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Characterization of TRBP1 and TRBP2

Stable stem-loop structure at the 5′ end of TRBP2 mRNA resembles HIV-1 TAR and is not found in its processed pseudogene

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Journal of Biomedical Science

Abstract

TRBP1 and TRBP2 cDNAs have been isolated based on the ability of the protein that they encode to bind HIV-1 TAR RNA. The two cDNAs have different 5′ end-termini resulting in 21 additional amino acids for TRBP2 protein compared to TRBP1. The corresponding gene is conserved in mammalian species. By PCR amplification of a human library, we have isolated an additional 22 nucleotides in the 5′ end of TRBP2 cDNA. Based on the addition of these 22 new nucleotides, the first 87 nucleotides of TRBP2 mRNA can fold into a stable stem-loop structure that resembles TAR RNA. We have also isolated the DNA sequence that represents the TRBP processed pseudogene. The absence of full alignment between TRBP2 full-length cDNA and this sequence suggests that the stemloop structure could have prevented a complete reverse transcription during pseudogene formation. Using different antibodies, three forms of TRBP can be identified in primate cells at 40, 43 and 50 kD, suggesting a differential expression from the cDNAs and post-translational modifications. Both TRBP1 and TRBP2 activate the basal and the Tat-activated level of the HIV-1 LTR in human and murine cells. Our data indicate that TRBP proteins act at a level prior to Tat function. TRBP could contribute to improved HIV expression in murine models.

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References

  1. Altschul S, Madden T, Schaffer A, Zhang J, Zhang Z, Miller W, Lipman D. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 25:3389–3402;1997.

    Google Scholar 

  2. Bass B, Hurst S, Singer J. Binding properties of newly identifiedXenopus proteins containing dsRNA-binding motifs. Curr Biol 4:301–314;1994.

    Google Scholar 

  3. Benkirane M, Neuveut C, Chun R, Smith S, Samuel C, Gatignol A, Jeang K-T. Oncogenic potential of TAR RNA-binding TRBP and its regulatory interaction with Protein Kinase PKR. EMBO J 16:611–624;1997.

    Google Scholar 

  4. Bieniasz PD, Grdina TA, Bogerd HP, Cullen BR. Recruitment of a protein complex containing Tat and cyclin T1 to TAR governs the species specificity of HIV-1 Tat. EMBO J 17:7056–7065;1998.

    Google Scholar 

  5. Blair E, Roberts C, Snowden B, Gatignol A, Benkirane M, Jeang K-T. Expression of TAR RNA-binding protein in baculovirus and co-immunoprecipitation with insect cell protein kinase. J Biomed Sci 2:322–329;1995.

    Google Scholar 

  6. Breathnach R, Chambon P. Organization and expression of eucaryotic split genes coding for proteins. Annu Rev Biochem 50:349–383;1981.

    Google Scholar 

  7. Chang Y-N, Kenan DJ, Keene JD, Gatignol A, Jeang K-T. Direct interactions between autoantigen La and human immunodeficiency virus leader RNA. J Virol 68:7008–7020;1994.

    Google Scholar 

  8. Cosentino GP, Venkatesan S, Serluca FC, Green SR, Mathews MB, Sonenberg N. Double-stranded-RNA-dependent protein kinase and TAR RNA-binding protein form homo- and heterodimers in vivo. Proc Natl Acad Sci USA 92:9445–9449;1995.

    Google Scholar 

  9. Daviet L, Erard M, Dorin D, Duarte M, Vaquero C, Gatignol A. The analysis of a binding difference between the two dsRNA binding domains in TRBP reveals the modular function of a KR-helix motif. Eur J Biochem 267:2419–2431;2000.

    Google Scholar 

  10. Devereux J, Haeberli P, Smithies O. A comprehensive set of sequence analysis programs for the VAX. Nucl Acids Res 12:387–395;1984.

    Google Scholar 

  11. Donzeau M, Winnacker EL, Meisterernst M. Specific repression of Tax trans-activation by TAR RNA-binding protein TRBP. J Virol 71:2628–2635;1997.

    Google Scholar 

  12. Eckmann C, Jantsch M. Xlrbpa, a double-stranded RNA-binding protein associated with ribosomes and heterogeneous nuclear RNPs. J Cell Biol 138:239–253;1997.

    Google Scholar 

  13. Erard M, Barker D, Amalric F, Jeang K-T, Gatignol A. An Arg/Lys-rich core peptide mimics TRBP binding to the HIV-1 TAR RNA upper-stem/loop. J Mol Biol 279:1085–1099;1998.

    Google Scholar 

  14. Garber ME, Wei P, Kewal Ramani V, Mayall TP, Herrmann C, Rice AP, Littman DR, Jones K. The interaction between HIV-1 Tat and human cyclin T1 requires zinc and a critical cysteine residue that is not conserved in the murine CycT1 protein. Genes Dev 12:3512–3527;1998.

    Google Scholar 

  15. Gatignol A, Buckler C, Jeang K-T. Relatedness of an RNA binding motif in HIV-1 TAR RNA binding protein TRBP to human P1/dsI kinase andDrosophila Staufen. Mol Cell Biol 13:2193–2202;1993.

    Google Scholar 

  16. 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 251:1597–1600;1991.

    Google Scholar 

  17. Gatignol A, Duarte M, Daviet L, Chang Y-N, Jeang K-T. Sequential steps in Tat trans-activation of HIV-1 mediated through cellular DNA, RNA, and protein binding factors. Gene Expr 5:217–228;1996.

    Google Scholar 

  18. Gatignol A, Jeang K-T. Expression cloning of genes encoding RNA binding proteins. In Adolph, K, ed. Methods in Molecular Genetics: Molecular Virology Techniques, part A. San Diego, Academic Press, 18–28;1994.

    Google Scholar 

  19. Gatignol A, Jeang K-T. Tat as a transcriptional activator and a potential therapeutic target for HIV-1. In Jeang, K-T, ed. Advances in Pharmacology; HIV: Molecular mechanisms and clinical applications. San Diego, Academic Press, 48:209–227;2000.

    Google Scholar 

  20. Ito T, Yang M, May WS. RAX, a cellular activator for double-stranded RNA-dependent protein kinase during stress signaling. J Biol Chem 274:15427–15432;1999.

    Google Scholar 

  21. Jeang K-T, Xiao H, Rich E. Multifaceted activities of the HIV-1 transactivator of transcription, Tat. J Biol Chem 274:28837–28840;1999.

    Google Scholar 

  22. Kharrat A, Macias MJ, Gibson TJ, Nilges M, Pastore A. Structure of the dsRNA binding domain ofE. coli RNase III. EMBO J 14:3572–3584;1995.

    Google Scholar 

  23. Klasens B, Huthoff H, Das A, Jeeninga R, Berkhout B. The effect of template RNA structure on elongation by HIV-1 reverse transcriptase. Biochim Biophys Acta 1444:355–370;1999.

    Google Scholar 

  24. Kozak C, Gatignol A, Graham K, Jeang K-T, McBride O. Genetic mapping in human and mouse of the locus encoding TRBP, a protein that binds the TAR region of the human immunodeficiency virus (HIV-1). Genomics 25:66–72;1995.

    Google Scholar 

  25. Lee K, Fajardo M, Braun R. A testis cytoplasmic RNA-binding protein that has the properties of a translational repressor. Mol Cell Biol 16:3023–3034;1996.

    Google Scholar 

  26. Mathews D, Sabina J, Zuker M, Turner D. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol 288:911–940;1999.

    Google Scholar 

  27. Notake M, Tobimatsu T, Watanabe Y, Takahashi H, Mishina M, Numa S. Isolation and characterization of the mouse corticotropin-beta-lipotropin precursor gene and a related pseudogene. FEBS Lett 156:67–71;1983.

    Google Scholar 

  28. Park H, Davies M, Langland J, Chang H-W, Nam YS, Tartaglia J, Paoletti E, Jacobs B, Kaufman R, Venkatesan S. TAR RNA-binding protein is an inhibitor of the interferon-induced protein kinase PKR. Proc Natl Acad Sci USA 91:4713–4717;1994.

    Google Scholar 

  29. Patel RC, Sen GC. PACT, a protein activator of the interferon-induced protein kinase, PKR. EMBO J 17:4379–4390;1998.

    Google Scholar 

  30. Rana T, Jeang K-T. Biochemical and functional interactions between HIV-1 Tat protein and TAR RNA. Arch Biochem Biophys 365:175–185;1999.

    Google Scholar 

  31. Reddy TR, Suhasini M, Rappaport J, Looney DJ, Kraus G, Wong-Staal F. Molecular cloning and characterization of a TAR-binding nuclear factor from T cells. AIDS Res Hum Ret 11:663–669;1995.

    Google Scholar 

  32. Roy S, Agy M, Hovanessian A, Sonenberg N, Katze M. The integrity of the stem structure of human immunodeficiency virus type 1 Tatresponsive sequence RNA is required for interaction with the interferon-induced 68,000-Mr protein kinase. J Virol 65:632–640;1991.

    Google Scholar 

  33. Sharp P. Split genes and RNA splicing. Cell 77:805–815;1994.

    Google Scholar 

  34. St Johnston D, Brown NH, Gall JG, Jantsch M. A conserved double-stranded RNA-binding domain. Proc Natl Acad Sci USA 89:10979–10983;1992.

    Google Scholar 

  35. Vanin E. Processed pseudogenes: Characteristics and evolution. Annu Rev Genet 19:253–272;1985.

    Google Scholar 

  36. Wei P, Garber ME, Fang SM, Fischer WH, Jones KA. A novel CDK9-associated C-type cyclin interacts directly with HIV-1 Tat and mediates its high-affinity, loop-specific binding to TAR RNA. Cell 92:451–462;1998.

    Google Scholar 

  37. Wilde C. Pseudogenes. CRC Crit Rev Biochem 19:323–352;1986.

    Google Scholar 

  38. Wu-Baer F, Lane WS, Gaynor RB. The cellular factor TRP-185 regulates RNA polymerase II binding to HIV-1 TAR RNA. EMBO J 14:5995–6009;1995.

    Google Scholar 

  39. Wu-Baer F, Sigman D, Gaynor RB. Specific binding of RNA polymerase II to the human immunodeficiency virus trans-asctivating region RNA is regulated by cellular cofactors and Tat. Proc Natl Acad Sci USA 92:7153–7157;1995.

    Google Scholar 

  40. Yankulov K, Bentley D. Transcriptional control: Tat cofactors and transcriptional elongation. Curr Biol 8:R447–449;1998.

    Google Scholar 

  41. Zhong J, Edelhoff S, Disteche C, Braun RE. The gene encoding PRBP, the mouse homolog of human TRBP, maps to distal chromosome 15. Mamm Genome 9:413–414;1998.

    Google Scholar 

  42. Zhong J, Peters AH, Lee K, Braun RE. A double-stranded RNA binding protein required for activation of repressed messages in mammalian germ cells. Nat Genet 22:171–174;1999.

    Google Scholar 

  43. Zuker M. On finding all suboptimal foldings of an RNA molecule. Science 244:48–52;1989.

    Google Scholar 

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Duarte, M., Graham, K., Daher, A. et al. Characterization of TRBP1 and TRBP2. J Biomed Sci 7, 494–506 (2000). https://doi.org/10.1007/BF02253365

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