Expression of 5 S rRNA genes linked to 35 S rDNA in plants, their epigenetic modification and regulatory element divergence
© Garcia et al.; licensee BioMed Central Ltd. 2012
Received: 2 February 2012
Accepted: 20 June 2012
Published: 20 June 2012
In plants, the 5 S rRNA genes usually occur as separate tandems (S-type arrangement) or, less commonly, linked to 35 S rDNA units (L-type). The activity of linked genes remains unknown so far. We studied the homogeneity and expression of 5 S genes in several species from family Asteraceae known to contain linked 35 S-5 S units. Additionally, their methylation status was determined using bisulfite sequencing. Fluorescence in situ hybridization was applied to reveal the sub-nuclear positions of rDNA arrays.
We found that homogenization of L-type units went to completion in most (4/6) but not all species. Two species contained major L-type and minor S-type units (termed Ls-type). The linked genes dominate 5 S rDNA expression while the separate tandems do not seem to be expressed. Members of tribe Anthemideae evolved functional variants of the polymerase III promoter in which a residing C-box element differs from the canonical angiosperm motif by as much as 30%. On this basis, a more relaxed consensus sequence of a plant C-box: (5’-RGSWTGGGTG-3’) is proposed. The 5 S paralogs display heavy DNA methylation similarly as to their unlinked counterparts. FISH revealed the close association of 35 S-5 S arrays with nucleolar periphery indicating that transcription of 5 S genes may occur in this territory.
We show that the unusual linked arrangement of 5 S genes, occurring in several plant species, is fully compatible with their expression and functionality. This extraordinary 5 S gene dynamics is manifested at different levels, such as variation in intrachromosomal positions, unit structure, epigenetic modification and considerable divergence of regulatory motifs.
Keywords5 S expression Artemisia Asteraceae C-box DNA methylation Pol III promoter divergence rDNA organization
Nuclear ribosomal DNA (rDNA) encoding 5 S, 5.8 S, 18 S and 26 S rRNA belong to the most important housekeeping genes playing a central role in cell metabolism . In plant genomes there may be from several hundred up to tens of thousands of highly homogeneous copies of each gene. A high copy number of these genes is probably important to ensure increased demand for proteosynthesis during plant development  but other functions, such as stabilization of the cell nucleus, have also been proposed . Each large 35 S (45 S in animals) rDNA unit contains 18 S, 5.8 S and 26 S rRNA genes, the internal transcribed spacers (ITSs), and an intergenic spacer (IGS) (for review see ). The 35 S units are organized in tandem arrays at one or several loci. The 5 S rDNA encoding a 120-bp-long transcript has been traditionally considered to occupy separate chromosomal locations (hereafter S-type) in seed plants [5–9]. However, physical linkage of 5 S and 35 S genes predominates the organization of rDNA in streptophyte algae and early diverging land plants such as mosses [10, 11]. These studies led to the hypothesis that “liberation” of 5 S genes from the 35 S unit might have occurred in a common angiosperm ancestor after the separation from early diverging plants. However, the linked arrangement of 35 S-5 S units (hereafter L-type) was later found in several species from the genus Artemisia (from family Asteraceae, considered one of the most phylogenetically derived groups of angiosperms), first based on cytogenetic evidence [12, 13] and subsequently confirmed through molecular studies . Additional studies showed that as many as 25% of Asteraceae members could have the unusual L-type arrangement of rDNA [15, 16] and the L-arrangement has recently been found in the living fossil gymnosperm Gingko biloba. Whether the L- or S-type was the ancestral rDNA status in angiosperm species remains to be determined. In most L-type genomes, the 5 S insertion occurs in the IGS within 1 kb downstream from the 26 S gene, and the corresponding transcript is encoded exclusively on the opposite DNA strand than the 26 S rRNA [15, 16].
Although, in the cell, there has to be a stoichiometric ratio of rRNA molecules, fundamental differences exist with respect to the transcriptional regulation of individual genes. The large polycistronic 35 S transcript produced by RNA polymerase I (Pol I) is endonucleolytically processed to produce mature 18 S, 5.8 S and 26 S rRNA molecules . The Pol I promoter, located within the 26-18 S intergenic spacer, binds to a complex of transcription factors . In contrast, transcription of 5 S genes is carried out by RNA polymerase III (Pol III) which requires an internal promoter within the gene in addition to the TFIIIA, TFIIIB and TFIIIC transcription factors. The tripartite structure of the Pol III internal promoter comprises an A-box, an IE (internal element) and a C-box, elements that are highly conserved in plants and animals . Epigenetic tools are another layer of expression control involved in the regulation of both types of rRNA genes. Silencing of non-transcribed gene copies is mediated by complex epigenetic mechanisms relying on chromatin modifications including DNA methylation [20, 21].
Do the L- and S-type loci occur simultaneously in a given genome? If, so which of them contribute to 5 S expression?
How much homogeneous are the 5 S rRNA pools? Are regulatory elements conserved between the S- and L-type genes?
What are the DNA methylation and chromatin condensation patterns of genes with linked and unlinked arrangements?
We analyzed expression by RT-PCR, cloning and sequencing approaches. Bisulfite sequencing and FISH were used to determine DNA methylation and chromatin condensation levels.
List of species studied with an indication of their origin and collection data
Spain: Catalonia, Setcases. S. Garcia and C. Ibarria ix. 2008.
Artemisia tridentata subsp. vaseyana
USA: Salt Creek Canyon, Juab. Co., Utah, USA. E. D. McArthur. 2008.
Mongolia: Southern Gobi. Sh. Dariimaa, Sh. Tsooj, J. Vallès and E. Yatamsuren. 2004.
Spain: Catalonia, Barcelona. Botanical Garden of Barcelona. S. Garcia. i.2007.
Czech Republic: Bohemia, Dobříš. Nohel Garden. S. Garcia i.2009.
Czech Republic: Bohemia, Dobříš. Nohel Garden. S. Garcia i.2009.
USA: Wyoming, Albany County. S. Garcia, E. D. McArthur, S. C. Sanderson and J. Vallès. ix.2008.
Czech Republic: Moravia, Brno. Near the Institute of Biophysics, T. Garnatje, x.2007.
Italy: Courmayeur. Giardino Botanico Alpino Saussurea
(Ref. 335 W). Index Seminum 2009.
Nucleic acids extractions, PCR and RT-PCR analysis
Genomic DNA (gDNA) was isolated following a CTAB protocol . RNAs were extracted from leaf material using the RNeasy Plant Mini kit (Qiagen, Germany). The purified RNAs were treated with TurboTM DNase (Ambion, Applied Biosystems, USA) to get rid of traces of DNA contamination. To prepare cDNA, about 2 μg of RNA was reverse transcribed by Superscript reverse transcriptase (Invitrogen, USA) employing random nonamer primers. The gDNA and cDNAs were analyzed by PCR using the following primers: 5SgF: 5’-GGTGCGATCATACCAGCACT-3’, 5SgR: GGTGCAACACGAGGACTT-3’, IGS1692: 5’-CGGAACYACCAAAGCGAGTAAG-3’ (newly designed) and 26Spr1: AGACGACTTTAAATACGCGAC . The 5 S regions delimited by the primer sets were amplified using Taq polymerase (Roche, Germany) with the following PCR program: one cycle at 94°C for 3 min; 29–35 (depending on amplicon) cycles at 55°C for 20 s, 72°C for 30 s, 92°C for 20 s; extension 72°C for 7 min. The PCR products were separated on a 1.2% agarose gel, stained with ethidium bromide and photodocumented (Ultralum, USA). Fragments corresponding to 5 S transcripts were cloned into the pDrive vector (Qiagen, Germany) and inserts were sequenced from both directions using the T7 and SP6 primers.
Bisulfite treatments were carried out on purified gDNA (~100 ng) using the EpiTect Bisulfite Kit (Qiagen, Germany). Primers amplifying the non-coding DNA strand designed with the aid of the BISPRIMER program  were as follows: forward primer 5'-GTTCGGATTCAAAAAAAGGGGT-3' and reverse primer 5'-CGATCATACCARCACTAAT-3' . The PCR program consisted on: one cycle at 94°C – 3 min; 35 cycles at 94°C – 20 s, 55°C – 20 s,72°C – 20 s; extension 72°C – 7 min. The PCR products were separated on 1.2% agarose gels, purified using a PCR purification kit (Macherey-Nagel, Germany) and cloned into a TA vector (pDrive, Qiagen, Germany). Positive clones were PCR-screened using vector SP6 and T7 primers. From 11 to 13 clones from each sample were sequenced (Eurofins MWG Operon, Germany).
Fluorescence in situ hybridization (FISH)
The fresh root tips of Helichrysum bracteatum were pretreated with an aqueous solution of colchicine 0.05% at room temperature, for 2.5 - 4 h and fixed in 3:1 (v/v) ethanol: acetic acid. Protoplasts were obtained using cellulolytic enzymes (0.4% pectinase (Macerozyme R10, Duchefa, Holland), 0.4% cytohelicase [Sigma C8274, USA], and 0.4% cellulase [Onozuka RS, Duchefa, Holland) in citrate buffer), dropped onto microscope slides, frozen and desiccated using liquid nitrogen and 70% ethanol. Before FISH, the slides were pre-treated with 50 μg mL-1 RNaseA for 1 h at 37°C in a humid chamber. After washing three times in 2× SSC (2× standard saline citrate + 0.1% (w/v) sodium dodecyl sulfate), slides were dehydrated in an ethanol series (50%, 70% and 100%) and air-dried. Remnants of cytoplasm were removed with pepsin treatment (10 μg mL-1 in 10 mM HCl, 4 min room temperature). The slides were then washed, dehydrated in ethanol and fixed for 10 min in 3.7% formaldehyde in 1× PBS, washed three times in 2× SSC, dehydrated again and air dried. The hybridization mix contained 50 ng μL-1 (1000 ng/slide), of Cy3-labeled (GE Healthcare, Chalfont, St Giles, England) 5 S probe a 116 bp-long insert of the cloned tobacco 5 S rRNA gene , and 20 ng μL-1 (400 ng/slide) of 35 S rDNA probe (a 2.5 kb fragment of 26 S rRNA gene from tomato labeled with Spectrum Green, Abbott Molecular, IL, USA). The FISH hybridization mixture (20 μL per slide) consisted of labeled DNA probes, 4 μL of a 50% solution of dextran sulfate, 10 μL pure formamide, 0.5 μL TE buffer and 2 μL 20 × SSC, and it was denatured at 75°C for 15 min and immediately cooled on ice. This was applied to the slides, which were denatured in a thermocycler using a flat plate: 5 min at 75°C, 2 min at 65°C, 2 min at 55°C, 2 min at 45°C, and transferred into a prewarmed humid chamber and put into an incubator. After overnight hybridization at 37°C, the slides were washed with 2× SSC, then 0.1× SSC (high stringency), at 42°C for 10 min each followed by washes with 2× SSC, 4× SSC + 0.1% Tween 20 at room temperature. Slides were rinsed in PBS and mounted in Vectashield (Vector Laboratories, Burlinghame, CA, USA) containing DAPI (1 μg/mL-1). FISH signals were observed using an Olympus AX 70 fluorescent microscope equipped with a digital camera. Images were analyzed and processed using ISIS software (MetaSystems, Altlussheim, Germany).
Sequences were assembled by BioEDIT Sequence Alignment Editor 22.214.171.124  and aligned. The bisulfite data were processed and methylation density calculated using CyMATE software . Secondary structure modeling was carried out through an online tool at the Mfold Web Server (The RNA Institute, College of Arts and Sciences, University of Albany, State University New York). Public database searches were carried out through BLAST . Additional 5 S sequences for comparative purposes were downloaded from the 5 S RNA database .
PCR on genomic DNA
Thus, A. tridentata and possibly G. luteoalbum contain rDNA in both linked and separate configurations of 5 S genes. The ratio of gene copies is, however, shifted to linked 35 S-5 S units. Therefore this type of genomic arrangement was called as “Ls”.
Size and cloning analysis of 5 S cDNA sequences
The products of cDNA amplification were purified, cloned and sequenced. The alignment of cDNA and gDNA clones is shown in Figure 2. It is evident that, in each species, the cDNA clones were nearly identical to the gDNA clones derived from 5 S rDNA1. Minor differences were attributed to only a few random mutations. Similarly, alignment of longer spacer sequences (IGS1692/5SgF) of cDNA and genomic clones also revealed nearly complete identity (Additional file 2). Consequently, phylogeny dendrograms (ML, NJ) constructed from both genomic and cDNA sequences revealed species-specific clustering (not shown). While comparison of gDNA and cDNA clones failed to reveal substantial intragenomic polymorphisms, up to seven conserved variable sites (occurring in all units) were detected across the species. Surprisingly, three of them located to the Pol III promoter element (C-box) in position 80–89 (Figure 2).
5 S regulatory motifs and secondary structure
As mentioned earlier, the internal Pol III promoter comprises a tripartite motif composed of an A-box, internal regulatory element (IE) and the C-box. Sequencing of multiple clones in the different analyzed species revealed high level of conservation of A-box and IE elements (Figure 2). However, the third part of the internal regulatory region, the C-box, located at 80–89, was only partially conserved. There were three substitutions in the 5’ region: one A > G transition at a position +80 and two G > C and A > T transversions at +82 and +83, respectively. The 3’end of the C-box was invariant. All cDNA clones (excepting random non-fixed mutations) from A. absinthium A. tridentata and M. matricarioides contained the same (5’-GGCTTGGGTG-3’) variant of the C-box (termed C*-box) whereas the other studied species displayed the canonical 5’-AGGATGGGTG-3’motif (Figures 2 and 4) . The upstream sequences were less conserved but the TATA box at about −20 was present in all genomic clones  including the one originating from minor separate loci in Ls species. In addition, there were multiple dT terminators in each IGS1, one or two immediately downstream of the last 5 S gene nucleotide (Additional file 2) while only a single terminator was found in the S-type genomic clones from A. tridentata (Additional file 1). We did not identify any repeated elements (using the REPFIND tool, Vienna server, http://molbioltools.ca/Repeats_secondary_structure/server) within the IGS1, proposed to function in the termination of transcription with Pol I .
DNA methylation analysis
Relationship between genomic organization and DNA methylation of 5 S genes in the studied species
Number of 5 S loci
1Position on chromosomes
In higher eukaryotes (plants and animals), 5 S genes occur either as separate arrays (S-type) or, less frequently, linked to large 35 S units (L-type). While the expression of S-type genes has been thoroughly studied in the past, expression of L-type genes has not yet been addressed in any of these organisms. Here we show that in several representative plant species the linked 5 S genes are expressed and dominantly contribute to cellular 5 S rRNA pools.
Low abundance of S-type loci in L-type genomes
Previous Southern blot and FISH analysis revealed largely homogenized 35 S-5 S units in several genera of the Asteraceae family . The current PCR analysis revealed minor 5 S-5 S tandems along with dominant 35-5 S units in two species (Artemisia tridentata and Gnaphalium luteoalbum). Separate tandems likely originate from loci that did not hybridize with the 26 S probe on Southern blots . Quantitative estimates suggest that they represent less than 10% of 5 S rDNA in Ls genomes . Contrast to linked 35 S-5 S genes, the 5 S-5 S tandems contained mutations in the A-box element (2/7 monomers) suggesting the occurrence of non-functional copies. However, more clones need to be analyzed to obtain statistical support for differential mutation frequencies between the arrays. The absence of S-type tandems in other L-type genomes (Figure 1) further indicates their frequent loss and/or rapid replacement by linked units. The question arises as to the location of minor S-type loci on chromosomes. While FISH on metaphase chromosomes of A. tridentata failed to reveal separate 35 S and 5 S signals, in the interphase some sites were labeled more strongly with the 5 S or 35 S rDNA probe . We therefore favor the hypothesis that minor 5 S-5 S tandems occur close to 35 S-5 S arrays or are interspersed between them.
Thus, four types of rDNA arrangement could be distinguished among different plant genera: (i) L-type, in which 35 S-5 S units are homogenized to completion (e.g., Helichrysum, Matricaria and Tagetes), (ii) LS-type, in which mostly linked 35 S-5 S units occur along with minor separate 5 S tandems (Artemisia and Gnaphalium), (iii) SL-type which is characterized by dominant independent 5 S-5 S tandems with a low abundance of 35 S-5 S units. Elachanthemum intricatum seems to be a representative of this group  and (iv) S-type, in which genomes contain independent 5 S tandems typical for most angiosperms.
Transcription of 35 S-5 S arrays
The Ls genomes harbor dominant L-type units and minor S-type units. Nevertheless, both loci encode potentially transcribed genes. Since only a fraction of rRNA genes is usually transcribed in the cell (the rest is epigenetically inactivated) it was of interest to determine the origin of 5 S rRNA transcripts, particularly in the Ls- and L-type genomes. The dominant expression of linked 5 S genes is supported by the following observations: (i) primary 5 S transcripts extending into IGS1 beyond the first termination signals were identified, which suggests that transcribed 5 S sequences actually stem from linked 5 S genes since a fraction of the IGS1 sequence is detected, (ii) no read-through transcripts were detected from tandemly arranged 5 S-5 S units in the Ls-type species, A. tridentata, (iii) the RNAs derived from linked genes adopted a secondary structure typical of a functional molecule according to the RNA folding simulations preformed and finally, (iv) linked arrays contained undermethylated and decondensed chromatin fractions (Table 2 and Figure 6), likely corresponding to active genes. We therefore presume that the contribution from low abundant tandem arrays or dispersed 5 S genes in Ls and L-type genomes to total rRNA pools is minor, if any.
One consequence of 5 S and 35 S linkage could be the putative transcription of both genes arising from read-through with both RNA Pol I and Pol III enzymes (Figure 3). In mung bean (Vigna radiata), termination of 35 S transcription occurs within 65 bp and 315 bp downstream of the 3'end of the 26 S rRNA coding region . In cucumber (Cucumis sativus), several termination signals in the IGS were observed, the first being 350 bp downstream of the 26 S gene . In Tagetes, the functional 5 S rDNA1 insertion occurs just within ~200 bp downstream from the last 26 S gene nucleotide (Additional file 2 and ), providing the possibility of formation of a long 35 S-5 S precursor and perhaps a double stranded RNA. However, we were unable to identify any transcripts containing both 26 S and 5 S sequences (Figure 3). Thus, the transcription of both genes is probably efficiently terminated in the IGS1 and/or genes are compartmentalized in cell nucleus (discussed further below).
As previously noticed , some genes in A. absinthium contain a second 5 S insertion (5SrDNA2) located distally to the 26 S gene. However, the PCR product corresponding to the 5 S rDNA2 transcription (Figure 2) was not detected among the sequenced clones, supporting the hypothesis that it may represent a pseudogene and therefore is not transcribed. Nevertheless, the duplication may have evolutionary significance since a similar duplication with one functional and one non-functional 5 S copy was observed in horsetail, Equisetum hyemale. Apparent parallelism may point to a common mechanism of 5 S integration, and/or similar selection pressures in different organisms maintaining gene functionality.
Evolution of pol III promoter variants: An updated plant C-box consensus sequence
There does not seem to be a simple correlation between the occurrence of the promoter variants and the genomic arrangement of rRNA genes. For example, the C*-box is found in some, but not all L-type species. The phylogeny study suggests its preferential occurrence in the tribe Anthemideae, but again, not all members seem to bear it (Figure 4). Sequence divergence may rather reflect the overall dynamics of locus undergoing frequent elimination/homogenization cycles in this group of plants. In this context, Asteraceae species show diverse positions of rDNA loci on chromosomes [13, 16, 49], substantial genome size variation , certain phylogenetic incongruence between 35 S and 5 S markers , and even rearrangements between telomeric and rDNA repeats . The C*-box variant appears to be of recent origin that perhaps evolved after the divergence of Anthemideae from the rest of Asteraceae less than few million years ago . To gain a better understanding of such C-box divergence, it will be interesting to analyze 5 S promoters in many other Asteraceae species, as well as the transcription factors binding to them, in order to detect their possible co-evolution. Of note, TFIIIA is known to evolve rapidly (yeast and animal genes share only 20% similarity) and splicing of its primary transcript seems to be influenced by an exonized 5 S insertion in plants .
Similar DNA methylation patterns of linked and separate 5 S rDNA
Both S- and L-type species showed CG, CHG and CHH methylation patterns typical for plant repetitive DNA . Consistently, the methylation density at different motifs had the identical tendency descending in this order: CG > CHG > CHH in line with previous studies of 5 S methylation [41, 55]. One can conclude that a relatively high level of methylation (usually higher than genome average) is not linked to tandem arrangement but also occurs when 5 S genes are organized as single or low copy insertions. In other words, the tandem arrangement does not seem to be essential for 5 S methylation. Within the tandemly arranged units, genes with low or no methylation levels are considered active while highly methylated genes are heterochromatic and inactive . Variation in methylation density between clones might reflect epiallelic heterogeneity of arrays. Significantly undermethylated genes with as little as 11% methylation (Table 2) were detected possibly originating from the highly active part of 35 S-5 S arrays. A relatively high level of methylation, particularly at non-CG motifs, was found in Helianthus (S-type). Helianthus annuus shows pericentromeric location of 5 S rDNA [15, 38] while the less methylated 5 S genes in Tagetes patula and Artemisia absinthium are located at (sub-)telomeric positions [12, 15]. In this sense, 5 S units located proximally to centromeres in Arabidopsis were more methylated than other distally located genes .
Relationship between chromatin condensation and expression of rDNA units
It is known that RNA Pol I (which transcribes the 35 S genes) occurs in the nucleolus while RNA Pol III (which transcribes 5 S genes) is a nucleoplasmic protein. Thus, a single 35 S-5 S unit actively transcribed by one polymerase cannot be transcribed at the same time by the other polymerase. Strict compartmentalization of 35 S and 5 S transcription may also explain our failure to detect products of bidirectional 26 S-5 S transcription (Figure 3). Several models of spatial control of rDNA expression can be envisaged. First, there could be frequent reshuffling of genes between the nucleolus and nucleoplasm. This is unlikely considering that different transcription machineries are needed to execute the transcription of 5 S and 35 S genes. The second possibility is that a part of the megabase-sized array could be transcribed by polymerase I while another part is transcribed with Pol III. Certainly, the L-type genomes harbor enough genes (several thousand copies ) allowing the separation of arrays into transcription domains. Finally, regulation may occur at the level of individual chromosome sites. For example, one chromosome homolog could be involved in organizing the nucleolus and the transcription of 35 S genes while the other homolog transcribes 5 S genes. The FISH experiment in Figure 7 may provide some experimental support for this hypothesis. In late anaphase/telophase of Helichrysum bracteatum the nucleoli were apparently assembled on one highly decondensed homolog, while the other was highly condensed and probably not involved in nucleolus assembly. Such a dramatic difference in condensation patterns was not seen in interphase in which rDNAs on both homologs were condensed and associated with the nucleolar periphery (Figure 7A-C). Interestingly, TFIIIA factor essential for 5 S transcription seems to be concentrated at several nuclear foci including the nucleolus in Arabidopsis suggesting that transcription of linked 5 S genes may occur in a close proximity of the nucleolus.
With the present study, evidence was obtained for a dominant contribution of linked 5 S genes to the overall 5 S rRNA pools in species with completely or partially homogenized 35 S-5 S arrays, that is, 5 S genes are entirely transcribed from these linked arrays. The unusual sequence variation found in the internal regulatory elements of 5 S genes seems to be fully compatible with transcription, and considering these variations, an updated C-box consensus sequence has therefore been proposed. The methylation patterns of linked genes seem to be similar to their unlinked counterparts. As for the nuclear topology, the 35 S-5 S arrays closely associate with the nucleolus, suggesting that 5 S transcription may occur in close proximity to the nucleolus, possibly at its periphery.
Intergenic spacer between the 26 S and 18 S rRNA genes
Linked arrangement of the 35 S and 5 S RNA genes
Separate arrangement of the 35 S and 5 S RNA genes
Linked arrangement with minor contribution of S arrangement
Separate arrangement with minor contribution of L arrangement
- Pol I:
RNA polymerase I
- Pol III:
RNA polymerase III
Internal controlling region
Fluorescent in situ hybridization.
We wish to thank Dr. Jiří Široký (Academy of Science, CZ) for his advice on FISH and the anonymous reviewers for their insightful comments. This research was funded by the Grant Agency of the Czech Republic (P501-10-0208 and P501/12/G090), Academy of Science CZ (RVO68081707) and by the Spanish and Catalan governments (projects CGL2010-22234-C02-01 and 02/BOS, and project 2009SGR00439, respectively). SG benefited from a Beatriu de Pinós postdoctoral contract with the support of the Comissionat per a Universitats i Recerca (CUR) del Departament d’Economia i Coneixement de la Generalitat de Catalunya (Catalan government), and from a Short-term EMBO (European Molecular Biology Organization) fellowship.
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