Home LiteratureArticle Details
PMID: 24850884 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

The SBP2 protein central to selenoprotein synthesis contacts the human ribosome at expansion segment 7L of the 28S rRNA.

RNA (New York, N.Y.) ·Vol. 20 ·No. 7 ·2014-07-00 ·Pages 1046-56

Kossinova O, Malygin A, Krol A, Karpova G

Abstract

SBP2 is a pivotal protein component in selenoprotein synthesis. It binds the SECIS stem-loop in the 3' UTR of selenoprotein mRNA and interacts with both the specialized translation elongation factor and the ribosome at the 60S subunit. In this work, our goal was to identify the binding partners of SBP2 on the ribosome. Cross-linking experiments with bifunctional reagents demonstrated that the SBP2-binding site on the human ribosome is mainly formed by the 28S rRNA. Direct hydroxyl radical probing of the entire 28S rRNA revealed that SBP2 bound to 80S ribosomes or 60S subunits protects helix ES7L-E in expansion segment 7 of the 28S rRNA. Diepoxybutane cross-linking confirmed the interaction of SBP2 with helix ES7L-E. Additionally, binding of SBP2 to the ribosome led to increased reactivity toward chemical probes of a few bases in ES7L-E and in the universally conserved helix H89, indicative of conformational changes in the 28S rRNA in response to SBP2 binding. This study revealed for the first time that SBP2 makes direct contacts with a discrete region of the human 28S rRNA.

Keywords
SECIS-binding protein 2 chemical probing cross-linking approach mammalian ribosome selenocysteine incorporation
MeSH Terms
Amino Acid Sequence Base Sequence Binding Sites Humans Models, Molecular Molecular Sequence Data Protein Binding RNA, Ribosomal, 28S/chemistry,metabolism RNA-Binding Proteins/chemistry,metabolism Ribosomes/chemistry,metabolism Selenoproteins/biosynthesis Sequence Homology, Nucleic Acid
Chemicals
RNA, Ribosomal, 28S RNA-Binding Proteins SECISBP2 protein, human Selenoproteins
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Kossinova Olga
Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 67084 Strasbourg, France.
Malygin Alexey
Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia.
Krol Alain
Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 67084 Strasbourg, France.
Karpova Galina
Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia.
References (41)
41 references, click to expand
  1. The ribosomal proteins of Escherichia coli. I. Purification of the 30S ribosomal proteins.
    Biochemistry. 1969 Jul;8(7):2897-905 PMID: 4897206
  2. The L7Ae RNA binding motif is a multifunctional domain required for the ribosome-dependent Sec incorporation activity of Sec insertion sequence binding protein 2.
    Mol Cell Biol. 2007 Sep;27(18):6350-60 PMID: 17636016
  3. Simulating movement of tRNA into the ribosome during decoding.
    Proc Natl Acad Sci U S A. 2005 Nov 1;102(44):15854-9 PMID: 16249344
  4. Position of eukaryotic initiation factor eIF5B on the 80S ribosome mapped by directed hydroxyl radical probing.
    EMBO J. 2007 Jul 11;26(13):3109-23 PMID: 17568775
  5. Altered RNA binding activity underlies abnormal thyroid hormone metabolism linked to a mutation in selenocysteine insertion sequence-binding protein 2.
    J Biol Chem. 2007 Nov 30;282(48):34653-62 PMID: 17901054
  6. Methyl 4-mercaptobutyrimidate as a cleavable cross-linking reagent and its application to the Escherichia coli 30S ribosome.
    Biochemistry. 1973 Aug 14;12(17):3266-73 PMID: 4581787
  7. A novel RNA binding protein, SBP2, is required for the translation of mammalian selenoprotein mRNAs.
    EMBO J. 2000 Jan 17;19(2):306-14 PMID: 10637234
  8. HCV IRES interacts with the 18S rRNA to activate the 40S ribosome for subsequent steps of translation initiation.
    Nucleic Acids Res. 2013 Oct;41(18):8706-14 PMID: 23873958
  9. A novel insight into the mechanism of mammalian selenoprotein synthesis.
    RNA. 2013 Aug;19(8):1147-58 PMID: 23788723
  10. Reconstitution of selenocysteine incorporation reveals intrinsic regulation by SECIS elements.
    J Mol Biol. 2013 Jul 24;425(14):2415-22 PMID: 23624110
  11. Intra-RNA and RNA-protein cross-linking techniques in Escherichia coli ribosomes.
    Methods Enzymol. 1988;164:287-309 PMID: 3071669
  12. The structure of helix 89 of 23S rRNA is important for peptidyl transferase function of Escherichia coli ribosome.
    FEBS Lett. 2011 Oct 3;585(19):3073-8 PMID: 21875584
  13. The mechanism of free base formation from DNA by bleomycin. A proposal based on site specific tritium release from Poly(dA.dU).
    J Biol Chem. 1983 Apr 25;258(8):4694-7 PMID: 6187741
  14. Chemical probing of RNA and RNA/protein complexes.
    Methods Enzymol. 2009;468:147-65 PMID: 20946769
  15. Isolation of ribosomal subunits containing intact rRNA from human placenta: estimation of functional activity of 80S ribosomes.
    Anal Biochem. 1991 Nov 1;198(2):219-23 PMID: 1799204
  16. Characterization of mSelB, a novel mammalian elongation factor for selenoprotein translation.
    EMBO J. 2000 Sep 1;19(17):4796-805 PMID: 10970870
  17. Cross-linking of ribosomes using 2-iminothiolane (methyl 4-mercaptobutyrimidate) and identification of cross-linked proteins by diagonal polyacrylamide/sodium dodecyl sulfate gel electrophoresis.
    Methods Enzymol. 1979;59:534-50 PMID: 374953
  18. Crystal structure of the eukaryotic 60S ribosomal subunit in complex with initiation factor 6.
    Science. 2011 Nov 18;334(6058):941-8 PMID: 22052974
  19. mRNA binding track in the human 80S ribosome for mRNA analogues randomly substituted with 4-thiouridine residues.
    Biochemistry. 1994 May 24;33(20):6201-6 PMID: 7514889
  20. cDNA cloning, expression pattern and RNA binding analysis of human selenocysteine insertion sequence (SECIS) binding protein 2.
    Gene. 2002 May 29;291(1-2):279-85 PMID: 12095701
  21. An improved definition of the RNA-binding specificity of SECIS-binding protein 2, an essential component of the selenocysteine incorporation machinery.
    Nucleic Acids Res. 2007;35(6):1868-84 PMID: 17332014
  22. The involvement of two distinct regions of 23 S ribosomal RNA in tRNA selection.
    J Mol Biol. 1995 Dec 15;254(5):838-47 PMID: 7500354
  23. The selenocysteine incorporation machinery: interactions between the SECIS RNA and the SECIS-binding protein SBP2.
    RNA. 2001 Oct;7(10):1442-53 PMID: 11680849
  24. Decoding apparatus for eukaryotic selenocysteine insertion.
    EMBO Rep. 2000 Aug;1(2):158-63 PMID: 11265756
  25. Inferring noncoding RNA families and classes by means of genome-scale structure-based clustering.
    PLoS Comput Biol. 2007 Apr 13;3(4):e65 PMID: 17432929
  26. Insight into mammalian selenocysteine insertion: domain structure and ribosome binding properties of Sec insertion sequence binding protein 2.
    Mol Cell Biol. 2001 Mar;21(5):1491-8 PMID: 11238886
  27. The SBP2 and 15.5 kD/Snu13p proteins share the same RNA binding domain: identification of SBP2 amino acids important to SECIS RNA binding.
    RNA. 2002 Oct;8(10):1308-18 PMID: 12403468
  28. Recognition of UGA as a selenocysteine codon in type I deiodinase requires sequences in the 3' untranslated region.
    Nature. 1991 Sep 19;353(6341):273-6 PMID: 1832744
  29. Specific DNA adducts induced by some mono-substituted epoxides in vitro and in vivo.
    Chem Biol Interact. 2000 Dec 15;129(3):209-29 PMID: 11137062
  30. Eukaryotic rpL10 drives ribosomal rotation.
    Nucleic Acids Res. 2014 Feb;42(3):2049-63 PMID: 24214990
  31. Yeast ribosomal protein L10 helps coordinate tRNA movement through the large subunit.
    Nucleic Acids Res. 2008 Nov;36(19):6187-98 PMID: 18824477
  32. Structures of the human and Drosophila 80S ribosome.
    Nature. 2013 May 2;497(7447):80-5 PMID: 23636399
  33. Initiation factor IF 2 binds to the alpha-sarcin loop and helix 89 of Escherichia coli 23S ribosomal RNA.
    RNA. 2001 Aug;7(8):1173-9 PMID: 11497435
  34. Selenocysteine insertion sequence (SECIS)-binding protein 2 alters conformational dynamics of residues involved in tRNA accommodation in 80 S ribosomes.
    J Biol Chem. 2012 Mar 23;287(13):10664-10673 PMID: 22308032
  35. RNA-protein neighbourhoods of the ribosome obtained by crosslinking.
    Eur J Biochem. 1978 Sep 1;89(2):353-9 PMID: 361392
  36. The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs.
    BMC Bioinformatics. 2002;3:2 PMID: 11869452
  37. The selenocysteine-specific elongation factor contains a novel and multi-functional domain.
    J Biol Chem. 2012 Nov 9;287(46):38936-45 PMID: 22992746
  38. Evolutionary history of selenocysteine incorporation from the perspective of SECIS binding proteins.
    BMC Evol Biol. 2009 Sep 10;9:229 PMID: 19744324
  39. A short motif in Drosophila SECIS Binding Protein 2 provides differential binding affinity to SECIS RNA hairpins.
    Nucleic Acids Res. 2009 Apr;37(7):2126-41 PMID: 19223320
  40. MUSCLE: multiple sequence alignment with high accuracy and high throughput.
    Nucleic Acids Res. 2004 Mar 19;32(5):1792-7 PMID: 15034147
  41. A novel protein domain induces high affinity selenocysteine insertion sequence binding and elongation factor recruitment.
    J Biol Chem. 2008 Dec 12;283(50):35129-39 PMID: 18948268
Article Info
Journal
RNA (New York, N.Y.)
Abbr.
RNA
ISSN
1469-9001
DOI
10.1261/rna.044917.114
Published
2014-07-00
Epub
2014-00-21
Pages
1046-56
Language
English
Region
United States
NLM ID
9509184
PMCID
PMC4114684
Subset
IM
External Links
PubMed source DOI: 10.1261/rna.044917.114 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2