• We are sorry, but NCBI web applications do not support your browser and may not function properly. More information
Logo of narLink to Publisher's site
Nucleic Acids Res. Dec 25, 1994; 22(25): 5582–5589.
PMCID: PMC310120

Binding of Y-box proteins to RNA: involvement of different protein domains.


Eukaryotic Y-box proteins are reported to interact with a wide variety of nucleic acid structures to act as transcription factors and mRNA masking proteins. The modular structure of Y-box proteins includes a highly conserved N-terminal cold-shock domain (CSD, equivalent to the bacterial cold-shock proteins) plus four basic C-terminal domains containing arginine clusters and aromatic residues. In addition, the basic domains are separated by acidic regions which contain several potential sites for serine/threonine phosphorylation. The interaction of Y-box proteins, isolated from Xenopus oocytes (FRGY2 type), with RNA molecules has been studied by UV crosslinking and protein fragmentation. We have identified two distinct binding activities. The CSD interacts preferentially with the polypurines poly(A,G) and poly(G) but not poly(A), this activity being sensitive to 5 mM MgCl2 but not to 5 mM spermidine. In the presence of 1 mM MgCl2 or 1 mM spermidine, the basic domains interact preferentially with poly(C,U), this activity being sensitive to 0.5 M NaCl. Binding of the basic domains is also sensitive to low concentrations of heparin. The basic domains can be crosslinked individually to labelled RNA. These results are discussed with reference to the various specificities noted in the binding of Y-box proteins to RNA and DNA.

Full text

Full text is available as a scanned copy of the original print version. Get a printable copy (PDF file) of the complete article (1.9M), or click on a page image below to browse page by page. Links to PubMed are also available for Selected References.

Images in this article

Click on the image to see a larger version.

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Wolffe AP, Tafuri S, Ranjan M, Familari M. The Y-box factors: a family of nucleic acid binding proteins conserved from Escherichia coli to man. New Biol. 1992 Apr;4(4):290–298. [PubMed]
  • Wolffe AP. Structural and functional properties of the evolutionarily ancient Y-box family of nucleic acid binding proteins. Bioessays. 1994 Apr;16(4):245–251. [PubMed]
  • Didier DK, Schiffenbauer J, Woulfe SL, Zacheis M, Schwartz BD. Characterization of the cDNA encoding a protein binding to the major histocompatibility complex class II Y box. Proc Natl Acad Sci U S A. 1988 Oct;85(19):7322–7326. [PMC free article] [PubMed]
  • Dorn A, Durand B, Marfing C, Le Meur M, Benoist C, Mathis D. Conserved major histocompatibility complex class II boxes--X and Y--are transcriptional control elements and specifically bind nuclear proteins. Proc Natl Acad Sci U S A. 1987 Sep;84(17):6249–6253. [PMC free article] [PubMed]
  • Kolluri R, Torrey TA, Kinniburgh AJ. A CT promoter element binding protein: definition of a double-strand and a novel single-strand DNA binding motif. Nucleic Acids Res. 1992 Jan 11;20(1):111–116. [PMC free article] [PubMed]
  • Grant CE, Deeley RG. Cloning and characterization of chicken YB-1: regulation of expression in the liver. Mol Cell Biol. 1993 Jul;13(7):4186–4196. [PMC free article] [PubMed]
  • Horwitz EM, Maloney KA, Ley TJ. A human protein containing a "cold shock" domain binds specifically to H-DNA upstream from the human gamma-globin genes. J Biol Chem. 1994 May 13;269(19):14130–14139. [PubMed]
  • Lenz J, Okenquist SA, LoSardo JE, Hamilton KK, Doetsch PW. Identification of a mammalian nuclear factor and human cDNA-encoded proteins that recognize DNA containing apurinic sites. Proc Natl Acad Sci U S A. 1990 May;87(9):3396–3400. [PMC free article] [PubMed]
  • Hasegawa SL, Doetsch PW, Hamilton KK, Martin AM, Okenquist SA, Lenz J, Boss JM. DNA binding properties of YB-1 and dbpA: binding to double-stranded, single-stranded, and abasic site containing DNAs. Nucleic Acids Res. 1991 Sep 25;19(18):4915–4920. [PMC free article] [PubMed]
  • Kandala JC, Guntaka RV. Cloning of Rous sarcoma virus enhancer factor genes. I. Evidence that RSV-EF-I is related to Y-box (inverted CCAAT) binding proteins and binds to multiple motifs in the RSV enhancer. Virology. 1994 Feb;198(2):514–523. [PubMed]
  • Sommerville J. RNA-binding proteins: masking proteins revealed. Bioessays. 1992 May;14(5):337–339. [PubMed]
  • Kwon YK, Murray MT, Hecht NB. Proteins homologous to the Xenopus germ cell-specific RNA-binding proteins p54/p56 are temporally expressed in mouse male germ cells. Dev Biol. 1993 Jul;158(1):99–100. [PubMed]
  • Tafuri SR, Familari M, Wolffe AP. A mouse Y box protein, MSY1, is associated with paternal mRNA in spermatocytes. J Biol Chem. 1993 Jun 5;268(16):12213–12220. [PubMed]
  • Wistow G. Cold shock and DNA binding. Nature. 1990 Apr 26;344(6269):823–824. [PubMed]
  • Schindelin H, Marahiel MA, Heinemann U. Universal nucleic acid-binding domain revealed by crystal structure of the B. subtilis major cold-shock protein. Nature. 1993 Jul 8;364(6433):164–168. [PubMed]
  • Schnuchel A, Wiltscheck R, Czisch M, Herrler M, Willimsky G, Graumann P, Marahiel MA, Holak TA. Structure in solution of the major cold-shock protein from Bacillus subtilis. Nature. 1993 Jul 8;364(6433):169–171. [PubMed]
  • Schindelin H, Jiang W, Inouye M, Heinemann U. Crystal structure of CspA, the major cold shock protein of Escherichia coli. Proc Natl Acad Sci U S A. 1994 May 24;91(11):5119–5123. [PMC free article] [PubMed]
  • Newkirk K, Feng W, Jiang W, Tejero R, Emerson SD, Inouye M, Montelione GT. Solution NMR structure of the major cold shock protein (CspA) from Escherichia coli: identification of a binding epitope for DNA. Proc Natl Acad Sci U S A. 1994 May 24;91(11):5114–5118. [PMC free article] [PubMed]
  • La Teana A, Brandi A, Falconi M, Spurio R, Pon CL, Gualerzi CO. Identification of a cold shock transcriptional enhancer of the Escherichia coli gene encoding nucleoid protein H-NS. Proc Natl Acad Sci U S A. 1991 Dec 1;88(23):10907–10911. [PMC free article] [PubMed]
  • Graumann P, Marahiel MA. The major cold shock protein of Bacillus subtilis CspB binds with high affinity to the ATTGG- and CCAAT sequences in single stranded oligonucleotides. FEBS Lett. 1994 Jan 31;338(2):157–160. [PubMed]
  • Doniger J, Landsman D, Gonda MA, Wistow G. The product of unr, the highly conserved gene upstream of N-ras, contains multiple repeats similar to the cold-shock domain (CSD), a putative DNA-binding motif. New Biol. 1992 Apr;4(4):389–395. [PubMed]
  • Tafuri SR, Wolffe AP. Xenopus Y-box transcription factors: molecular cloning, functional analysis and developmental regulation. Proc Natl Acad Sci U S A. 1990 Nov;87(22):9028–9032. [PMC free article] [PubMed]
  • Murray MT, Schiller DL, Franke WW. Sequence analysis of cytoplasmic mRNA-binding proteins of Xenopus oocytes identifies a family of RNA-binding proteins. Proc Natl Acad Sci U S A. 1992 Jan 1;89(1):11–15. [PMC free article] [PubMed]
  • Deschamps S, Viel A, Garrigos M, Denis H, le Maire M. mRNP4, a major mRNA-binding protein from Xenopus oocytes is identical to transcription factor FRG Y2. J Biol Chem. 1992 Jul 15;267(20):13799–13802. [PubMed]
  • Burd CG, Dreyfuss G. Conserved structures and diversity of functions of RNA-binding proteins. Science. 1994 Jul 29;265(5172):615–621. [PubMed]
  • Cummings A, Barrett P, Sommerville J. Multiple modifications in the phosphoproteins bound to stored messenger RNA in Xenopus oocytes. Biochim Biophys Acta. 1989 Dec 14;1014(3):319–326. [PubMed]
  • Deschamps S, Viel A, Denis H, le Maire M. Purification of two thermostable components of messenger ribonucleoprotein particles (mRNPs) from Xenopus laevis oocytes, belonging to a novel class of RNA-binding proteins. FEBS Lett. 1991 Apr 22;282(1):110–114. [PubMed]
  • Murray MT, Krohne G, Franke WW. Different forms of soluble cytoplasmic mRNA binding proteins and particles in Xenopus laevis oocytes and embryos. J Cell Biol. 1991 Jan;112(1):1–11. [PMC free article] [PubMed]
  • Marello K, LaRovere J, Sommerville J. Binding of Xenopus oocyte masking proteins to mRNA sequences. Nucleic Acids Res. 1992 Nov 11;20(21):5593–5600. [PMC free article] [PubMed]
  • Nute PE, Mahoney WC. Complete amino acid sequence of the gamma chain from the major fetal hemoglobin of the pig-tailed macaque, Macaca nemestrina. Biochemistry. 1979 Feb 6;18(3):467–472. [PubMed]
  • Enfield DL, Ericsson LH, Fujikawa K, Walsh KA, Neurath H, Titani K. Amino acid sequence of the light chain of bovine factor X1 (Stuart factor). Biochemistry. 1980 Feb 19;19(4):659–667. [PubMed]
  • Jacquemin-Sablon H, Triqueneaux G, Deschamps S, le Maire M, Doniger J, Dautry F. Nucleic acid binding and intracellular localization of unr, a protein with five cold shock domains. Nucleic Acids Res. 1994 Jul 11;22(13):2643–2650. [PMC free article] [PubMed]
  • Ranjan M, Tafuri SR, Wolffe AP. Masking mRNA from translation in somatic cells. Genes Dev. 1993 Sep;7(9):1725–1736. [PubMed]
  • Spitkovsky DD, Royer-Pokora B, Delius H, Kisseljov F, Jenkins NA, Gilbert DJ, Copeland NG, Royer HD. Tissue restricted expression and chromosomal localization of the YB-1 gene encoding a 42 kD nuclear CCAAT binding protein. Nucleic Acids Res. 1992 Feb 25;20(4):797–803. [PMC free article] [PubMed]
  • Gai XX, Lipson KE, Prystowsky MB. Unusual DNA binding characteristics of an in vitro translation product of the CCAAT binding protein mYB-1. Nucleic Acids Res. 1992 Feb 11;20(3):601–606. [PMC free article] [PubMed]
  • Kashanchi F, Duvall JF, Dittmer J, Mireskandari A, Reid RL, Gitlin SD, Brady JN. Involvement of transcription factor YB-1 in human T-cell lymphotropic virus type I basal gene expression. J Virol. 1994 Jan;68(1):561–565. [PMC free article] [PubMed]
  • Ozer J, Faber M, Chalkley R, Sealy L. Isolation and characterization of a cDNA clone for the CCAAT transcription factor EFIA reveals a novel structural motif. J Biol Chem. 1990 Dec 25;265(36):22143–22152. [PubMed]
  • Firulli AB, Maibenco DC, Kinniburgh AJ. The identification of a tandem H-DNA structure in the c-myc nuclease sensitive promoter element. Biochem Biophys Res Commun. 1992 May 29;185(1):264–270. [PubMed]
  • Laing LG, Gluick TC, Draper DE. Stabilization of RNA structure by Mg ions. Specific and non-specific effects. J Mol Biol. 1994 Apr 15;237(5):577–587. [PubMed]
  • Bendall AJ, Molloy PL. Base preferences for DNA binding by the bHLH-Zip protein USF: effects of MgCl2 on specificity and comparison with binding of Myc family members. Nucleic Acids Res. 1994 Jul 25;22(14):2801–2810. [PMC free article] [PubMed]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press


Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...


Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...