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PMID: 15769874 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S.

Binding specificity and mRNA targets of a C. elegans PUF protein, FBF-1.

RNA (New York, N.Y.) ·Vol. 11 ·No. 4 ·2005-04-00 ·Pages 447-58

Bernstein D, Hook B, Hajarnavis A, Opperman L, Wickens M

Abstract

Sequence-specific RNA-protein interactions underlie regulation of many mRNAs. Here we analyze the RNA sequence specificity of Caenorhabditis elegans FBF-1, a founding member of the PUF protein family. Like other PUF proteins, FBF-1 binds to the 3' UTR of target mRNAs and decreases expression of those target genes. Here, we show that FBF-1 and its close relative, FBF-2, bind with similar affinity to multiple RNA sites. We use mutagenesis and in vivo selection experiments to identify nucleotides that are essential for FBF-1 binding. The binding elements comprise a "core" central region and flanking sequences. The core region is similar but distinct from the binding sites of other PUF proteins. We combine the identification of binding elements with informatics to predict new FBF-1 binding sites in a C. elegans 3' UTR database. These data identify a set of new candidate mRNA targets of FBF-1 and FBF-2.

MeSH Terms
Amino Acid Sequence Animals Binding Sites Caenorhabditis elegans/genetics,metabolism Caenorhabditis elegans Proteins/genetics,metabolism Molecular Sequence Data Protein Binding RNA, Helminth/metabolism RNA, Messenger/metabolism RNA-Binding Proteins/genetics,metabolism Two-Hybrid System Techniques Yeasts/genetics,metabolism
Chemicals
Caenorhabditis elegans Proteins RNA, Helminth RNA, Messenger RNA-Binding Proteins fem-3-binding protein, C elegans
Authors & Affiliations
5 authors, click to expand affiliations / ORCID
Bernstein David
Department of Biochemistry, University of Wisconsin, 433 Babcock Drive, Madison, WI 53706, USA.
Hook Brad
Hajarnavis Ashwin
Opperman Laura
Wickens Marvin
References (32)
32 references, click to expand
  1. FBF-1 and FBF-2 regulate the size of the mitotic region in the C. elegans germline.
    Dev Cell. 2004 Nov;7(5):697-707 PMID: 15525531
  2. NANOS-3 and FBF proteins physically interact to control the sperm-oocyte switch in Caenorhabditis elegans.
    Curr Biol. 1999 Sep 23;9(18):1009-18 PMID: 10508609
  3. Recruitment of Nanos to hunchback mRNA by Pumilio.
    Genes Dev. 1999 Oct 15;13(20):2704-12 PMID: 10541556
  4. Computational identification of cis-acting elements affecting post-transcriptional control of gene expression in Saccharomyces cerevisiae.
    Nucleic Acids Res. 2000 Apr 1;28(7):1604-17 PMID: 10710427
  5. CPEB proteins control two key steps in spermatogenesis in C. elegans.
    Genes Dev. 2000 Oct 15;14(20):2596-609 PMID: 11040214
  6. The Puf3 protein is a transcript-specific regulator of mRNA degradation in yeast.
    EMBO J. 2000 Dec 1;19(23):6602-11 PMID: 11101532
  7. Post-transcriptional regulation through the HO 3'-UTR by Mpt5, a yeast homolog of Pumilio and FBF.
    EMBO J. 2001 Feb 1;20(3):552-61 PMID: 11157761
  8. Drosophila Brain Tumor is a translational repressor.
    Genes Dev. 2001 Mar 15;15(6):762-73 PMID: 11274060
  9. Structure of Pumilio reveals similarity between RNA and peptide binding motifs.
    Cell. 2001 Apr 20;105(2):281-9 PMID: 11336677
  10. Crystal structure of a Pumilio homology domain.
    Mol Cell. 2001 Apr;7(4):855-65 PMID: 11336708
  11. Biochemical identification of Xenopus Pumilio as a sequence-specific cyclin B1 mRNA-binding protein that physically interacts with a Nanos homolog, Xcat-2, and a cytoplasmic polyadenylation element-binding protein.
    J Biol Chem. 2001 Jun 15;276(24):20945-53 PMID: 11283000
  12. PUM2, a novel murine puf protein, and its consensus RNA-binding site.
    RNA. 2001 Dec;7(12):1855-66 PMID: 11780640
  13. A PUF family portrait: 3'UTR regulation as a way of life.
    Trends Genet. 2002 Mar;18(3):150-7 PMID: 11858839
  14. A conserved RNA-binding protein controls germline stem cells in Caenorhabditis elegans.
    Nature. 2002 Jun 6;417(6889):660-3 PMID: 12050669
  15. Analyzing mRNA-protein complexes using a yeast three-hybrid system.
    Methods. 2002 Feb;26(2):123-41 PMID: 12054889
  16. Modular recognition of RNA by a human pumilio-homology domain.
    Cell. 2002 Aug 23;110(4):501-12 PMID: 12202039
  17. GLD-3, a bicaudal-C homolog that inhibits FBF to control germline sex determination in C. elegans.
    Dev Cell. 2002 Nov;3(5):697-710 PMID: 12431376
  18. Involvement of Xenopus Pumilio in the translational regulation that is specific to cyclin B1 mRNA during oocyte maturation.
    Mech Dev. 2003 Aug;120(8):865-80 PMID: 12963108
  19. Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast.
    PLoS Biol. 2004 Mar;2(3):E79 PMID: 15024427
  20. Recruitment of the Puf3 protein to its mRNA target for regulation of mRNA decay in yeast.
    RNA. 2004 Oct;10(10):1625-36 PMID: 15337848
  21. GLD-3 and control of the mitosis/meiosis decision in the germline of Caenorhabditis elegans.
    Genetics. 2004 Sep;168(1):147-60 PMID: 15454534
  22. Computer prediction of RNA structure.
    Methods Enzymol. 1989;180:262-88 PMID: 2482418
  23. The Caenorhabditis elegans sex determining gene fem-3 is regulated post-transcriptionally.
    EMBO J. 1992 Jun;11(6):2303-10 PMID: 1376249
  24. Specificity of ribonucleoprotein interaction determined by RNA folding during complex formulation.
    Nature. 1996 Apr 18;380(6575):646-50 PMID: 8602269
  25. Molecular control of vertebrate iron metabolism: mRNA-based regulatory circuits operated by iron, nitric oxide, and oxidative stress.
    Proc Natl Acad Sci U S A. 1996 Aug 6;93(16):8175-82 PMID: 8710843
  26. A conserved RNA-binding protein that regulates sexual fates in the C. elegans hermaphrodite germ line.
    Nature. 1997 Dec 4;390(6659):477-84 PMID: 9393998
  27. The Pumilio protein binds RNA through a conserved domain that defines a new class of RNA-binding proteins.
    RNA. 1997 Dec;3(12):1421-33 PMID: 9404893
  28. Searching for patterns in genomic data.
    Trends Genet. 1997 Dec;13(12):497-8 PMID: 9433140
  29. The Pumilio RNA-binding domain is also a translational regulator.
    Mol Cell. 1998 May;1(6):863-72 PMID: 9660969
  30. The PUMILIO-RNA interaction: a single RNA-binding domain monomer recognizes a bipartite target sequence.
    Biochemistry. 1999 Jan 12;38(2):596-604 PMID: 9888799
  31. Starvation promotes Dictyostelium development by relieving PufA inhibition of PKA translation through the YakA kinase pathway.
    Development. 1999 Jun;126(14):3263-74 PMID: 10375515
  32. RNA-protein interactions in the yeast three-hybrid system: affinity, sensitivity, and enhanced library screening.
    RNA. 2005 Feb;11(2):227-33 PMID: 15613539
Article Info
Journal
RNA (New York, N.Y.)
Abbr.
RNA
ISSN
1355-8382
DOI
10.1261/rna.7255805
Published
2005-04-00
Pages
447-58
Language
English
Region
United States
NLM ID
9509184
PMCID
PMC1370734
Subset
IM
Grants
NIGMS NIH HHS · GM50942 · United States
NIGMS NIH HHS · R01 GM050942 · United States
NIGMS NIH HHS · R37 GM031892 · United States
NIGMS NIH HHS · GM31892 · United States
NIGMS NIH HHS · R01 GM031892 · United States
External Links
PubMed source DOI: 10.1261/rna.7255805 PMC Full Text View journal details
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