551
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Ben Chaabane S, Liu R, Chinnusamy V, Kwon Y, Park JH, Kim SY, Zhu JK, Yang SW, Lee BH. STA1, an Arabidopsis pre-mRNA processing factor 6 homolog, is a new player involved in miRNA biogenesis. Nucleic Acids Res 2012; 41:1984-97. [PMID: 23268445 PMCID: PMC3561960 DOI: 10.1093/nar/gks1309] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
MicroRNAs (miRNAs) are small regulatory RNAs that have important regulatory roles in numerous developmental and metabolic processes in most eukaryotes. In Arabidopsis, DICER-LIKE1 (DCL1), HYPONASTIC LEAVES 1, SERRATE, HUA ENHANCER1 and HASTY are involved in processing of primary miRNAs (pri-miRNAs) to yield precursor miRNAs (pre-miRNAs) and eventually miRNAs. In addition to these components, mRNA cap-binding proteins, CBP80/ABA HYPERSENSITIVE1 and CBP20, also participate in miRNA biogenesis. Here, we show that STABILIZED1 (STA1), an Arabidopsis pre-mRNA processing factor 6 homolog, is also involved in the biogenesis of miRNAs. Similar to other miRNA biogenesis-defective mutants, sta1-1 accumulated significantly lower levels of mature miRNAs and concurrently higher levels of pri-miRNAs than wild type. The dramatic reductions of mature miRNAs were associated with the accumulation of their target gene transcripts and developmental defects. Furthermore, sta1-1 impaired splicing of intron containing pri-miRNAs and decreased transcript levels of DCL1. These results suggest that STA1 is involved in miRNA biogenesis directly by functioning in pri-miRNA splicing and indirectly by modulating the DCL1 transcript level.
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Affiliation(s)
- Samir Ben Chaabane
- Department of Plant Biology and Biotechnology, Faculty of Life Science, University of Copenhagen, Thovanlsensvej 40, 1871 Frederiksberg, Copenhagen, Denmark
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552
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Eldem V, Çelikkol Akçay U, Ozhuner E, Bakır Y, Uranbey S, Unver T. Genome-wide identification of miRNAs responsive to drought in peach (Prunus persica) by high-throughput deep sequencing. PLoS One 2012; 7:e50298. [PMID: 23227166 PMCID: PMC3515591 DOI: 10.1371/journal.pone.0050298] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Accepted: 10/18/2012] [Indexed: 12/13/2022] Open
Abstract
Peach (Prunus persica L.) is one of the most important worldwide fresh fruits. Since fruit growth largely depends on adequate water supply, drought stress is considered as the most important abiotic stress limiting fleshy fruit production and quality in peach. Plant responses to drought stress are regulated both at transcriptional and post-transcriptional level. As post-transcriptional gene regulators, miRNAs (miRNAs) are small (19–25 nucleotides in length), endogenous, non-coding RNAs. Recent studies indicate that miRNAs are involved in plant responses to drought. Therefore, Illumina deep sequencing technology was used for genome-wide identification of miRNAs and their expression profile in response to drought in peach. In this study, four sRNA libraries were constructed from leaf control (LC), leaf stress (LS), root control (RC) and root stress (RS) samples. We identified a total of 531, 471, 535 and 487 known mature miRNAs in LC, LS, RC and RS libraries, respectively. The expression level of 262 (104 up-regulated, 158 down-regulated) of the 453 miRNAs changed significantly in leaf tissue, whereas 368 (221 up-regulated, 147 down-regulated) of the 465 miRNAs had expression levels that changed significantly in root tissue upon drought stress. Additionally, a total of 197, 221, 238 and 265 novel miRNA precursor candidates were identified from LC, LS, RC and RS libraries, respectively. Target transcripts (137 for LC, 133 for LS, 148 for RC and 153 for RS) generated significant Gene Ontology (GO) terms related to DNA binding and catalytic activites. Genome-wide miRNA expression analysis of peach by deep sequencing approach helped to expand our understanding of miRNA function in response to drought stress in peach and Rosaceae. A set of differentially expressed miRNAs could pave the way for developing new strategies to alleviate the adverse effects of drought stress on plant growth and development.
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Affiliation(s)
- Vahap Eldem
- Cankırı Karatekin University, Faculty of Science, Department of Biology, Cankiri, Turkey
- Istanbul University, Faculty of Science, Department of Biology, Istanbul, Turkey
| | - Ufuk Çelikkol Akçay
- Suleyman Demirel University, Faculty of Agriculture, Department of Agricultural Biotechnology, Isparta, Turkey
| | - Esma Ozhuner
- Cankırı Karatekin University, Faculty of Science, Department of Biology, Cankiri, Turkey
| | - Yakup Bakır
- Marmara University, Faculty of Arts and Science, Department of Biology, Istanbul, Turkey
| | - Serkan Uranbey
- Cankırı Karatekin University, Faculty of Science, Department of Biology, Cankiri, Turkey
| | - Turgay Unver
- Cankırı Karatekin University, Faculty of Science, Department of Biology, Cankiri, Turkey
- * E-mail:
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553
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Alabi OJ, Zheng Y, Jagadeeswaran G, Sunkar R, Naidu RA. High-throughput sequence analysis of small RNAs in grapevine (Vitis vinifera L.) affected by grapevine leafroll disease. MOLECULAR PLANT PATHOLOGY 2012; 13:1060-76. [PMID: 22827483 PMCID: PMC6638782 DOI: 10.1111/j.1364-3703.2012.00815.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Grapevine leafroll disease (GLRD) is one of the most economically important virus diseases of grapevine (Vitis spp.) worldwide. In this study, we used high-throughput sequencing of cDNA libraries made from small RNAs (sRNAs) to compare profiles of sRNA populations recovered from own-rooted Merlot grapevines with and without GLRD symptoms. The data revealed the presence of sRNAs specific to Grapevine leafroll-associated virus 3, Hop stunt viroid (HpSVd), Grapevine yellow speckle viroid 1 (GYSVd-1) and Grapevine yellow speckle viroid 2 (GYSVd-2) in symptomatic grapevines and sRNAs specific only to HpSVd, GYSVd-1 and GYSVd-2 in nonsymptomatic grapevines. In addition to 135 previously identified conserved microRNAs in grapevine (Vvi-miRs), we identified 10 novel and several candidate Vvi-miRs in both symptomatic and nonsymptomatic grapevine leaves based on the cloning of miRNA star sequences. Quantitative real-time reverse transcriptase-polymerase chain reaction (RT-PCR) of selected conserved Vvi-miRs indicated that individual members of an miRNA family are differentially expressed in symptomatic and nonsymptomatic leaves. The high-resolution mapping of sRNAs specific to an ampelovirus and three viroids in mixed infections, the identification of novel Vvi-miRs and the modulation of certain conserved Vvi-miRs offers resources for the further elucidation of compatible host-pathogen interactions and for the provision of ecologically relevant information to better understand host-pathogen-environment interactions in a perennial fruit crop.
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Affiliation(s)
- Olufemi J Alabi
- Department of Plant Pathology, Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, WA 99350, USA
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554
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Cominelli E, Conti L, Tonelli C, Galbiati M. Challenges and perspectives to improve crop drought and salinity tolerance. N Biotechnol 2012; 30:355-61. [PMID: 23165101 DOI: 10.1016/j.nbt.2012.11.001] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 11/05/2012] [Indexed: 11/29/2022]
Abstract
Drought and high salinity are two major abiotic stresses affecting crop productivity. Therefore, the development of crops better adapted to cope with these stresses represents a key goal to ensure global food security to an increasing world population. Although many genes involved in the response to these abiotic stresses have been extensively characterised and some stress tolerant plants developed, the success rate in producing stress-tolerant crops for field conditions has been thus far limited. In this review we discuss different factors hampering the successful transfer of beneficial genes from model species to crops, emphasizing some limitations in the phenotypic characterisation and definition of the stress tolerant plants developed so far. We also highlight some technological advances and different approaches that may help in developing cultivated stress tolerant plants.
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Affiliation(s)
- Eleonora Cominelli
- Istituto di Biologia e Biotecnologia Agraria, CNR, Via E. Bassini 15, 20133 Milano, Italy
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555
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Guzman F, Almerão MP, Körbes AP, Loss-Morais G, Margis R. Identification of microRNAs from Eugenia uniflora by high-throughput sequencing and bioinformatics analysis. PLoS One 2012; 7:e49811. [PMID: 23166775 PMCID: PMC3499529 DOI: 10.1371/journal.pone.0049811] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Accepted: 10/17/2012] [Indexed: 11/27/2022] Open
Abstract
Background microRNAs or miRNAs are small non-coding regulatory RNAs that play important functions in the regulation of gene expression at the post-transcriptional level by targeting mRNAs for degradation or inhibiting protein translation. Eugenia uniflora is a plant native to tropical America with pharmacological and ecological importance, and there have been no previous studies concerning its gene expression and regulation. To date, no miRNAs have been reported in Myrtaceae species. Results Small RNA and RNA-seq libraries were constructed to identify miRNAs and pre-miRNAs in Eugenia uniflora. Solexa technology was used to perform high throughput sequencing of the library, and the data obtained were analyzed using bioinformatics tools. From 14,489,131 small RNA clean reads, we obtained 1,852,722 mature miRNA sequences representing 45 conserved families that have been identified in other plant species. Further analysis using contigs assembled from RNA-seq allowed the prediction of secondary structures of 25 known and 17 novel pre-miRNAs. The expression of twenty-seven identified miRNAs was also validated using RT-PCR assays. Potential targets were predicted for the most abundant mature miRNAs in the identified pre-miRNAs based on sequence homology. Conclusions This study is the first large scale identification of miRNAs and their potential targets from a species of the Myrtaceae family without genomic sequence resources. Our study provides more information about the evolutionary conservation of the regulatory network of miRNAs in plants and highlights species-specific miRNAs.
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Affiliation(s)
- Frank Guzman
- PPGGBM, Departamento de Genética, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Rio Grande do Sul, Brazil
- PPGBCM, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Rio Grande do Sul, Brazil
| | - Mauricio P. Almerão
- PPGBCM, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Rio Grande do Sul, Brazil
| | - Ana P. Körbes
- PPGGBM, Departamento de Genética, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Rio Grande do Sul, Brazil
| | - Guilherme Loss-Morais
- PPGBCM, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Rio Grande do Sul, Brazil
| | - Rogerio Margis
- PPGGBM, Departamento de Genética, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Rio Grande do Sul, Brazil
- PPGBCM, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Rio Grande do Sul, Brazil
- Departamento de Biofisica, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Rio Grande do Sul, Brazil
- * E-mail:
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556
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Marín-González E, Suárez-López P. "And yet it moves": cell-to-cell and long-distance signaling by plant microRNAs. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2012; 196:18-30. [PMID: 23017896 DOI: 10.1016/j.plantsci.2012.07.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Revised: 07/17/2012] [Accepted: 07/21/2012] [Indexed: 05/07/2023]
Abstract
MicroRNAs (miRNAs) are key regulators of numerous genes in many eukaryotes. Some plant miRNAs are involved in developmental and physiological processes that require intercellular or inter-organ signaling. Movement of other small RNAs within plants has been established. Recent findings also demonstrate intercellular signaling by miRNAs and strongly support that a subset of these regulatory molecules move from one cell to another or over long distances. Phloem exudates contain diverse miRNAs and at least two of them, involved in responses to nutrient availability, are transmitted through grafts, indicating long-distance movement. Two miRNAs that regulate developmental processes are present in cells outside their domains of expression. Several results strongly support that one of them moves from cell to cell. Research on a mutant affected in plasmodesmata trafficking indicates that these intercellular channels are required for transmission of miRNA activity to adjacent cells. Moreover, ARGONAUTE proteins might be involved in the regulation of miRNA trafficking. Hypothesis on the features and mechanisms that may determine miRNA mobility are presented. Future challenges include identifying other mobile miRNAs; demonstrating that miRNA movement is required for non-cell autonomous action; and characterizing the mechanisms of translocation and genetic pathways that regulate miRNA movement.
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Affiliation(s)
- Esther Marín-González
- Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Bellaterra-Cerdanyola del Vallès, 08193 Barcelona, Spain
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557
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Knight MR, Knight H. Low-temperature perception leading to gene expression and cold tolerance in higher plants. THE NEW PHYTOLOGIST 2012; 195:737-751. [PMID: 22816520 DOI: 10.1111/j.1469-8137.2012.04239.x] [Citation(s) in RCA: 221] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Plant species exhibit a range of tolerances to low temperatures, and these constitute a major determinant of their geographical distribution and use as crops. When tolerance is insufficient, either chilling or freezing injuries result. A variety of mechanisms are employed to evade the ravages of extreme or sub-optimal temperatures. Many of these involve cold-responsive gene expression and require that the drop in temperature is first sensed by the plant. Despite intensive research over the last 100 yr or longer, we still cannot easily answer the question of how plants sense low temperature. Over recent years, genomic and post-genomic approaches have produced a wealth of information relating to the sequence of events leading from cold perception to appropriate and useful responses. However, there are also crucial and significant gaps in the pathways constructed from these data. We describe the literature pertaining to the current understanding of cold perception, signalling and regulation of low-temperature-responsive gene expression in higher plants, raising some of the key questions that still intrigue plant biologists today and that could be targets for future work. Our review focuses on the control of gene expression in the pathways leading from cold perception to chilling and freezing tolerance.
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Affiliation(s)
- Marc R Knight
- Durham Centre for Crop Improvement Technology, School of Biological and Biomedical Sciences, Durham University, South Road, Durham DH1 3LE, UK
| | - Heather Knight
- Durham Centre for Crop Improvement Technology, School of Biological and Biomedical Sciences, Durham University, South Road, Durham DH1 3LE, UK
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558
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Colaiacovo M, Bernardo L, Centomani I, Crosatti C, Giusti L, Orrù L, Tacconi G, Lamontanara A, Cattivelli L, Faccioli P. A Survey of MicroRNA Length Variants Contributing to miRNome Complexity in Peach (Prunus Persica L.). FRONTIERS IN PLANT SCIENCE 2012; 3:165. [PMID: 22855688 PMCID: PMC3405489 DOI: 10.3389/fpls.2012.00165] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Accepted: 07/04/2012] [Indexed: 05/13/2023]
Abstract
MicroRNAs (miRNAs) are short non-coding RNA molecules produced from hairpin structures and involved in gene expression regulation with major roles in plant development and stress response. Although each annotated miRNA in miRBase (www.mirbase.org) is a single defined sequence with no further details on possible variable sequence length, isomiRs - namely the population of variants of miRNAs coming from the same precursors - have been identified in several species and could represent a way of broadening the regulatory network of the cell. Next-gen-based sequencing makes it possible to comprehensively and accurately assess the entire miRNA repertoire including isomiRs. The aim of this work was to survey the complexity of the peach miRNome by carrying out Illumina high-throughput sequencing of miRNAs in three replicates of five biological samples arising from a set of different peach organs and/or phenological stages. Three hundred-ninety-two isomiRs (miRNA and miRNA*-related) corresponding to 26 putative miRNA coding loci, have been highlighted by mirDeep-P and analyzed. The presence of the same isomiRs in different biological replicates of a sample and in different tissues demonstrates that the generation of most of the detected isomiRs is not random. The degree of mature sequence heterogeneity is very different for each individual locus. Results obtained in the present work can thus contribute to a deeper view of the miRNome complexity and to better explore the mechanism of action of these tiny regulators.
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Affiliation(s)
| | | | | | | | | | - Luigi Orrù
- CRA Genomics Research Centre, Fiorenzuola d’ArdaItaly
| | | | | | | | - Primetta Faccioli
- CRA Genomics Research Centre, Fiorenzuola d’ArdaItaly
- *Correspondence: Primetta Faccioli, CRA Genomics Research Centre, via S.Protaso 302, I-29017 Fiorenzuola d’Arda (Pc), Italy. e-mail:
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