Sequence and functional diversification of miR391-directed PTGS modules in plants



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MicroRNA (miRNA)-directed posttranscriptional gene silencing (miR-PTGS) is an integral component of gene regulatory networks governing plant development and responses to the environment. The sequence homology between Sly-miR4376, a miRNA common to Solanaceae and reported to target autoinhibited Ca2+-ATPase 10 (ACA10) messenger RNA (mRNA) in tomato, and Arabidopsis miR391 (Ath-miR391), previously annotated as a non-conserved member of the deeply conserved miR390 family, has prompted us to revisit the function of Ath-miR391, as well as its regulatory conservation. A combination of genetic, molecular, and bioinformatic analyses revealed a hidden conservation for miR-PTGS of ACA10 homologs in spermatophytes. We found that the Arabidopsis ACA10 mRNA undergoes miR391-directed cleavage in vivo. Furthermore, transgenic overexpression of miR391 recapitulated the compact inflorescence (cif) phenotypes characteristic of ACA10 loss-of-function mutants, due to miR391-directed PTGS of ACA10. Significantly, comprehensive data mining revealed robust evidence for widespread PTGS of ACA10 homologs directed by a superfamily of related miRNAs sharing a conserved sequence core. Intriguingly, the ACA-targeting miRNAs in Poaceae also direct PTGS for calmodulin-like proteins which are putative Ca2+ sensors. The PTGS of ACA10 homologs is therefore directed by a miRNA superfamily that is of ancient origin and has undergone rapid sequence diversification associated with functional innovation by virtue of the miRNA-interacting site in the non-coding region. Developing cotton fibers which are extremely elongated seed trichomes also serve as a unique single-celled platform for studying cell growth and cell wall biogenesis. As an integral step towards understanding the gene regulatory networks governing fiber production, here we report a comprehensive analysis on small RNA (sRNA)-directed posttranscriptional gene silencing (PTGS) in upland cotton (Gossypium hirsutum L.). Sequencing and analysis of twelve sRNA libraries representing diverse tissue samples including developing fibers enabled global identification of sRNA-producing loci and revealed sRNA expression profiles. A total of 386 MicroRNA (MIRNA) loci which give rise to mature miRNAs of 166 distinct sequences belonging to 55 families were identified in the G. hirsutum genome, of which 2 have not been previously reported in cotton. Targets for sRNA-directed PTGS were identified through integrated computational prediction and degradome sequencing. Several conserved miRNAs and trans-acting small interfering RNAs (ta-siRNA) targeting auxin signaling components were highly enriched in early stage developing fibers, indicating an important regulatory role of sRNAs in auxin-mediated fiber initiation and elongation. Intriguingly, members of a miRNA superfamily targeting plasma membrane calcium transporters (Ca2+-ATPases) were highly expressed in developing fibers, suggesting a potentially important role of Ca2+ signaling in the rapid polar growth of fiber cells. Finally, novel, fiber-expressed miRNAs, as well as 21-nt siRNAs derived from a diverse set of protein-coding transcripts were identified, providing further insights into the dynamic posttranscriptional regulation of the cotton fiber transcriptome. These data collectively indicate that emergence of novel morphological traits in plants, such as the seed trichomes in Gossypium species implicated regulatory innovations including sRNA-mediated PTGS.

Embargo status: Restricted until 09/2024. To request the author grant access, click on the PDF link to the left.



Arabidopsis, Autoinhibited Calcium-ATPase (ACA), Calcium signaling, Calmodulin-like (CML), EF hand (EF-h), miR391, posttranscriptional gene silencing (PTGS), spermatophytes, Cotton, Fiber development, miRNA-directed PTGS (miR-PTGS), Auxin signaling, phasiRNAs