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Proc Natl Acad Sci U S A. 2018 Jul 31;115(31):8037-8042. doi: 10.1073/pnas.1807403115. Epub 2018 Jul 16.

Biogenesis of a 22-nt microRNA in Phaseoleae species by precursor-programmed uridylation.

Author information

Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711.
Donald Danforth Plant Science Center, St. Louis, MO 63132.
Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521.
Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637.
Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637.
Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, 518060 Shenzhen, China.
Donald Danforth Plant Science Center, St. Louis, MO 63132;
Division of Plant Sciences, University of Missouri, Columbia, MO 65211.


Phased, secondary siRNAs (phasiRNAs) represent a class of small RNAs in plants generated via distinct biogenesis pathways, predominantly dependent on the activity of 22-nt miRNAs. Most 22-nt miRNAs are processed by DCL1 from miRNA precursors containing an asymmetric bulge, yielding a 22/21-nt miRNA/miRNA* duplex. Here we show that miR1510, a soybean miRNA capable of triggering phasiRNA production from numerous nucleotide-binding leucine-rich repeat (NB-LRRs), previously described as 21 nt in its mature form, primarily accumulates as a 22-nt isoform via monouridylation. We demonstrate that, in Arabidopsis, this uridylation is performed by HESO1. Biochemical experiments showed that the 3' terminus of miR1510 is only partially 2'-O-methylated because of the terminal mispairing in the miR1510/miR1510* duplex that inhibits HEN1 activity in soybean. miR1510 emerged in the Phaseoleae ∼41-42 million years ago with a conserved precursor structure yielding a 22-nt monouridylated form, yet a variant in mung bean is processed directly in a 22-nt mature form. This analysis of miR1510 yields two observations: (i) plants can utilize postprocessing modification to generate abundant 22-nt miRNA isoforms to more efficiently regulate target mRNA abundances; and (ii) comparative analysis demonstrates an example of selective optimization of precursor processing of a young plant miRNA.


disease resistance; microRNA; plant evolution; soybean; uridylation

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