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Abstract
MicroRNAs (miRNAs) are negative regulators of gene expression in eukaryotic organisms, whereas small interfering RNAs (siRNAs) guide host-cell defence against viruses, transposons and transgenes. A key issue in plant biology is whether miRNAs act only in cells in which they are formed, or if, like siRNAs, they also function after passive diffusion or active transportation into other cells. Recent reports show that miRNAs are indeed able to move between plant cells to direct developmental programming of gene expression. In both leaf and root development, miRNAs establish intercellular gradients of gene expression that are essential for cell and tissue differentiation. Gradients in gene expression also play crucial roles in animal development, and there is strong evidence for intercellular movement of miRNAs in animals. Thus, intercellular movement of miRNAs may be crucial to animal developmental biology as well as plants.
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Affiliation(s)
- Nial R Gursanscky
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
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153
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Kulcheski FR, de Oliveira LFV, Molina LG, Almerão MP, Rodrigues FA, Marcolino J, Barbosa JF, Stolf-Moreira R, Nepomuceno AL, Marcelino-Guimarães FC, Abdelnoor RV, Nascimento LC, Carazzolle MF, Pereira GAG, Margis R. Identification of novel soybean microRNAs involved in abiotic and biotic stresses. BMC Genomics 2011; 12:307. [PMID: 21663675 PMCID: PMC3141666 DOI: 10.1186/1471-2164-12-307] [Citation(s) in RCA: 204] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2011] [Accepted: 06/10/2011] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Small RNAs (19-24 nt) are key regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in eukaryotes. Current studies have demonstrated that microRNAs (miRNAs) act in several plant pathways associated with tissue proliferation, differentiation, and development and in response to abiotic and biotic stresses. In order to identify new miRNAs in soybean and to verify those that are possibly water deficit and rust-stress regulated, eight libraries of small RNAs were constructed and submitted to Solexa sequencing. RESULTS The libraries were developed from drought-sensitive and tolerant seedlings and rust-susceptible and resistant soybeans with or without stressors. Sequencing the library and subsequent analyses detected 256 miRNAs. From this total, we identified 24 families of novel miRNAs that had not been reported before, six families of conserved miRNAs that exist in other plants species, and 22 families previously reported in soybean. We also observed the presence of several isomiRNAs during our analyses. To validate novel miRNAs, we performed RT-qPCR across the eight different libraries. Among the 11 miRNAs analyzed, all showed different expression profiles during biotic and abiotic stresses to soybean. The majority of miRNAs were up-regulated during water deficit stress in the sensitive plants. However, for the tolerant genotype, most of the miRNAs were down regulated. The pattern of miRNAs expression was also different for the distinct genotypes submitted to the pathogen stress. Most miRNAs were down regulated during the fungus infection in the susceptible genotype; however, in the resistant genotype, most miRNAs did not vary during rust attack. A prediction of the putative targets was carried out for conserved and novel miRNAs families. CONCLUSIONS Validation of our results with quantitative RT-qPCR revealed that Solexa sequencing is a powerful tool for miRNA discovery. The identification of differentially expressed plant miRNAs provides molecular evidence for the possible involvement of miRNAs in the process of water deficit- and rust-stress responses.
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Affiliation(s)
- Franceli R Kulcheski
- Centre of Biotechnology and PPGBCM, Laboratory of Genomes and Plant Population, building 43431, Federal University of Rio Grande do Sul - UFRGS, P.O. Box 15005, CEP 91501-970, Porto Alegre, RS, Brazil
| | - Luiz FV de Oliveira
- Centre of Biotechnology and PPGBCM, Laboratory of Genomes and Plant Population, building 43431, Federal University of Rio Grande do Sul - UFRGS, P.O. Box 15005, CEP 91501-970, Porto Alegre, RS, Brazil
- PPGGBM at Federal University of Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil
| | - Lorrayne G Molina
- Centre of Biotechnology and PPGBCM, Laboratory of Genomes and Plant Population, building 43431, Federal University of Rio Grande do Sul - UFRGS, P.O. Box 15005, CEP 91501-970, Porto Alegre, RS, Brazil
- PPGGBM at Federal University of Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil
| | - Maurício P Almerão
- Centre of Biotechnology and PPGBCM, Laboratory of Genomes and Plant Population, building 43431, Federal University of Rio Grande do Sul - UFRGS, P.O. Box 15005, CEP 91501-970, Porto Alegre, RS, Brazil
| | - Fabiana A Rodrigues
- EMBRAPA Soja, Rodovia Carlos João Strass, Distrito de Warta, CEP 86001-970, Londrina, PR, Brazil
| | - Juliana Marcolino
- EMBRAPA Soja, Rodovia Carlos João Strass, Distrito de Warta, CEP 86001-970, Londrina, PR, Brazil
| | - Joice F Barbosa
- EMBRAPA Soja, Rodovia Carlos João Strass, Distrito de Warta, CEP 86001-970, Londrina, PR, Brazil
| | - Renata Stolf-Moreira
- EMBRAPA Soja, Rodovia Carlos João Strass, Distrito de Warta, CEP 86001-970, Londrina, PR, Brazil
| | - Alexandre L Nepomuceno
- EMBRAPA Soja, Rodovia Carlos João Strass, Distrito de Warta, CEP 86001-970, Londrina, PR, Brazil
| | | | - Ricardo V Abdelnoor
- EMBRAPA Soja, Rodovia Carlos João Strass, Distrito de Warta, CEP 86001-970, Londrina, PR, Brazil
| | - Leandro C Nascimento
- Institute of Biology, Laboratory of Genomic and Expression, State University of Campinas, CEP 13083-970, Campinas, SP, Brazil
| | - Marcelo F Carazzolle
- Institute of Biology, Laboratory of Genomic and Expression, State University of Campinas, CEP 13083-970, Campinas, SP, Brazil
- National Center for High Performance Processing (CENAPAD-SP), State University of Campinas, CEP 13083-970, Campinas, SP, Brazil
| | - Gonçalo AG Pereira
- Institute of Biology, Laboratory of Genomic and Expression, State University of Campinas, CEP 13083-970, Campinas, SP, Brazil
| | - Rogério Margis
- Centre of Biotechnology and PPGBCM, Laboratory of Genomes and Plant Population, building 43431, Federal University of Rio Grande do Sul - UFRGS, P.O. Box 15005, CEP 91501-970, Porto Alegre, RS, Brazil
- PPGGBM at Federal University of Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil
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154
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Kantar M, Lucas SJ, Budak H. miRNA expression patterns of Triticum dicoccoides in response to shock drought stress. PLANTA 2011; 233:471-84. [PMID: 21069383 DOI: 10.1007/s00425-010-1309-4] [Citation(s) in RCA: 200] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2010] [Accepted: 10/25/2010] [Indexed: 05/18/2023]
Abstract
Drought is a major environmental stress factor that affects plant growth and development worldwide. Wild emmer wheat (Triticum turgidum ssp. dicoccoides), the ancestor of domesticated durum wheat (Triticum turgidum ssp. durum), has great potential for improving the understanding of the wheat drought response. MicroRNAs (miRNAs) are a recently discovered class of gene expression regulators that have also been linked to several plant stress responses; however, this relationship is just beginning to be understood. miRNA expression patterns of drought-resistant wild emmer wheat in response to drought stress were investigated using a plant miRNA microarray platform. Expression was detected to be 205 miRNAs in control and 438 miRNAs in drought-stressed leaf and root tissues. Of these miRNAs, the following 13 were differentially regulated in response to drought: miR1867, miR896, miR398, miR528, miR474, miR1450, miR396, miR1881, miR894, miR156, miR1432, miR166 and miR171. Regulation of miRNAs upon 4 and 8 h drought stress applications observed by qRT-PCR. Target transcripts of differentially regulated miRNAs were computationally predicted. In addition to miRNA microarray study, five new conserved T. turgidum miRNAs were identified through a homology-based approach, and their secondary structures and putative targets were predicted. These findings both computationally and experimentally highlight the presence of miRNAs in T. dicoccoides and further extend the role of miRNAs under shock drought stress conditions.
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Affiliation(s)
- Melda Kantar
- Biological Sciences and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
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