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Diversity, expression and mRNA targeting abilities of Argonaute-targeting miRNAs among selected vascular plants.

Jagtap S, Shivaprasad PV - BMC Genomics (2014)

Bottom Line: Sequences of miR168 and miR403 are not conserved among plant lineages, but surprisingly they differ drastically in their sequence diversity and expression levels even among closely related plants.Variation in miR168 expression among plants correlates well with secondary structures/length of loop sequences of their precursors.We also show that rapid evolution and likely loss of expression of miR168 isoforms in tobacco is related to the insertion of MITE-like transposons between miRNA and miRNA* sequences, a possible mechanism showing how miRNAs are lost in few plant lineages even though other close relatives have abundantly expressing miRNAs.

View Article: PubMed Central - PubMed

Affiliation: National Centre for Biological Sciences, GKVK Campus, Bellary Road, Bangalore 560 065, India. shivaprasad@ncbs.res.in.

ABSTRACT

Background: Micro (mi)RNAs are important regulators of plant development. Across plant lineages, Dicer-like 1 (DCL1) proteins process long ds-like structures to produce micro (mi) RNA duplexes in a stepwise manner. These miRNAs are incorporated into Argonaute (AGO) proteins and influence expression of RNAs that have sequence complementarity with miRNAs. Expression levels of AGOs are greatly regulated by plants in order to minimize unwarranted perturbations using miRNAs to target mRNAs coding for AGOs. AGOs may also have high promoter specificity-sometimes expression of AGO can be limited to just a few cells in a plant. Viral pathogens utilize various means to counter antiviral roles of AGOs including hijacking the host encoded miRNAs to target AGOs. Two host encoded miRNAs namely miR168 and miR403 that target AGOs have been described in the model plant Arabidopsis and such a mechanism is thought to be well conserved across plants because AGO sequences are well conserved.

Results: We show that the interaction between AGO mRNAs and miRNAs is species-specific due to the diversity in sequences of two miRNAs that target AGOs, sequence diversity among corresponding target regions in AGO mRNAs and variable expression levels of these miRNAs among vascular plants. We used miRNA sequences from 68 plant species representing 31 plant families for this analysis. Sequences of miR168 and miR403 are not conserved among plant lineages, but surprisingly they differ drastically in their sequence diversity and expression levels even among closely related plants. Variation in miR168 expression among plants correlates well with secondary structures/length of loop sequences of their precursors.

Conclusions: Our data indicates a complex AGO targeting interaction among plant lineages due to miRNA sequence diversity and sequences of miRNA targeting regions among AGO mRNAs, thus leading to the assumption that the perturbations by viruses that use host miRNAs to target antiviral AGOs can only be species-specific. We also show that rapid evolution and likely loss of expression of miR168 isoforms in tobacco is related to the insertion of MITE-like transposons between miRNA and miRNA* sequences, a possible mechanism showing how miRNAs are lost in few plant lineages even though other close relatives have abundantly expressing miRNAs.

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Accumulation of miR168 a,b,c and miR168 d,e isoforms among tobacco tissues (floral and leaf). Reads of miRNA or miRNA* per million reads was taken from GEO accession GSE28977. Similar ratio between a,b,c and d,e were observed among tobacco pods. miR168 sequences were retrieved as discussed in methods section.
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Fig5: Accumulation of miR168 a,b,c and miR168 d,e isoforms among tobacco tissues (floral and leaf). Reads of miRNA or miRNA* per million reads was taken from GEO accession GSE28977. Similar ratio between a,b,c and d,e were observed among tobacco pods. miR168 sequences were retrieved as discussed in methods section.

Mentions: Because structures of these miRNA precursors are crucial for their biogenesis, a secondary structure prediction of all miR168 precursors was carried out using RNA-fold (Figure 4B, Additional file 5: Figure S4). Among the dicots, the typical secondary structure had one or two small loops and short branches. Monocots having very short loops had a simple stem loop with high sequence complementarity. Usually high sequence complementarity beyond miR and miR* sequences indicate their recent evolution. Among the Solanaceae, those with shorter loops had structures similar to other dicots, but as expected the structures of miR168 isoforms with long loops were complex. The nta miR168d and e precursors have long loop sequences similar to each other but extremely different from any other miR168 precursor (Figure 4C). A closer look showed high sequence similarity between fragments of loop sequences between these two precursors and Miniature Inverted repeat Transposable Elements (MITE) from few dicots (Additional file 6: Figure S5). MITEs are cut and paste type transposon elements typically leaving short fragments when they jump to newer locations. The presence of MITE-like sequences in the loop region for any miRNA has not been reported so far. It is important to note that Piriyapongsa et al. [31] have proposed that miRNAs encoded by MITEs evolved from corresponding ancestral full-length (autonomous) elements that originally encoded short interfering (si)RNAs. For miR168 though this may have been in a reverse order. A systematic search using published genomes identified other regions that could have been miR168 precursors that invited other repeat elements to become transcriptionally inactive (data not shown).In tobacco, identification of mature miRNAs corresponding to isoforms a, b, c (without MITE insertion) and d, e (with MITE insertion) is possible due to the sequence divergence between these isoforms. We hypothesized that insertion of MITEs might interfere with Pri-miR168 transcription or biogenesis steps and therefore those isoforms with insertion should be less abundant compared to their counterparts. Strikingly, tobacco miR168d,e isoforms were ~15 times low abundant than a,b,c isoforms in leaves and flowers (Figure 5), supporting the idea that long loop-containing precursors of miR168 yield less abundant mature miRNAs.Figure 5


Diversity, expression and mRNA targeting abilities of Argonaute-targeting miRNAs among selected vascular plants.

Jagtap S, Shivaprasad PV - BMC Genomics (2014)

Accumulation of miR168 a,b,c and miR168 d,e isoforms among tobacco tissues (floral and leaf). Reads of miRNA or miRNA* per million reads was taken from GEO accession GSE28977. Similar ratio between a,b,c and d,e were observed among tobacco pods. miR168 sequences were retrieved as discussed in methods section.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4300679&req=5

Fig5: Accumulation of miR168 a,b,c and miR168 d,e isoforms among tobacco tissues (floral and leaf). Reads of miRNA or miRNA* per million reads was taken from GEO accession GSE28977. Similar ratio between a,b,c and d,e were observed among tobacco pods. miR168 sequences were retrieved as discussed in methods section.
Mentions: Because structures of these miRNA precursors are crucial for their biogenesis, a secondary structure prediction of all miR168 precursors was carried out using RNA-fold (Figure 4B, Additional file 5: Figure S4). Among the dicots, the typical secondary structure had one or two small loops and short branches. Monocots having very short loops had a simple stem loop with high sequence complementarity. Usually high sequence complementarity beyond miR and miR* sequences indicate their recent evolution. Among the Solanaceae, those with shorter loops had structures similar to other dicots, but as expected the structures of miR168 isoforms with long loops were complex. The nta miR168d and e precursors have long loop sequences similar to each other but extremely different from any other miR168 precursor (Figure 4C). A closer look showed high sequence similarity between fragments of loop sequences between these two precursors and Miniature Inverted repeat Transposable Elements (MITE) from few dicots (Additional file 6: Figure S5). MITEs are cut and paste type transposon elements typically leaving short fragments when they jump to newer locations. The presence of MITE-like sequences in the loop region for any miRNA has not been reported so far. It is important to note that Piriyapongsa et al. [31] have proposed that miRNAs encoded by MITEs evolved from corresponding ancestral full-length (autonomous) elements that originally encoded short interfering (si)RNAs. For miR168 though this may have been in a reverse order. A systematic search using published genomes identified other regions that could have been miR168 precursors that invited other repeat elements to become transcriptionally inactive (data not shown).In tobacco, identification of mature miRNAs corresponding to isoforms a, b, c (without MITE insertion) and d, e (with MITE insertion) is possible due to the sequence divergence between these isoforms. We hypothesized that insertion of MITEs might interfere with Pri-miR168 transcription or biogenesis steps and therefore those isoforms with insertion should be less abundant compared to their counterparts. Strikingly, tobacco miR168d,e isoforms were ~15 times low abundant than a,b,c isoforms in leaves and flowers (Figure 5), supporting the idea that long loop-containing precursors of miR168 yield less abundant mature miRNAs.Figure 5

Bottom Line: Sequences of miR168 and miR403 are not conserved among plant lineages, but surprisingly they differ drastically in their sequence diversity and expression levels even among closely related plants.Variation in miR168 expression among plants correlates well with secondary structures/length of loop sequences of their precursors.We also show that rapid evolution and likely loss of expression of miR168 isoforms in tobacco is related to the insertion of MITE-like transposons between miRNA and miRNA* sequences, a possible mechanism showing how miRNAs are lost in few plant lineages even though other close relatives have abundantly expressing miRNAs.

View Article: PubMed Central - PubMed

Affiliation: National Centre for Biological Sciences, GKVK Campus, Bellary Road, Bangalore 560 065, India. shivaprasad@ncbs.res.in.

ABSTRACT

Background: Micro (mi)RNAs are important regulators of plant development. Across plant lineages, Dicer-like 1 (DCL1) proteins process long ds-like structures to produce micro (mi) RNA duplexes in a stepwise manner. These miRNAs are incorporated into Argonaute (AGO) proteins and influence expression of RNAs that have sequence complementarity with miRNAs. Expression levels of AGOs are greatly regulated by plants in order to minimize unwarranted perturbations using miRNAs to target mRNAs coding for AGOs. AGOs may also have high promoter specificity-sometimes expression of AGO can be limited to just a few cells in a plant. Viral pathogens utilize various means to counter antiviral roles of AGOs including hijacking the host encoded miRNAs to target AGOs. Two host encoded miRNAs namely miR168 and miR403 that target AGOs have been described in the model plant Arabidopsis and such a mechanism is thought to be well conserved across plants because AGO sequences are well conserved.

Results: We show that the interaction between AGO mRNAs and miRNAs is species-specific due to the diversity in sequences of two miRNAs that target AGOs, sequence diversity among corresponding target regions in AGO mRNAs and variable expression levels of these miRNAs among vascular plants. We used miRNA sequences from 68 plant species representing 31 plant families for this analysis. Sequences of miR168 and miR403 are not conserved among plant lineages, but surprisingly they differ drastically in their sequence diversity and expression levels even among closely related plants. Variation in miR168 expression among plants correlates well with secondary structures/length of loop sequences of their precursors.

Conclusions: Our data indicates a complex AGO targeting interaction among plant lineages due to miRNA sequence diversity and sequences of miRNA targeting regions among AGO mRNAs, thus leading to the assumption that the perturbations by viruses that use host miRNAs to target antiviral AGOs can only be species-specific. We also show that rapid evolution and likely loss of expression of miR168 isoforms in tobacco is related to the insertion of MITE-like transposons between miRNA and miRNA* sequences, a possible mechanism showing how miRNAs are lost in few plant lineages even though other close relatives have abundantly expressing miRNAs.

Show MeSH
Related in: MedlinePlus