun Meng
- School of Computer Science and Technology, Dalian University of Technology, Dalian, China
- *Correspondence: Jun Meng, Yu-shi Luan,
| | - Jun Cui
- School of Life Sciences and Biotechnology, Dalian University of Technology, Dalian, China
| | - Yu-shi Luan
- School of Life Sciences and Biotechnology, Dalian University of Technology, Dalian, China
- *Correspondence: Jun Meng, Yu-shi Luan,
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Achkar NP, Cambiagno DA, Manavella PA. miRNA Biogenesis: A Dynamic Pathway. TRENDS IN PLANT SCIENCE 2016; 21:1034-1044. [PMID: 27793495 DOI: 10.1016/j.tplants.2016.09.003] [Citation(s) in RCA: 169] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 09/14/2016] [Accepted: 09/26/2016] [Indexed: 05/18/2023]
Abstract
MicroRNAs (miRNAs) modulate plant homeostasis through the inactivation of specific mRNAs, especially those encoding transcription factors. A delicate spatial/temporal balance between a miRNA and its targets is central to achieving the appropriate biological outcomes. In this review we discuss our growing understanding of the dynamic regulation of miRNA biogenesis. We put special emphasis on crosstalk between miRNA biogenesis and other cellular processes such as transcription and splicing. We also discuss how the pathway is regulated in specific tissues to achieve harmonious plant development through a subtle balance between gene expression and silencing.
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Affiliation(s)
- Natalia P Achkar
- Instituto de Agrobiotecnología del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Facultad de Bioquímica y Ciencias Biológicas (FBCB), Universidad Nacional del Litoral (UNL), Paraje El Pozo, 3000 Santa Fe, Argentina
| | - Damián A Cambiagno
- Instituto de Agrobiotecnología del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Facultad de Bioquímica y Ciencias Biológicas (FBCB), Universidad Nacional del Litoral (UNL), Paraje El Pozo, 3000 Santa Fe, Argentina
| | - Pablo A Manavella
- Instituto de Agrobiotecnología del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Facultad de Bioquímica y Ciencias Biológicas (FBCB), Universidad Nacional del Litoral (UNL), Paraje El Pozo, 3000 Santa Fe, Argentina.
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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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Yu L, Shao C, Ye X, Meng Y, Zhou Y, Chen M. miRNA Digger: a comprehensive pipeline for genome-wide novel miRNA mining. Sci Rep 2016; 6:18901. [PMID: 26732371 PMCID: PMC4702050 DOI: 10.1038/srep18901] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 11/27/2015] [Indexed: 11/09/2022] Open
Abstract
MicroRNAs (miRNAs) are important regulators of gene expression. The recent advances in high-throughput sequencing (HTS) technique have greatly facilitated large-scale detection of the miRNAs. However, thoroughly discovery of novel miRNAs from the available HTS data sets remains a major challenge. In this study, we observed that Dicer-mediated cleavage sites for the processing of the miRNA precursors could be mapped by using degradome sequencing data in both animals and plants. In this regard, a novel tool, miRNA Digger, was developed for systematical discovery of miRNA candidates through genome-wide screening of cleavage signals based on degradome sequencing data. To test its sensitivity and reliability, miRNA Digger was applied to discover miRNAs from four organs of Arabidopsis. The results revealed that a majority of already known mature miRNAs along with their miRNA*s expressed in these four organs were successfully recovered. Notably, a total of 30 novel miRNA-miRNA* pairs that have not been registered in miRBase were discovered by miRNA Digger. After target prediction and degradome sequencing data-based validation, eleven miRNA-target interactions involving six of the novel miRNAs were identified. Taken together, miRNA Digger could be applied for sensitive detection of novel miRNAs and it could be freely downloaded from http://www.bioinfolab.cn/miRNA_Digger/index.html.
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Affiliation(s)
- Lan Yu
- College of Life Sciences, Huzhou University, Huzhou 313000, P.R. China
| | - Chaogang Shao
- College of Life Sciences, Huzhou University, Huzhou 313000, P.R. China
| | - Xinghuo Ye
- College of Life Sciences, Huzhou University, Huzhou 313000, P.R. China
| | - Yijun Meng
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, P.R. China
| | - Yincong Zhou
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, P. R. China
| | - Ming Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, P. R. China
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Thatcher SR, Burd S, Wright C, Lers A, Green PJ. Differential expression of miRNAs and their target genes in senescing leaves and siliques: insights from deep sequencing of small RNAs and cleaved target RNAs. PLANT, CELL & ENVIRONMENT 2015; 38:188-200. [PMID: 24965556 PMCID: PMC4304344 DOI: 10.1111/pce.12393] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Accepted: 06/06/2014] [Indexed: 05/03/2023]
Abstract
MicroRNAs (miRNAs) are a class of small RNAs, which typically function by guiding cleavage of target mRNAs. They are known to play roles in a variety of plant processes including development, responses to environmental stresses and senescence. To identify senescence regulation of miRNAs in Arabidopsis thaliana, eight small RNA libraries were constructed and sequenced at four different stages of development and senescence from both leaves and siliques, resulting in more than 200 million genome-matched sequences. Parallel analysis of RNA ends libraries, which enable the large-scale examination of miRNA-guided cleavage products, were constructed and sequenced, resulting in over 750 million genome-matched sequences. These large datasets led to the identification a new senescence-inducible small RNA locus, as well as new regulation of known miRNAs and their target genes during senescence, many of which have established roles in nutrient responsiveness and cell structural integrity. In keeping with remobilization of nutrients thought to occur during senescence, many miRNAs and targets had opposite expression pattern changes between leaf and silique tissues during the progression of senescence. Taken together, these findings highlight the integral role that miRNAs may play in the remobilization of resources and alteration of cellular structure that is known to occur in senescence.
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Affiliation(s)
- Shawn R Thatcher
- Delaware Biotechnology Institute, University of Delaware, Newark, DE, 19711, USA
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13
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Sorin C, Declerck M, Christ A, Blein T, Ma L, Lelandais-Brière C, Njo MF, Beeckman T, Crespi M, Hartmann C. A miR169 isoform regulates specific NF-YA targets and root architecture in Arabidopsis. THE NEW PHYTOLOGIST 2014; 202:1197-1211. [PMID: 24533947 DOI: 10.1111/nph.12735] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 01/21/2014] [Indexed: 05/20/2023]
Abstract
In plants, roots are essential for water and nutrient acquisition. MicroRNAs (miRNAs) regulate their target mRNAs by transcript cleavage and/or inhibition of protein translation and are known as major post-transcriptional regulators of various developmental pathways and stress responses. In Arabidopsis thaliana, four isoforms of miR169 are encoded by 14 different genes and target diverse mRNAs, encoding subunits A of the NF-Y transcription factor complex. These miRNA isoforms and their targets have previously been linked to nutrient signalling in plants. By using mimicry constructs against different isoforms of miR169 and miR-resistant versions of NF-YA genes we analysed the role of specific miR169 isoforms in root growth and branching. We identified a regulatory node involving the particular miR169defg isoform and NF-YA2 and NF-YA10 genes that acts in the control of primary root growth. The specific expression of MIM169defg constructs altered specific cell type numbers and dimensions in the root meristem. Preventing miR169defg-regulation of NF-YA2 indirectly affected laterial root initiation. We also showed that the miR169defg isoform affects NF-YA2 transcripts both at mRNA stability and translation levels. We propose that a specific miR169 isoform and the NF-YA2 target control root architecture in Arabidopsis.
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Affiliation(s)
- Céline Sorin
- Institut des Sciences du Végétal (ISV), CNRS, UPR2355, Saclay Plant Sciences, F-91198, Gif-sur-Yvette Cedex, France
- Université Paris Diderot, Sorbonne Paris Cité, F-75205, Paris Cedex 13, France
| | - Marie Declerck
- Institut des Sciences du Végétal (ISV), CNRS, UPR2355, Saclay Plant Sciences, F-91198, Gif-sur-Yvette Cedex, France
| | - Aurélie Christ
- Institut des Sciences du Végétal (ISV), CNRS, UPR2355, Saclay Plant Sciences, F-91198, Gif-sur-Yvette Cedex, France
| | - Thomas Blein
- Institut des Sciences du Végétal (ISV), CNRS, UPR2355, Saclay Plant Sciences, F-91198, Gif-sur-Yvette Cedex, France
- INRA, Institut JP Bourgin, Route de Saint-Cyr, 78026, Versailles Cedex, France
| | - Linnan Ma
- Institut des Sciences du Végétal (ISV), CNRS, UPR2355, Saclay Plant Sciences, F-91198, Gif-sur-Yvette Cedex, France
| | - Christine Lelandais-Brière
- Institut des Sciences du Végétal (ISV), CNRS, UPR2355, Saclay Plant Sciences, F-91198, Gif-sur-Yvette Cedex, France
- Université Paris Diderot, Sorbonne Paris Cité, F-75205, Paris Cedex 13, France
| | - Maria Fransiska Njo
- Department of Plant Systems Biology, Flanders Institute for Biotechnology, Technologiepark 927, 9052, Ghent, Belgium
- Department Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | - Tom Beeckman
- Department of Plant Systems Biology, Flanders Institute for Biotechnology, Technologiepark 927, 9052, Ghent, Belgium
- Department Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | - Martin Crespi
- Institut des Sciences du Végétal (ISV), CNRS, UPR2355, Saclay Plant Sciences, F-91198, Gif-sur-Yvette Cedex, France
| | - Caroline Hartmann
- Institut des Sciences du Végétal (ISV), CNRS, UPR2355, Saclay Plant Sciences, F-91198, Gif-sur-Yvette Cedex, France
- Université Paris Diderot, Sorbonne Paris Cité, F-75205, Paris Cedex 13, France
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14
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Patra D, Fasold M, Langenberger D, Steger G, Grosse I, Stadler PF. plantDARIO: web based quantitative and qualitative analysis of small RNA-seq data in plants. FRONTIERS IN PLANT SCIENCE 2014; 5:708. [PMID: 25566282 PMCID: PMC4274896 DOI: 10.3389/fpls.2014.00708] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 11/26/2014] [Indexed: 05/11/2023]
Abstract
High-throughput sequencing techniques have made it possible to assay an organism's entire repertoire of small non-coding RNAs (ncRNAs) in an efficient and cost-effective manner. The moderate size of small RNA-seq datasets makes it feasible to provide free web services to the research community that provide many basic features of a small RNA-seq analysis, including quality control, read normalization, ncRNA quantification, and the prediction of putative novel ncRNAs. DARIO is one such system that so far has been focussed on animals. Here we introduce an extension of this system to plant short non-coding RNAs (sncRNAs). It includes major modifications to cope with plant-specific sncRNA processing. The current version of plantDARIO covers analyses of mapping files, small RNA-seq quality control, expression analyses of annotated sncRNAs, including the prediction of novel miRNAs and snoRNAs from unknown expressed loci and expression analyses of user-defined loci. At present Arabidopsis thaliana, Beta vulgaris, and Solanum lycopersicum are covered. The web tool links to a plant specific visualization browser to display the read distribution of the analyzed sample. The easy-to-use platform of plantDARIO quantifies RNA expression of annotated sncRNAs from different sncRNA databases together with new sncRNAs, annotated by our group. The plantDARIO website can be accessed at http://plantdario.bioinf.uni-leipzig.de/.
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Affiliation(s)
- Deblina Patra
- Institut für Informatik, Martin-Luther-Universität Halle-WittenbergHalle (Saale), Germany
- Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University LeipzigLeipzig, Germany
| | - Mario Fasold
- Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University LeipzigLeipzig, Germany
- ecSeq BioinformaticsLeipzig, Germany
| | - David Langenberger
- Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University LeipzigLeipzig, Germany
- ecSeq BioinformaticsLeipzig, Germany
| | - Gerhard Steger
- Institut für Pysikalische Biologie, Heinrich-Heine-UniversitätDüsseldorf, Germany
| | - Ivo Grosse
- Institut für Informatik, Martin-Luther-Universität Halle-WittenbergHalle (Saale), Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-LeipzigLeipzig, Germany
| | - Peter F. Stadler
- Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University LeipzigLeipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-LeipzigLeipzig, Germany
- Max Planck Institute for Mathematics in the SciencesLeipzig, Germany
- Fraunhofer Institute for Cell Therapy and ImmunologyLeipzig, Germany
- Department of Theoretical Chemistry of the University of ViennaVienna, Austria
- Center for RNA in Technology and Health, University of CopenhagenFrederiksberg, Denmark
- Santa Fe InstituteSanta Fe, USA
- *Correspondence: Peter F. Stadler, Bioinformatics Group, Department of Computer Science, University Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany e-mail:
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Jeong DH, Thatcher SR, Brown RS, Zhai J, Park S, Rymarquis LA, Meyers BC, Green PJ. Comprehensive investigation of microRNAs enhanced by analysis of sequence variants, expression patterns, ARGONAUTE loading, and target cleavage. PLANT PHYSIOLOGY 2013; 162:1225-45. [PMID: 23709668 PMCID: PMC3707554 DOI: 10.1104/pp.113.219873] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
MicroRNAs (miRNAs) are a class of small RNAs that typically function by guiding the cleavage of target messenger RNAs. They have been shown to play major roles in a variety of plant processes, including development, and responses to pathogens and environmental stresses. To identify new miRNAs and regulation in Arabidopsis (Arabidopsis thaliana), 27 small RNA libraries were constructed and sequenced from various tissues, stresses, and small RNA biogenesis mutants, resulting in 95 million genome-matched sequences. The use of rdr2 to enrich the miRNA population greatly enhanced this analysis and led to the discovery of new miRNAs arising from both known and new precursors, increasing the total number of Arabidopsis miRNAs by about 10%. Parallel Analysis of RNA Ends data provide evidence that the majority guide target cleavage. Many libraries represented novel stress/tissue conditions, such as submergence-stressed flowers, which enabled the identification of new stress regulation of both miRNAs and their targets, all of which were validated in wild-type plants. By combining small RNA expression analysis with ARGONAUTE immunoprecipitation data and global target cleavage data from Parallel Analysis of RNA Ends, a much more complete picture of Arabidopsis miRNAs was obtained. In particular, the discovery of ARGONAUTE loading and target cleavage biases gave important insights into tissue-specific expression patterns, pathogen responses, and the role of sequence variation among closely related miRNA family members that would not be evident without this combinatorial approach.
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