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Novel Mir390-Dependent Transacting Sirna Precursors in Plants Revealed by a PCR-Based Experimental Approach and Database Analysis Hindawi Publishing Corporation Journal of Biomedicine and Biotechnology Volume 2009, Article ID 952304, 9 pages doi:10.1155/2009/952304 Research Article Novel miR390-Dependent Transacting siRNA Precursors in Plants Revealed by a PCR-Based Experimental Approach and Database Analysis M. S. Krasnikova,1 I. A. Milyutina,2 V. K. Bobrova, 2 L. V. Ozerova,3 A. V. Troitsky,2 A. G. Solovyev,1, 2 andS.Y.Morozov2 1 Institute of Agricultural Biotechnology, Russian Academy of Agricultural Sciences, Timiryazevskaya 42, 127550 Moscow, Russia 2 A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119992 Moscow, Russia 3 Main Botanic Garden Russian Academy of Sciences, Botanicheskaya 4, 127276 Moscow, Russia CorrespondenceshouldbeaddressedtoS.Y.Morozov,[email protected] Received 28 February 2009; Accepted 31 July 2009 Recommended by Zhumur Ghosh TAS loci in plant genomes encode transacting small interfering RNAs (ta-siRNAs) that regulate expression of a number of genes. The function of TAS3 precursor in Arabidopsis thaliana is controlled by two miR390 target sites flanking two ta-siARF sequences targeting mRNAs of ARF transcription factors. Cleavage of the 3-miR390-site initiates ta-siRNAs biogenesis. Here we describe the new method for identification of plant ta-siRNA precursors based on PCR with oligodeoxyribonucleotide primers mimicking miR390. The method was found to be efficient for dicotiledonous plants, cycads, and mosses. Based on sequences of amplified loci and a database analysis, a novel type of miR390-dependent TAS sequences was identified in dicots. These TAS loci are characterized by a smaller distance between miR390 sites compared to TAS3, a single copy of ta-siARF, and a sequence conservation pattern pointing to the possibility that processing of novel TAS-like locus is initiated by cleavage of the 5-terminal miR390 target site. Copyright © 2009 M. S. Krasnikova et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 1. Introduction in the nucleus by RNaseIII-like protein DCL1 to give an imperfect RNA duplex with 2 nt 3 overhangsoneachstrand Small RNA-mediated gene silencing plays important roles [5, 14, 15]. In total, several dozens of plant miRNA fami- in many cellular processes, including development, genome lies (hundreds of individual miRNA species) are currently maintenance and integrity, and adaptive responses to biotic identified and found to target mainly protein-coding mRNAs and abiotic stress in most eukaryotes. Small RNAs, usually [7, 12, 13, 15, 16]. However, some microRNAs guide the 20–25 nucleotides (nt) in length, guide heterochromatin cleavage of the non-protein-coding primary transcripts of formation, mRNA degradation, translational inhibition, and TAS genes directing the formation of trans-acting siRNAs DNA elimination. In plants, small RNAs are highly diverse (ta-siRNAs). In this case, miRNAs represent a cleavage guider and significant progress has been achieved in unraveling the for ARGONAUTE (AGO) proteins with RNaseH-like activity components and mechanisms involved in their biogenesis that cleaves TAS single-stranded RNA transcript in the region and function [1–8]. MicroRNAs (miRNAs) are a class of complementary to small RNA [4].TAScleavageproduct(s) small noncoding RNAs (21-22-nt long) transcribed from the is converted by cooperative action of RNA-binding protein genomes of all multicellular organisms and some viruses SGS3 and RNA-polymerase RDR6 to double-stranded form [5, 9–13]. Plant miRNA biogenesis starts with the transcrip- and subsequently processed by DCL4 to produce a cluster tion of miRNA precursors by RNA polymerase II. These of ta-siRNAs that are phased in 21 nt increment relative to precursors contain the mature miRNA sequence within the the original cleavage site on both strands [4, 5, 13, 17, 18]. stem of a long imperfect RNA hairpin which is processed The generated 21 nt ta-siRNAs further work as components 2 Journal of Biomedicine and Biotechnology of RISC complex to guide AGO-dependent cleavage of their (for mosses), and an extending temperature of 72◦C, each target mRNAs. Recent studies have reported that some ta- for 30 seconds, followed by a final extension at 72◦Cfor3 siRNAs also work as cleavage guiders to cut other TAS minutes. PCR products were visualized by electrophoresis of RNA precursors similarly to microRNA and thus generate samples in 1% agarose gel. For cloning, the PCR-amplified secondary ta-siRNAs with new specificity [19]. Most TAS DNA bands were isolated from gel and ligated into pGEM- RNA precursors have only single miRNA target motif (e.g., T (Promega). In each case, 7–18 independent clones were miR173) positioned 5 to ta-siRNA-producing site, and the sequenced. Sequences of 20–50% of clones depending on target motif is cleaved by AGO1 guided by the respective particular plant species showed no presence of tasi-ARF RNA miRNA. However, two miR390 target sites (5 and 3 to ta- sequences and these clones were regarded as false ones. In siRNA site) were shown to be necessary for TAS3 precursor some cases (less than 10% of clones), nucleotide sequences RNA cleavage that appeared to be dependent on specific of tasi-ARF precursor genes have the ends (primer sites) interaction between AGO7 and miR390 [4, 18, 20]. which are different by single nucleotide substitutions or In this study, we analyzed TAS3-related sequences deletions from the primer sequences. We propose that this encoded by genomes of different land plants. Using multiple discrepancy may result from rare mutations after cloning of alignments of TAS3-like RNAs in dicotyledonous plants [17, PCR products in Escherichia coli. 18], we synthesized oligonucleotide primers complementary to miR390 target sites positioned 5 and 3 to ta-siRNA 2.3. GeneBank Accession Numbers. DNA sequences were site. In a control PCR reaction with Arabidopsis thaliana deposited at NCBI databank under the following acces- chromosomal DNA, we obtained a PCR product of expected sion numbers: Nicotiana benthamiana—FJ804742; Nicotiana size. However, in Nicotiana benthamiana and tobacco, in tabacum—FJ804743 (“short” TAS) and FJ804751 (classical addition to the PCR products corresponding to TAS3-like TAS); Datura stramonium—FJ804744; Solanum demissum— RNAs, we found smaller PCR fragments. Sequencing of these FJ804745; Physalis longifolia—FJ804746; Brachythecium lat- fragments and further database analysis revealed that they ifolium (clone 50 Br)—FJ804747; Brachythecium latifolium represent a new, previously undescribed, type of miR390- (clone 47 Br)—FJ804748; Hookeria lucens—FJ804749; Cycas mediated TAS genes producing potential precursors of ta- revolute—FJ804750. siARF RNA in different dicotyledonous plants. 2. Materials and Methods 3. Results To design primers for PCR and cloning of TAS3-like genes 2.1. Plant Material. Plants were taken from collections of from Nicotiana benthamiana and Nicotiana tabacum,we Main Botanic Garden of the Russian Academy of Sciences used a multiple alignment of TAS3-like RNA precursors and Department of Virology, Moscow State University. from flowering plants published by Axtell and others [18]. Solanaceous plants were germinated in standard growth PCR analysis was performed with two pairs of primers: P- chamber conditions for several weeks until stage of 6–8 Tas3 corresponded to the 5 miR390 target site and either leaves. M-Tas3/caa or M-Tas3/aca, both complementary to the 3 miR390 target/cleavage site [18, 20]. Control PCR reaction 2.2. Analysis of Nucleic Acids. Genomic plant DNA was using chromosomal Arabidopsis thaliana DNAastemplate isolated from 200 mg of plant material by DNA extraction and both paires of primers resulted in efficient synthesis kit (Macherey-Nagel) according to the protocol of the of a single PCR-fragments with expected size of 260 bp manufacturer. Total RNA was isolated from young tobacco (Figure 1(a)) that was in agreement with calculated distance leaves with the Trizol reagent according to the manufacturer’s between 5 and 3 miR390 target sites in Arabidopsis ta-siARF instructions (Invitrogen). Digestion of any contaminating precursor RNAs [17, 18]. Sequencing of these PCR-amplified DNA was achieved by treatment of samples with RQI and cloned DNA fragments confirmed specific amplification RNase-free DNase (Promega). Reverse transcription was of at least two of three known A. thaliana TAS3 chromosomal performed with 1 µg of total RNA and oligo (dT)-primer loci (data not shown) [17, 21]. using the RT system (Invitrogen) according to the protocol PCR amplification of chromosomal DNA from Nicotiana of the manufacturer. Primers for dicotiledonous plants benthamiana and Nicotiana tabacum (cv. Samsun) also and Cycas revoluta were: forward primer: TAS-P 5-GGT- resulted in synthesis of one major band of 250 bp and 280 bp, GCTATCCTATCTGAGCTT-3 and reverse primers TAS- respectively (Figure 1(a) and data not shown). Cloning and Mcaa 5-AGCTCAGGAGGGATAGCAA-3 and TAS-Maca sequencing of the obtained DNA bands revealed that the 5-AGCTCAGGAGGGATAGACA-3. amplified sequences contained putative ta-siARF site com- The primers for mosses (Physcomitrella-specific) were: posed of two tandem copies of ARF-specific ta-siRNAs and forward primers: Bryo TAS-P1 5-GGCGCTATCCCTCCT- located between miR390 target sites corresponding to PCR GAGCT-3 and Bryo TAS-P3 5-GACGCTACCCTTCCT- primers. Moreover, amplified sequences showed obvious GAGCT-3, reverse primer: Bryo TAS-M 5-TAGCTCAGG- similarity to TAS3-like genes from other dicotyledonous AGTGATA(G/T)A(C/A)AA-3. For PCR, 25–35 cycles were plants (Figure 2)[17, 18]. Bioinformatic analysis of the used for amplification with a melting temperature of 95◦C, putative TAS3-like sequences from Nicotiana benthamiana an annealing temperature of 58◦C (for seed plants) or 60◦C and Nicotiana tabacum using NCBI Blast revealed closely Journal of Biomedicine and Biotechnology 3 1234M 123M 500 400 500 300 400 300 200 200 100 100 (a) (b) Figure 1: Agarose gel analysis of PCR products.
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