Home LiteratureArticle Details
PMID: 7682716 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S.

Role of RNA structure in arginine recognition of TAR RNA.

Proceedings of the National Academy of Sciences of the United States of America ·Vol. 90 ·No. 8 ·1993-04-15 ·Pages 3680-4

Puglisi JD, Chen L, Frankel AD, Williamson JR

Abstract

The human immunodeficiency virus Tat protein binds specifically to an RNA stem-loop structure (TAR) that contains two helical stem regions separated by a three-nucleotide bulge. A single arginine within the basic region of Tat mediates specific binding to TAR, and arginine as the free amino acid also binds specifically to TAR. We have previously proposed a model in which interaction of the arginine guanidinium group with guanosine-26 (G26) and with a pair of phosphates is stabilized by formation of a base triple between U23 in the bulge and A27.U38 in the upper helix. Here we show by NMR spectroscopy that formation of the base triple is critical for arginine binding to TAR. Mutants of TAR that cannot form the base triple or that remove the guanine contact do not bind arginine specifically. These mutants also showed reduced transactivation by Tat. A triple mutant designed to form an isomorphous base triple between C23 and G27.C38 binds arginine and adopts the same conformation as wild-type TAR. These results demonstrate the importance of RNA structure for arginine binding and further demonstrate the direct correspondence between arginine and Tat binding.

MeSH Terms
Arginine Base Sequence Binding Sites Chloramphenicol O-Acetyltransferase/genetics,metabolism Gene Products, tat/metabolism HIV/genetics,metabolism HIV Long Terminal Repeat HeLa Cells Humans Magnetic Resonance Spectroscopy/methods Models, Structural Molecular Sequence Data Mutagenesis Nucleic Acid Conformation RNA/chemistry,metabolism RNA-Binding Proteins/metabolism Transcriptional Activation Transfection tat Gene Products, Human Immunodeficiency Virus
Chemicals
Gene Products, tat RNA-Binding Proteins tat Gene Products, Human Immunodeficiency Virus trans-activation responsive RNA-binding protein RNA Arginine Chloramphenicol O-Acetyltransferase
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Puglisi J D
Department of Chemistry, Massachusetts Institute of Technology, Cambridge 02139.
Chen L
Frankel A D
Williamson J R
References (37)
37 references, click to expand
  1. Detailed molecular model for transfer ribonucleic acid.
    Nature. 1969 Nov 22;224(5221):759-63 PMID: 5361649
  2. tRNA structure and aminoacylation efficiency.
    Prog Nucleic Acid Res Mol Biol. 1993;45:129-206 PMID: 8341800
  3. A specific amino acid binding site composed of RNA.
    Science. 1988 Jun 24;240(4860):1751-8 PMID: 3381099
  4. Evidence for several higher order structural elements in ribosomal RNA.
    Proc Natl Acad Sci U S A. 1989 May;86(9):3119-22 PMID: 2654936
  5. Structure of E. coli glutaminyl-tRNA synthetase complexed with tRNA(Gln) and ATP at 2.8 A resolution.
    Science. 1989 Dec 1;246(4934):1135-42 PMID: 2479982
  6. RNA bulges and the helical periodicity of double-stranded RNA.
    Nature. 1990 Feb 1;343(6257):484-7 PMID: 2300191
  7. Z-RNA: the solution NMR structure of r(CGCGCG).
    Biopolymers. 1990 Jan;29(1):109-22 PMID: 1691662
  8. Formation of a stable triplex from a single DNA strand.
    Nature. 1990 Jun 28;345(6278):836-8 PMID: 2359461
  9. Conformation of an RNA pseudoknot.
    J Mol Biol. 1990 Jul 20;214(2):437-53 PMID: 1696318
  10. Fragments of the HIV-1 Tat protein specifically bind TAR RNA.
    Science. 1990 Sep 14;249(4974):1281-5 PMID: 2205002
  11. Phylogenetic and genetic evidence for base-triples in the catalytic domain of group I introns.
    Nature. 1990 Oct 11;347(6293):578-80 PMID: 2215683
  12. A bulge structure in HIV-1 TAR RNA is required for Tat binding and Tat-mediated trans-activation.
    Genes Dev. 1990 Aug;4(8):1365-73 PMID: 2227414
  13. Sequence-specific interaction of Tat protein and Tat peptides with the transactivation-responsive sequence element of human immunodeficiency virus type 1 in vitro.
    Proc Natl Acad Sci U S A. 1990 Nov;87(22):8985-9 PMID: 2247474
  14. HIV-1 tat protein stimulates transcription by binding to a U-rich bulge in the stem of the TAR RNA structure.
    EMBO J. 1990 Dec;9(12):4145-53 PMID: 2249668
  15. Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis.
    J Mol Biol. 1990 Dec 5;216(3):585-610 PMID: 2258934
  16. Analysis of arginine-rich peptides from the HIV Tat protein reveals unusual features of RNA-protein recognition.
    Genes Dev. 1991 Feb;5(2):201-10 PMID: 1899841
  17. Zinc finger-DNA recognition: crystal structure of a Zif268-DNA complex at 2.1 A.
    Science. 1991 May 10;252(5007):809-17 PMID: 2028256
  18. Specific interaction between RNA phage coat proteins and RNA.
    Prog Nucleic Acid Res Mol Biol. 1991;40:185-220 PMID: 2031083
  19. Arginine-mediated RNA recognition: the arginine fork.
    Science. 1991 May 24;252(5009):1167-71 PMID: 1709522
  20. Class II aminoacyl transfer RNA synthetases: crystal structure of yeast aspartyl-tRNA synthetase complexed with tRNA(Asp).
    Science. 1991 Jun 21;252(5013):1682-9 PMID: 2047877
  21. Structural basis of anticodon loop recognition by glutaminyl-tRNA synthetase.
    Nature. 1991 Jul 18;352(6332):213-8 PMID: 1857417
  22. RNA recognition by Tat-derived peptides: interaction in the major groove?
    Cell. 1991 Aug 9;66(3):577-88 PMID: 1907891
  23. Structural elements in RNA.
    Prog Nucleic Acid Res Mol Biol. 1991;41:131-77 PMID: 1715587
  24. Detailed mutational analysis of TAR RNA: critical spacing between the bulge and loop recognition domains.
    Nucleic Acids Res. 1991 Nov 25;19(22):6169-76 PMID: 1956776
  25. RNA structure and NMR spectroscopy.
    Q Rev Biophys. 1991 Nov;24(4):479-532 PMID: 1723809
  26. Specific binding of arginine to TAR RNA.
    Proc Natl Acad Sci U S A. 1992 Apr 1;89(7):2723-6 PMID: 1557378
  27. Conserved nucleotides in the TAR RNA stem of human immunodeficiency virus type 1 are critical for Tat binding and trans activation: model for TAR RNA tertiary structure.
    J Virol. 1992 May;66(5):3018-25 PMID: 1560535
  28. Synthesis and purification of large amounts of RNA oligonucleotides.
    Biotechniques. 1991 Dec;11(6):764-9 PMID: 1809333
  29. Three-dimensional structures of bulge-containing DNA fragments.
    J Mol Biol. 1992 May 20;225(2):397-431 PMID: 1593627
  30. Co-optimization of ribozyme substrate stacking and L-arginine binding.
    J Mol Biol. 1992 Jun 20;225(4):945-9 PMID: 1613800
  31. Conformation of the TAR RNA-arginine complex by NMR spectroscopy.
    Science. 1992 Jul 3;257(5066):76-80 PMID: 1621097
  32. Activation of HIV transcription by Tat.
    Curr Opin Genet Dev. 1992 Apr;2(2):293-8 PMID: 1638124
  33. RNA binding assays for Tat-derived peptides: implications for specificity.
    Biochemistry. 1992 Oct 27;31(42):10281-7 PMID: 1384694
  34. Circular dichroism studies suggest that TAR RNA changes conformation upon specific binding of arginine or guanidine.
    Biochemistry. 1992 Oct 27;31(42):10288-94 PMID: 1384695
  35. A base-triple structural domain in RNA.
    Biochemistry. 1992 Dec 29;31(51):12733-41 PMID: 1463745
  36. Electrostatic interactions modulate the RNA-binding and transactivation specificities of the human immunodeficiency virus and simian immunodeficiency virus Tat proteins.
    Proc Natl Acad Sci U S A. 1993 Feb 15;90(4):1571-5 PMID: 8434019
  37. Sequence-specific recognition of double helical nucleic acids by proteins.
    Proc Natl Acad Sci U S A. 1976 Mar;73(3):804-8 PMID: 1062791
Article Info
Journal
Proceedings of the National Academy of Sciences of the United States of America
Abbr.
Proc Natl Acad Sci U S A
ISSN
0027-8424
DOI
10.1073/pnas.90.8.3680
Published
1993-04-15
Pages
3680-4
Language
English
Region
United States
NLM ID
7505876
PMCID
PMC46365
Subset
IM
Grants
NIAID NIH HHS · AI08591 · United States
NIAID NIH HHS · AI29135 · United States
NIGMS NIH HHS · GM46314 · United States
External Links
PubMed source DOI: 10.1073/pnas.90.8.3680 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