RISC-Interacting Clearing 3’- 5’ Exoribonucleases (RICEs) degrade uridylated cleavage fragments to maintain functional RISC in Arabidopsis

  1. Zhonghui Zhang
  2. Fuqu Hu
  3. Min Woo Sung
  4. Chang Shu
  5. Claudia Castillo-González
  6. Hisashi Koiwa
  7. Guiliang Tang
  8. Marty Dickman
  9. Pingwei Li  Is a corresponding author
  10. Xiuren Zhang  Is a corresponding author
  1. Texas A&M University, United States
  2. Michigan Technological University, United States

Abstract

RNA-induced Silencing Complex (RISC) is composed of miRNAs and AGO proteins. AGOs use miRNAs as guides to slice target mRNAs to produce truncated 5' and 3' RNA fragments. The 5' cleaved RNA fragments are marked with uridylation for degradation. Here, we identified novel cofactors of Arabidopsis AGOs, named RICE1 and RICE2. RICE proteins specifically degraded single-strand (ss) RNAs in vitro; but neither miRNAs nor miRNA*s in vivo. RICE1 exhibited a DnaQ-like exonuclease fold and formed a homohexamer with the active sites located at the interfaces between RICE1 subunits. Notably, ectopic expression of catalytically-inactive RICE1 not only significantly reduced miRNA levels; but also increased 5' cleavage RISC fragments with extended uridine tails. We conclude that RICEs act to degrade uridylated 5’ products of AGO cleavage to maintain functional RISC. Our study also suggests a possible link between decay of cleaved target mRNAs and miRNA stability in RISC.

Data availability

The following data sets were generated
    1. Zhang Z
    2. Zhang X
    (2017) small RNAs in RICE mutants
    Publicly available at the NCBI Gene Expression Omnibus (accession no: GSE96951).
    1. Min Woo Sung
    2. Pingwei Li
    3. and Xiuren Zhang
    (2017) protein structure of RICE1
    Publicly available at the RCSB Protein Data Bank (accession no. 5V5F).

Article and author information

Author details

  1. Zhonghui Zhang

    Department of Biochemistry and Biophysics, Texas A&M University, College Station, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Fuqu Hu

    Department of Biochemistry and Biophysics, Texas A&M University, College Station, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Min Woo Sung

    Department of Biochemistry and Biophysics, Texas A&M University, College Station, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Chang Shu

    Department of Biochemistry and Biophysics, Texas A&M University, College Station, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Claudia Castillo-González

    Department of Biochemistry and Biophysics, Texas A&M University, College Station, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Hisashi Koiwa

    Department of Horticulture, Texas A&M University, College Station, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Guiliang Tang

    Department of Biological Sciences, Michigan Technological University, Houghton, United States
    Competing interests
    The authors declare that no competing interests exist.
  8. Marty Dickman

    Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6091-6921
  9. Pingwei Li

    Department of Biochemistry and Biophysics, Texas A&M University, College Station, United States
    For correspondence
    pingwei@tamu.edu
    Competing interests
    The authors declare that no competing interests exist.
  10. Xiuren Zhang

    Department of Biochemistry and Biophysics, Texas A&M University, College Station, United States
    For correspondence
    xiuren.zhang@tamu.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-8982-2999

Funding

National Science Foundation (CAREER MCB-1253369)

  • Xiuren Zhang

Cancer Prevention and Research Institute of Texas (RP160822)

  • Xiuren Zhang

The authors declare that there was no funding for this work.

Reviewing Editor

  1. David Baulcombe, University of Cambridge, United Kingdom

Publication history

  1. Received: December 21, 2016
  2. Accepted: April 29, 2017
  3. Accepted Manuscript published: May 2, 2017 (version 1)
  4. Version of Record published: May 31, 2017 (version 2)
  5. Version of Record updated: June 5, 2017 (version 3)

Copyright

© 2017, Zhang et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 3,007
    Page views
  • 674
    Downloads
  • 35
    Citations

Article citation count generated by polling the highest count across the following sources: Scopus, Crossref, PubMed Central.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Zhonghui Zhang
  2. Fuqu Hu
  3. Min Woo Sung
  4. Chang Shu
  5. Claudia Castillo-González
  6. Hisashi Koiwa
  7. Guiliang Tang
  8. Marty Dickman
  9. Pingwei Li
  10. Xiuren Zhang
(2017)
RISC-Interacting Clearing 3’- 5’ Exoribonucleases (RICEs) degrade uridylated cleavage fragments to maintain functional RISC in Arabidopsis
eLife 6:e24466.
https://doi.org/10.7554/eLife.24466

Further reading

    1. Biochemistry and Chemical Biology
    2. Microbiology and Infectious Disease
    Abhinay Ramaprasad, Paul-Christian Burda ... Michael J Blackman
    Research Article Updated

    The malaria parasite Plasmodium falciparum synthesizes significant amounts of phospholipids to meet the demands of replication within red blood cells. De novo phosphatidylcholine (PC) biosynthesis via the Kennedy pathway is essential, requiring choline that is primarily sourced from host serum lysophosphatidylcholine (lysoPC). LysoPC also acts as an environmental sensor to regulate parasite sexual differentiation. Despite these critical roles for host lysoPC, the enzyme(s) involved in its breakdown to free choline for PC synthesis are unknown. Here, we show that a parasite glycerophosphodiesterase (PfGDPD) is indispensable for blood stage parasite proliferation. Exogenous choline rescues growth of PfGDPD-null parasites, directly linking PfGDPD function to choline incorporation. Genetic ablation of PfGDPD reduces choline uptake from lysoPC, resulting in depletion of several PC species in the parasite, whilst purified PfGDPD releases choline from glycerophosphocholine in vitro. Our results identify PfGDPD as a choline-releasing glycerophosphodiesterase that mediates a critical step in PC biosynthesis and parasite survival.

    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics
    Jiemin Shen, Azaan Saalim Wilbon ... Yaping Pan
    Research Article Updated

    Ferroportin (Fpn) is a transporter that releases ferrous ion (Fe2+) from cells and is important for homeostasis of iron in circulation. Export of one Fe2+ by Fpn is coupled to import of two H+ to maintain charge balance. Here, we show that human Fpn (HsFpn) binds to and mediates Ca2+ transport. We determine the structure of Ca2+-bound HsFpn and identify a single Ca2+ binding site distinct from the Fe2+ binding sites. Further studies validate the Ca2+ binding site and show that Ca2+ transport is not coupled to transport of another ion. In addition, Ca2+ transport is significantly inhibited in the presence of Fe2+ but not vice versa. Function of Fpn as a Ca2+ uniporter may allow regulation of iron homeostasis by Ca2+.