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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

1
Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711.
2
Donald Danforth Plant Science Center, St. Louis, MO 63132.
3
Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521.
4
Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637.
5
Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637.
6
Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, 518060 Shenzhen, China.
7
Donald Danforth Plant Science Center, St. Louis, MO 63132; bmeyers@danforthcenter.org.
8
Division of Plant Sciences, University of Missouri, Columbia, MO 65211.

Abstract

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.

KEYWORDS:

disease resistance; microRNA; plant evolution; soybean; uridylation

PMID:
30012624
PMCID:
PMC6077734
DOI:
10.1073/pnas.1807403115
[Indexed for MEDLINE]
Free PMC Article

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