Abstract
TRBP is a human cellular protein that binds the human immunodeficiency virus type 1 TAR RNA. Here, we show that the intact presence of amino acids 247 to 267 in TRBP correlates with its ability to bind RNA. This region contains a lysine- and arginine-rich motif, KKLAKRNAAAKMLLRVHTVPLDAR. A 24-amino-acid synthetic peptide (TR1) of this sequence bound TAR RNA with affinities similar to that of the entire TRBP, thus suggesting that this short motif contains a sufficient RNA-binding activity. Using RNA probe-shift analysis, we determined that TR1 does not bind all double-stranded RNAs but prefers TAR and other double-stranded RNAs with G+C-rich characteristics. Immunoprecipitation of TRBP from human immunodeficiency virus type 1-infected T lymphocytes recovered TAR RNA. This is consistent with a TRBP-TAR ribonucleoprotein during viral infection. Computer alignment revealed that TR1 is highly homologous to the RNA-binding domain of human P1/dsI protein kinase and two regions within Drosophila Staufen. We suggest that these proteins are related by virtue of sharing a common RNA-binding moiety.
Full text
PDF









Images in this article
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Adachi A., Gendelman H. E., Koenig S., Folks T., Willey R., Rabson A., Martin M. A. Production of acquired immunodeficiency syndrome-associated retrovirus in human and nonhuman cells transfected with an infectious molecular clone. J Virol. 1986 Aug;59(2):284–291. doi: 10.1128/jvi.59.2.284-291.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. Basic local alignment search tool. J Mol Biol. 1990 Oct 5;215(3):403–410. doi: 10.1016/S0022-2836(05)80360-2. [DOI] [PubMed] [Google Scholar]
- Bandziulis R. J., Swanson M. S., Dreyfuss G. RNA-binding proteins as developmental regulators. Genes Dev. 1989 Apr;3(4):431–437. doi: 10.1101/gad.3.4.431. [DOI] [PubMed] [Google Scholar]
- Bell L. R., Maine E. M., Schedl P., Cline T. W. Sex-lethal, a Drosophila sex determination switch gene, exhibits sex-specific RNA splicing and sequence similarity to RNA binding proteins. Cell. 1988 Dec 23;55(6):1037–1046. doi: 10.1016/0092-8674(88)90248-6. [DOI] [PubMed] [Google Scholar]
- Berkhout B., Jeang K. T. Functional roles for the TATA promoter and enhancers in basal and Tat-induced expression of the human immunodeficiency virus type 1 long terminal repeat. J Virol. 1992 Jan;66(1):139–149. doi: 10.1128/jvi.66.1.139-149.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Berkhout B., Silverman R. H., Jeang K. T. Tat trans-activates the human immunodeficiency virus through a nascent RNA target. Cell. 1989 Oct 20;59(2):273–282. doi: 10.1016/0092-8674(89)90289-4. [DOI] [PubMed] [Google Scholar]
- Calnan B. J., Biancalana S., Hudson D., Frankel A. D. Analysis of arginine-rich peptides from the HIV Tat protein reveals unusual features of RNA-protein recognition. Genes Dev. 1991 Feb;5(2):201–210. doi: 10.1101/gad.5.2.201. [DOI] [PubMed] [Google Scholar]
- Calnan B. J., Tidor B., Biancalana S., Hudson D., Frankel A. D. Arginine-mediated RNA recognition: the arginine fork. Science. 1991 May 24;252(5009):1167–1171. doi: 10.1126/science.252.5009.1167. [DOI] [PubMed] [Google Scholar]
- Casey J. L., Koeller D. M., Ramin V. C., Klausner R. D., Harford J. B. Iron regulation of transferrin receptor mRNA levels requires iron-responsive elements and a rapid turnover determinant in the 3' untranslated region of the mRNA. EMBO J. 1989 Dec 1;8(12):3693–3699. doi: 10.1002/j.1460-2075.1989.tb08544.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Chang Y. N., Jeang K. T. The basic RNA-binding domain of HIV-2 Tat contributes to preferential trans-activation of a TAR2-containing LTR. Nucleic Acids Res. 1992 Oct 25;20(20):5465–5472. doi: 10.1093/nar/20.20.5465. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Cordingley M. G., LaFemina R. L., Callahan P. L., Condra J. H., Sardana V. V., Graham D. J., Nguyen T. M., LeGrow K., Gotlib L., Schlabach A. J. 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):8985–8989. doi: 10.1073/pnas.87.22.8985. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Cullen B. R., Malim M. H. The HIV-1 Rev protein: prototype of a novel class of eukaryotic post-transcriptional regulators. Trends Biochem Sci. 1991 Sep;16(9):346–350. doi: 10.1016/0968-0004(91)90141-h. [DOI] [PubMed] [Google Scholar]
- Daly T. J., Cook K. S., Gray G. S., Maione T. E., Rusche J. R. Specific binding of HIV-1 recombinant Rev protein to the Rev-responsive element in vitro. Nature. 1989 Dec 14;342(6251):816–819. doi: 10.1038/342816a0. [DOI] [PubMed] [Google Scholar]
- Dang C. V., Lee W. M. Nuclear and nucleolar targeting sequences of c-erb-A, c-myb, N-myc, p53, HSP70, and HIV tat proteins. J Biol Chem. 1989 Oct 25;264(30):18019–18023. [PubMed] [Google Scholar]
- Delling U., Reid L. S., Barnett R. W., Ma M. Y., Climie S., Sumner-Smith M., Sonenberg N. 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):3018–3025. doi: 10.1128/jvi.66.5.3018-3025.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Delling U., Roy S., Sumner-Smith M., Barnett R., Reid L., Rosen C. A., Sonenberg N. The number of positively charged amino acids in the basic domain of Tat is critical for trans-activation and complex formation with TAR RNA. Proc Natl Acad Sci U S A. 1991 Jul 15;88(14):6234–6238. doi: 10.1073/pnas.88.14.6234. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Dingwall C., Ernberg I., Gait M. J., Green S. M., Heaphy S., Karn J., Lowe A. D., Singh M., Skinner M. A. 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):4145–4153. doi: 10.1002/j.1460-2075.1990.tb07637.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Dingwall C., Ernberg I., Gait M. J., Green S. M., Heaphy S., Karn J., Lowe A. D., Singh M., Skinner M. A., Valerio R. Human immunodeficiency virus 1 tat protein binds trans-activation-responsive region (TAR) RNA in vitro. Proc Natl Acad Sci U S A. 1989 Sep;86(18):6925–6929. doi: 10.1073/pnas.86.18.6925. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Gatignol A., Buckler-White A., Berkhout B., Jeang K. T. Characterization of a human TAR RNA-binding protein that activates the HIV-1 LTR. Science. 1991 Mar 29;251(5001):1597–1600. doi: 10.1126/science.2011739. [DOI] [PubMed] [Google Scholar]
- Gatignol A., Kumar A., Rabson A., Jeang K. T. Identification of cellular proteins that bind to the human immunodeficiency virus type 1 trans-activation-responsive TAR element RNA. Proc Natl Acad Sci U S A. 1989 Oct;86(20):7828–7832. doi: 10.1073/pnas.86.20.7828. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Gaynor R., Soultanakis E., Kuwabara M., Garcia J., Sigman D. S. Specific binding of a HeLa cell nuclear protein to RNA sequences in the human immunodeficiency virus transactivating region. Proc Natl Acad Sci U S A. 1989 Jul;86(13):4858–4862. doi: 10.1073/pnas.86.13.4858. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Ghisolfi L., Joseph G., Amalric F., Erard M. The glycine-rich domain of nucleolin has an unusual supersecondary structure responsible for its RNA-helix-destabilizing properties. J Biol Chem. 1992 Feb 15;267(5):2955–2959. [PubMed] [Google Scholar]
- Gooding L. R. Virus proteins that counteract host immune defenses. Cell. 1992 Oct 2;71(1):5–7. doi: 10.1016/0092-8674(92)90259-f. [DOI] [PubMed] [Google Scholar]
- Grove J. R., Banerjee P., Balasubramanyam A., Coffer P. J., Price D. J., Avruch J., Woodgett J. R. Cloning and expression of two human p70 S6 kinase polypeptides differing only at their amino termini. Mol Cell Biol. 1991 Nov;11(11):5541–5550. doi: 10.1128/mcb.11.11.5541. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Harper J. W., Logsdon N. J. Refolded HIV-1 tat protein protects both bulge and loop nucleotides in TAR RNA from ribonucleolytic cleavage. Biochemistry. 1991 Aug 13;30(32):8060–8066. doi: 10.1021/bi00246a026. [DOI] [PubMed] [Google Scholar]
- Heaphy S., Dingwall C., Ernberg I., Gait M. J., Green S. M., Karn J., Lowe A. D., Singh M., Skinner M. A. HIV-1 regulator of virion expression (Rev) protein binds to an RNA stem-loop structure located within the Rev response element region. Cell. 1990 Feb 23;60(4):685–693. doi: 10.1016/0092-8674(90)90671-z. [DOI] [PubMed] [Google Scholar]
- Holland S. M., Ahmad N., Maitra R. K., Wingfield P., Venkatesan S. Human immunodeficiency virus rev protein recognizes a target sequence in rev-responsive element RNA within the context of RNA secondary structure. J Virol. 1990 Dec;64(12):5966–5975. doi: 10.1128/jvi.64.12.5966-5975.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Jeang K. T., Chang Y., Berkhout B., Hammarskjöld M. L., Rekosh D. Regulation of HIV expression: mechanisms of action of Tat and Rev. AIDS. 1991;5 (Suppl 2):S3–14. [PubMed] [Google Scholar]
- Kamine J., Loewenstein P., Green M. Mapping of HIV-1 Tat protein sequences required for binding to Tar RNA. Virology. 1991 Jun;182(2):570–577. doi: 10.1016/0042-6822(91)90598-6. [DOI] [PubMed] [Google Scholar]
- Katze M. G., Wambach M., Wong M. L., Garfinkel M., Meurs E., Chong K., Williams B. R., Hovanessian A. G., Barber G. N. Functional expression and RNA binding analysis of the interferon-induced, double-stranded RNA-activated, 68,000-Mr protein kinase in a cell-free system. Mol Cell Biol. 1991 Nov;11(11):5497–5505. doi: 10.1128/mcb.11.11.5497. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kenan D. J., Query C. C., Keene J. D. RNA recognition: towards identifying determinants of specificity. Trends Biochem Sci. 1991 Jun;16(6):214–220. doi: 10.1016/0968-0004(91)90088-d. [DOI] [PubMed] [Google Scholar]
- Koromilas A. E., Roy S., Barber G. N., Katze M. G., Sonenberg N. Malignant transformation by a mutant of the IFN-inducible dsRNA-dependent protein kinase. Science. 1992 Sep 18;257(5077):1685–1689. doi: 10.1126/science.1382315. [DOI] [PubMed] [Google Scholar]
- Lamond A. I., Gibson T. J. Catalytic RNA and the origin of genetic systems. Trends Genet. 1990 May;6(5):145–149. doi: 10.1016/0168-9525(90)90148-y. [DOI] [PubMed] [Google Scholar]
- Lazinski D., Grzadzielska E., Das A. Sequence-specific recognition of RNA hairpins by bacteriophage antiterminators requires a conserved arginine-rich motif. Cell. 1989 Oct 6;59(1):207–218. doi: 10.1016/0092-8674(89)90882-9. [DOI] [PubMed] [Google Scholar]
- Malim M. H., Cullen B. R. HIV-1 structural gene expression requires the binding of multiple Rev monomers to the viral RRE: implications for HIV-1 latency. Cell. 1991 Apr 19;65(2):241–248. doi: 10.1016/0092-8674(91)90158-u. [DOI] [PubMed] [Google Scholar]
- Marciniak R. A., Garcia-Blanco M. A., Sharp P. A. Identification and characterization of a HeLa nuclear protein that specifically binds to the trans-activation-response (TAR) element of human immunodeficiency virus. Proc Natl Acad Sci U S A. 1990 May;87(9):3624–3628. doi: 10.1073/pnas.87.9.3624. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Mattaj I. W. A selective review of RNA-protein interactions in eukaryotes. Mol Biol Rep. 1990;14(2-3):151–155. doi: 10.1007/BF00360454. [DOI] [PubMed] [Google Scholar]
- McClure W. R. Mechanism and control of transcription initiation in prokaryotes. Annu Rev Biochem. 1985;54:171–204. doi: 10.1146/annurev.bi.54.070185.001131. [DOI] [PubMed] [Google Scholar]
- McCormack S. J., Thomis D. C., Samuel C. E. Mechanism of interferon action: identification of a RNA binding domain within the N-terminal region of the human RNA-dependent P1/eIF-2 alpha protein kinase. Virology. 1992 May;188(1):47–56. doi: 10.1016/0042-6822(92)90733-6. [DOI] [PubMed] [Google Scholar]
- Meurs E., Chong K., Galabru J., Thomas N. S., Kerr I. M., Williams B. R., Hovanessian A. G. Molecular cloning and characterization of the human double-stranded RNA-activated protein kinase induced by interferon. Cell. 1990 Jul 27;62(2):379–390. doi: 10.1016/0092-8674(90)90374-n. [DOI] [PubMed] [Google Scholar]
- Mott L. Alar: the aftermath. Science. 1992 Feb 7;255(5045):665–665. doi: 10.1126/science.1738835. [DOI] [PubMed] [Google Scholar]
- Pearson W. R., Lipman D. J. Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A. 1988 Apr;85(8):2444–2448. doi: 10.1073/pnas.85.8.2444. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Qian Z. W., Wilusz J. An RNA-binding protein specifically interacts with a functionally important domain of the downstream element of the simian virus 40 late polyadenylation signal. Mol Cell Biol. 1991 Oct;11(10):5312–5320. doi: 10.1128/mcb.11.10.5312. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Query C. C., Bentley R. C., Keene J. D. A common RNA recognition motif identified within a defined U1 RNA binding domain of the 70K U1 snRNP protein. Cell. 1989 Apr 7;57(1):89–101. doi: 10.1016/0092-8674(89)90175-x. [DOI] [PubMed] [Google Scholar]
- Rounseville M. P., Kumar A. Binding of a host cell nuclear protein to the stem region of human immunodeficiency virus type 1 trans-activation-responsive RNA. J Virol. 1992 Mar;66(3):1688–1694. doi: 10.1128/jvi.66.3.1688-1694.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Roy S., Agy M., Hovanessian A. G., Sonenberg N., Katze M. G. The integrity of the stem structure of human immunodeficiency virus type 1 Tat-responsive sequence of RNA is required for interaction with the interferon-induced 68,000-Mr protein kinase. J Virol. 1991 Feb;65(2):632–640. doi: 10.1128/jvi.65.2.632-640.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Roy S., Delling U., Chen C. H., Rosen C. A., Sonenberg N. A bulge structure in HIV-1 TAR RNA is required for Tat binding and Tat-mediated trans-activation. Genes Dev. 1990 Aug;4(8):1365–1373. doi: 10.1101/gad.4.8.1365. [DOI] [PubMed] [Google Scholar]
- Römisch K., Webb J., Lingelbach K., Gausepohl H., Dobberstein B. The 54-kD protein of signal recognition particle contains a methionine-rich RNA binding domain. J Cell Biol. 1990 Nov;111(5 Pt 1):1793–1802. doi: 10.1083/jcb.111.5.1793. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Sheline C. T., Milocco L. H., Jones K. A. Two distinct nuclear transcription factors recognize loop and bulge residues of the HIV-1 TAR RNA hairpin. Genes Dev. 1991 Dec;5(12B):2508–2520. doi: 10.1101/gad.5.12b.2508. [DOI] [PubMed] [Google Scholar]
- St Johnston D., Beuchle D., Nüsslein-Volhard C. Staufen, a gene required to localize maternal RNAs in the Drosophila egg. Cell. 1991 Jul 12;66(1):51–63. doi: 10.1016/0092-8674(91)90138-o. [DOI] [PubMed] [Google Scholar]
- St Johnston D., Brown N. H., Gall J. G., Jantsch M. A conserved double-stranded RNA-binding domain. Proc Natl Acad Sci U S A. 1992 Nov 15;89(22):10979–10983. doi: 10.1073/pnas.89.22.10979. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Subramanian T., Kuppuswamy M., Venkatesh L., Srinivasan A., Chinnadurai G. Functional substitution of the basic domain of the HIV-1 trans-activator, Tat, with the basic domain of the functionally heterologous Rev. Virology. 1990 May;176(1):178–183. doi: 10.1016/0042-6822(90)90242-j. [DOI] [PubMed] [Google Scholar]
- Swanson M. S. Heterogeneous nuclear ribonucleoprotein complexes. Mol Biol Rep. 1990;14(2-3):79–82. doi: 10.1007/BF00360424. [DOI] [PubMed] [Google Scholar]
- Taylor W. R. Identification of protein sequence homology by consensus template alignment. J Mol Biol. 1986 Mar 20;188(2):233–258. doi: 10.1016/0022-2836(86)90308-6. [DOI] [PubMed] [Google Scholar]
- Toyoshima H., Itoh M., Inoue J., Seiki M., Takaku F., Yoshida M. Secondary structure of the human T-cell leukemia virus type 1 rex-responsive element is essential for rex regulation of RNA processing and transport of unspliced RNAs. J Virol. 1990 Jun;64(6):2825–2832. doi: 10.1128/jvi.64.6.2825-2832.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Weeks K. M., Ampe C., Schultz S. C., Steitz T. A., Crothers D. M. Fragments of the HIV-1 Tat protein specifically bind TAR RNA. Science. 1990 Sep 14;249(4974):1281–1285. doi: 10.1126/science.2205002. [DOI] [PubMed] [Google Scholar]
- Weeks K. M., Crothers D. M. RNA recognition by Tat-derived peptides: interaction in the major groove? Cell. 1991 Aug 9;66(3):577–588. doi: 10.1016/0092-8674(81)90020-9. [DOI] [PubMed] [Google Scholar]
- Wei N., Morris T. J. Interactions between viral coat protein and a specific binding region on turnip crinkle virus RNA. J Mol Biol. 1991 Dec 5;222(3):437–443. doi: 10.1016/0022-2836(91)90483-m. [DOI] [PubMed] [Google Scholar]
- Wu F., Garcia J., Sigman D., Gaynor R. tat regulates binding of the human immunodeficiency virus trans-activating region RNA loop-binding protein TRP-185. Genes Dev. 1991 Nov;5(11):2128–2140. doi: 10.1101/gad.5.11.2128. [DOI] [PubMed] [Google Scholar]
- Zamore P. D., Zapp M. L., Green M. R. Gene expression. RNA binding: beta s and basics. Nature. 1990 Dec 6;348(6301):485–486. doi: 10.1038/348485a0. [DOI] [PubMed] [Google Scholar]
- Zapp M. L., Green M. R. Sequence-specific RNA binding by the HIV-1 Rev protein. Nature. 1989 Dec 7;342(6250):714–716. doi: 10.1038/342714a0. [DOI] [PubMed] [Google Scholar]
- Zapp M. L., Hope T. J., Parslow T. G., Green M. R. Oligomerization and RNA binding domains of the type 1 human immunodeficiency virus Rev protein: a dual function for an arginine-rich binding motif. Proc Natl Acad Sci U S A. 1991 Sep 1;88(17):7734–7738. doi: 10.1073/pnas.88.17.7734. [DOI] [PMC free article] [PubMed] [Google Scholar]