Distinct and cooperative activities of HESO1 and URT1 nucleotidyl transferases in microRNA turnover in Arabidopsis.
3' uridylation is increasingly recognized as a conserved RNA modification process associated with RNA turnover in eukaryotes. 2'-O-methylation on the 3' terminal ribose protects micro(mi)RNAs from 3' truncation and 3' uridylation in Arabidopsis. Previously, we identified HESO1 as the nucleotidyl transferase that uridylates most unmethylated miRNAs in vivo, but substantial 3' tailing of miRNAs still remains in heso1 loss-of-function mutants. In this study, we found that among nine other potential nucleotidyl transferases, UTP:RNA uridylyltransferase 1 (URT1) is the single most predominant nucleotidyl transferase that tails miRNAs. URT1 and HESO1 prefer substrates with different 3' end nucleotides in vitro and act cooperatively to tail different forms of the same miRNAs in vivo. Moreover, both HESO1 and URT1 exhibit nucleotidyl transferase activity on AGO1-bound miRNAs. Although these enzymes are able to add long tails to AGO1-bound miRNAs, the tailed miRNAs remain associated with AGO1. Moreover, tailing of AGO1-bound miRNA165/6 drastically reduces the slicing activity of AGO1-miR165/6, suggesting that tailing reduces miRNA activity. However, monouridylation of miR171a by URT1 endows the miRNA the ability to trigger the biogenesis of secondary siRNAs. Therefore, 3' tailing could affect the activities of miRNAs in addition to leading to miRNA degradation.
Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, California, United States of America; Rice Research Institute, Sichuan Agricultural University, Chengdu Wenjiang, Sichuan, China.
Bin
B
Tu
Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, California, United States of America; Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences, Shenzhen University, Shenzhen, China.
Li
L
Liu
Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences, Shenzhen University, Shenzhen, China.
Chi
C
Xu
Department of Plant & Soil Sciences, and Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, United States of America.
Jixian
J
Zhai
Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, California, United States of America.
Shengben
S
Li
Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, California, United States of America.
Miguel A
MA
Lopez
Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, California, United States of America.
Yuanyuan
Y
Zhao
Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, California, United States of America.
Yu
Y
Yu
Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, California, United States of America.
Vanitharani
V
Ramachandran
Center for Plant Science Innovation & School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America.
Guodong
G
Ren
Center for Plant Science Innovation & School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America.
Bin
B
Yu
Rice Research Institute, Sichuan Agricultural University, Chengdu Wenjiang, Sichuan, China.
Shigui
S
Li
Department of Plant & Soil Sciences, and Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, United States of America.
Blake C
BC
Meyers
Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences, Shenzhen University, Shenzhen, China.
Beixin
B
Mo
Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, California, United States of America; Howard Hughes Medical Institute, University of California, Riverside, Riverside, California, United States of America.
Xuemei
X
Chen
D017360:Arabidopsis / Q000201:enzymology / Q000235:genetics; D029681:Arabidopsis Proteins / Q000235:genetics*; D060565:Argonaute Proteins / Q000235:genetics; D008745:Methylation; D035683:MicroRNAs / Q000235:genetics*; D009713:Nucleotidyltransferases / Q000235:genetics*; D012316:RNA Nucleotidyltransferases / Q000235:genetics*; D020871:RNA Stability / Q000235:genetics*; D034741:RNA, Small Interfering / Q000235:genetics; D014529:Uridine / Q000378:metabolism
C117457:AGO1 protein, Arabidopsis; D029681:Arabidopsis Proteins; D060565:Argonaute Proteins; C556250:MIRN171 microRNA, Arabidopsis; D035683:MicroRNAs; D034741:RNA, Small Interfering; C576617:HESO1 protein, Arabidopsis; D009713:Nucleotidyltransferases; D012316:RNA Nucleotidyltransferases; C584074:URT1 protein, Arabidopsis; D014529:Uridine