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Zimmerman K, Pegler JL, Oultram JMJ, Collings DA, Wang MB, Grof CPL, Eamens AL. Molecular Manipulation of the miR160/ AUXIN RESPONSE FACTOR Expression Module Impacts Root Development in Arabidopsis thaliana. Genes (Basel) 2024; 15:1042. [PMID: 39202402 PMCID: PMC11353855 DOI: 10.3390/genes15081042] [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: 07/07/2024] [Revised: 07/31/2024] [Accepted: 08/05/2024] [Indexed: 09/03/2024] Open
Abstract
In Arabidopsis thaliana (Arabidopsis), microRNA160 (miR160) regulates the expression of AUXIN RESPONSE FACTOR10 (ARF10), ARF16 and ARF17 throughout development, including the development of the root system. We have previously shown that in addition to DOUBLE-STRANDED RNA BINDING1 (DRB1), DRB2 is also involved in controlling the rate of production of specific miRNA cohorts in the tissues where DRB2 is expressed in wild-type Arabidopsis plants. In this study, a miR160 overexpression transgene (MIR160B) and miR160-resistant transgene versions of ARF10 and ARF16 (mARF10 and mARF16) were introduced into wild-type Arabidopsis plants and the drb1 and drb2 single mutants to determine the degree of requirement of DRB2 to regulate the miR160 expression module as part of root development. Via this molecular modification approach, we show that in addition to DRB1, DRB2 is required to regulate the level of miR160 production from its precursor transcripts in Arabidopsis roots. Furthermore, we go on to correlate the altered abundance of miR160 or its ARF10, ARF16 and ARF17 target genes in the generated series of transformant lines with the enhanced development of the root system displayed by these plant lines. More specifically, promotion of primary root elongation likely stemmed from enhancement of miR160-directed ARF17 expression repression, while the promotion of lateral and adventitious root formation was the result of an elevated degree of miR160-directed regulation of ARF17 expression, and to a lesser degree, ARF10 and ARF16 expression. Taken together, the results presented in this study identify the requirement of the functional interplay between DRB1 and DRB2 to tightly control the rate of miR160 production, to in turn ensure the appropriate degree of miR160-directed ARF10, ARF16 and ARF17 gene expression regulation as part of normal root system development in Arabidopsis.
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Affiliation(s)
- Kim Zimmerman
- Centre for Plant Science, School of Environmental and Life Sciences, College of Engineering, Science and Environment University of Newcastle, Callaghan, NSW 2308, Australia; (K.Z.); (J.L.P.); (J.M.J.O.); (D.A.C.); (C.P.L.G.)
| | - Joseph L. Pegler
- Centre for Plant Science, School of Environmental and Life Sciences, College of Engineering, Science and Environment University of Newcastle, Callaghan, NSW 2308, Australia; (K.Z.); (J.L.P.); (J.M.J.O.); (D.A.C.); (C.P.L.G.)
| | - Jackson M. J. Oultram
- Centre for Plant Science, School of Environmental and Life Sciences, College of Engineering, Science and Environment University of Newcastle, Callaghan, NSW 2308, Australia; (K.Z.); (J.L.P.); (J.M.J.O.); (D.A.C.); (C.P.L.G.)
| | - David A. Collings
- Centre for Plant Science, School of Environmental and Life Sciences, College of Engineering, Science and Environment University of Newcastle, Callaghan, NSW 2308, Australia; (K.Z.); (J.L.P.); (J.M.J.O.); (D.A.C.); (C.P.L.G.)
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - Ming-Bo Wang
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia;
| | - Christopher P. L. Grof
- Centre for Plant Science, School of Environmental and Life Sciences, College of Engineering, Science and Environment University of Newcastle, Callaghan, NSW 2308, Australia; (K.Z.); (J.L.P.); (J.M.J.O.); (D.A.C.); (C.P.L.G.)
- School of Agriculture and Food Sustainability, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Andrew L. Eamens
- Seaweed Research Group, School of Health, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia
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Pegler JL, Oultram JMJ, Mann CWG, Carroll BJ, Grof CPL, Eamens AL. Miniature Inverted-Repeat Transposable Elements: Small DNA Transposons That Have Contributed to Plant MICRORNA Gene Evolution. PLANTS (BASEL, SWITZERLAND) 2023; 12:1101. [PMID: 36903960 PMCID: PMC10004981 DOI: 10.3390/plants12051101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 02/23/2023] [Accepted: 02/24/2023] [Indexed: 06/18/2023]
Abstract
Angiosperms form the largest phylum within the Plantae kingdom and show remarkable genetic variation due to the considerable difference in the nuclear genome size of each species. Transposable elements (TEs), mobile DNA sequences that can amplify and change their chromosome position, account for much of the difference in nuclear genome size between individual angiosperm species. Considering the dramatic consequences of TE movement, including the complete loss of gene function, it is unsurprising that the angiosperms have developed elegant molecular strategies to control TE amplification and movement. Specifically, the RNA-directed DNA methylation (RdDM) pathway, directed by the repeat-associated small-interfering RNA (rasiRNA) class of small regulatory RNA, forms the primary line of defense to control TE activity in the angiosperms. However, the miniature inverted-repeat transposable element (MITE) species of TE has at times avoided the repressive effects imposed by the rasiRNA-directed RdDM pathway. MITE proliferation in angiosperm nuclear genomes is due to their preference to transpose within gene-rich regions, a pattern of transposition that has enabled MITEs to gain further transcriptional activity. The sequence-based properties of a MITE results in the synthesis of a noncoding RNA (ncRNA), which, after transcription, folds to form a structure that closely resembles those of the precursor transcripts of the microRNA (miRNA) class of small regulatory RNA. This shared folding structure results in a MITE-derived miRNA being processed from the MITE-transcribed ncRNA, and post-maturation, the MITE-derived miRNA can be used by the core protein machinery of the miRNA pathway to regulate the expression of protein-coding genes that harbor homologous MITE insertions. Here, we outline the considerable contribution that the MITE species of TE have made to expanding the miRNA repertoire of the angiosperms.
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Affiliation(s)
- Joseph L. Pegler
- Centre for Plant Science, School of Environmental and Life Sciences, College of Engineering, Science and Environment, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Jackson M. J. Oultram
- Centre for Plant Science, School of Environmental and Life Sciences, College of Engineering, Science and Environment, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Christopher W. G. Mann
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Bernard J. Carroll
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Christopher P. L. Grof
- Centre for Plant Science, School of Environmental and Life Sciences, College of Engineering, Science and Environment, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Andrew L. Eamens
- School of Health, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia
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Pegler JL, Grof CPL, Eamens AL. The Plant microRNA Pathway: The Production and Action Stages. Methods Mol Biol 2019; 1932:15-39. [PMID: 30701489 DOI: 10.1007/978-1-4939-9042-9_2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Plant microRNAs are an endogenous class of small regulatory RNA central to the posttranscriptional regulation of gene expression in plant development and environmental stress adaptation or in response to pathogen challenge. The plant microRNA pathway is readily separated into two distinct stages: (1) the production stage, which is localized to the plant cell nucleus and where the microRNA small RNA is processed from a double-stranded RNA precursor transcript, and (2) the action stage, which is localized to the plant cell cytoplasm and where the mature microRNA small RNA is loaded into an effector complex and is used by the complex as a sequence specificity guide to direct expression repression of target genes harboring highly complementary microRNA target sequences. Historical research indicated that the plant microRNA pathway was a highly structured, almost linear pathway requiring a small set of core machinery proteins. However, contemporary research has demonstrated that the plant microRNA pathway is highly dynamic, and to allow for this flexibility, a large and highly functionally diverse set of machinery proteins is now known to be required. For example, recent research has shown that plant microRNAs can regulate target gene expression via a translational repression mechanism of RNA silencing in addition to the standard messenger RNA cleavage-based mechanism of RNA silencing: a mode of RNA silencing originally assigned to all plant microRNAs. Using Arabidopsis thaliana as our model system, here we report on both the core and auxiliary sets of machinery proteins now known to be required for both microRNA production and microRNA action in plants.
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Affiliation(s)
- Joseph L Pegler
- Faculty of Science, Centre for Plant Science, School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, Australia
| | - Christopher P L Grof
- Faculty of Science, Centre for Plant Science, School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, Australia
| | - Andrew L Eamens
- Faculty of Science, Centre for Plant Science, School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, Australia.
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MicroRNA expression profiles during cotton (Gossypium hirsutum L) fiber early development. Sci Rep 2017; 7:44454. [PMID: 28327647 PMCID: PMC5361117 DOI: 10.1038/srep44454] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 02/08/2017] [Indexed: 12/24/2022] Open
Abstract
The role of microRNAs (miRNAs) during cotton fiber development remains unclear. Here, a total of 54 miRNAs belonging to 39 families were selected to characterize miRNA regulatory mechanism in eight different fiber development stages in upland cotton cv BM-1. Among 54 miRNAs, 18 miRNAs were involved in cotton fiber initiation and eight miRNAs were related to fiber elongation and secondary wall biosynthesis. Additionally, 3,576 protein-coding genes were candidate target genes of these miRNAs, which are potentially involved in cotton fiber development. We also investigated the regulatory network of miRNAs and corresponding targets in fiber initiation and elongation, and secondary wall formation. Our Gene Ontology-based term classification and KEGG-based pathway enrichment analyses showed that the miRNA targets covered 220 biological processes, 67 molecular functions, 45 cellular components, and 10 KEGG pathways. Three of ten KEGG pathways were involved in lignan synthesis, cell elongation, and fatty acid biosynthesis, all of which have important roles in fiber development. Overall, our study shows the potential regulatory roles of miRNAs in cotton fiber development and the importance of miRNAs in regulating different cell types. This is helpful to design miRNA-based biotechnology for improving fiber quality and yield.
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Sun XH, Zhao LP, Zou Q, Wang ZB. Identification of microRNA genes and their mRNA targets in Festuca arundinacea. Appl Biochem Biotechnol 2014; 172:3875-87. [PMID: 24577674 DOI: 10.1007/s12010-014-0805-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 02/12/2014] [Indexed: 01/26/2023]
Abstract
MicroRNAs (miRNAs) have emerged as a novel class of endogenous, small, non-coding RNAs of 22 nucleotides (nts) in length, which plays important roles in post-transcriptional degradation of target mRNA or inhibition of protein synthesis through binding the specific sites of target mRNA. Growing evidences have shown that miRNAs play an important role in various biological processes, including growth and development, signal transduction, apoptosis, proliferation, stress responses, maintenance of genome stability, and so on. In our study, we used bioinformatic tools to predict miRNA and the corresponding target genes of Festuca arundinacea. We used known miRNAs of other plants from miRBase to search against expressed sequence tags (EST) databases and genome survey sequences (GSS) of F. arundinacea. A total of 8 potential miRNAs were predicted. Phylogenetic analysis of the predicted miRNAs revealed that miRNA398c of F. arundinacea species was evolutionary highly conserved with Populus trichocarpa. The 8 potential miRNAs corresponding to 20 target genes were found. Most of the miRNA target genes were predicted to encode transcription factors that regulate cell growth and development, signaling, metabolism, and other biology processes. By bioinformatics methods, we can effectively predict novel miRNAs and its target genes and add information to F. arundinacea miRNA database. Moreover, it shows a path for the prediction and analysis of miRNAs to those species whose genomes are not available through bioinformatics tools.
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Affiliation(s)
- Xi Hong Sun
- Animal Science and Technology College, Henan University of Science and Technology, Luoyang City, 471003, Henan Province, People's Republic of China
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Abstract
RNA interference, or RNAi, is arguably one of the most significant discoveries in biology in the last several decades. First recognized in plants (where it was called post-transcriptional gene silencing, PTGS) RNAi is a gene down-regulation mechanism since demonstrated to exist in all eukaryotes. In RNAi, small RNAs (of about 21-24 nucleotides) function to guide specific effector proteins (members of the Argonaute protein family) to a target nucleotide sequence by complementary base pairing. The effector protein complex then down-regulates the expression of the targeted RNA or DNA. Small RNA-directed gene regulation systems were independently discovered (and named) in plants, fungi, worms, flies, and mammalian cells. Collectively, PTGS, RNA silencing, and co-suppression (in plants); quelling (in fungi and algae); and RNAi (in Caenorhabditis elegans, Drosophila, and mammalian cells) are all examples of small RNA-based gene regulation systems. From the very beginning, plant research has had a major impact on our understanding of RNAi. The purpose of this chapter is to provide an historical perspective and overview on the discovery, characterization, and applications of RNAi in plants.
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Affiliation(s)
- John A Lindbo
- Campbell's Seeds, Campbells Soup Company, R&D, Davis, CA, USA.
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Dalakouras A, Tzanopoulou M, Tsagris M, Wassenegger M, Kalantidis K. Hairpin transcription does not necessarily lead to efficient triggering of the RNAi pathway. Transgenic Res 2011; 20:293-304. [PMID: 20582569 DOI: 10.1007/s11248-010-9416-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2010] [Accepted: 06/04/2010] [Indexed: 11/30/2022]
Abstract
Previously, we had shown that stable expression of a hairpin RNA sharing homology with the coat protein (CP) of the Cucumber mosaic virus (CMV) (hpRNA(CMV)) produced CMV resistant Nicotiana tabacum plants. However, only 17% of the hpRNA(CMV)-expressing plants generated substantial amounts of siRNAs that mediated CMV resistance (siRNAs(CMV)). Here, we demonstrate that the transcription of a hpRNA(CMV) per se is not sufficient to trigger cytoplasmic and nuclear RNAi. A multiple-transgene copy line showed a strong resistance phenotype. Segregation of individual copies revealed that in one locus, the transgene-produced hpRNA(CMV) transcript was processed into 21-nt and 24-nt siRNAs(CMV) and lines containing this locus were resistant. At a second locus, where the transgene was shown to be transcribed, no siRNAs(CMV) were produced and lines harbouring only this locus were susceptible. In addition, the second locus failed to trigger de novo RNA-directed DNA methylation (RdDM) in cis, of its cognate sequence. However, after being induced in trans, methylation in the transcribed region of the transgene was maintained in both CG and CHG residues. Sequence-specific maintenance of methylation in transcribed regions, as well as diverse RNA degradation pathways in plants are discussed in view of our observations.
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Affiliation(s)
- Athanasios Dalakouras
- RLP AgroScience GmbH, AlPlanta-Institute for Plant Research, 67435, Neustadt, Germany
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Ruan MB, Zhao YT, Meng ZH, Wang XJ, Yang WC. Conserved miRNA analysis in Gossypium hirsutum through small RNA sequencing. Genomics 2009; 94:263-8. [PMID: 19628031 DOI: 10.1016/j.ygeno.2009.07.002] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2009] [Revised: 06/09/2009] [Accepted: 07/12/2009] [Indexed: 12/20/2022]
Abstract
Several miRNA family and their targets in cotton had been identified by computational methods based on the conserved characterization of miRNAs. So far, there are no experiments to validate the existence of miRNAs in cotton. In this study, to analyze the miRNAs in cotton, a small RNA library of sequences from 18 to 26 nt of Gossypium hirsutum seedling has been built by high-throughput sequencing. In this library, 34 conserved miRNA families were identified by homology search and the miRNA sequences of them were also found in the library. Furthermore, potential targets of these conserved miRNA families were predicted in cotton TC library. However, based on the mature miRNAs and their miR sequences, only 8 conserved miRNA encoding loci (miR156, miR157a, miR157b, miR162, miR164, miR393, miR399, miR827) were identified from cotton EST sequences. Multiple encoding loci of some miRNAs were identified by comparing the cloned miRNA and miR sequences.
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Affiliation(s)
- Meng-Bin Ruan
- Key Laboratory of Molecular and Developmental Biology, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100080, China
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