Selection of peptides interfering with a ribosomal frameshift in the human immunodeficiency virus type 1

RNA

Volumn 14, Issue 5, 2008, Pages 981-991

  Dulude, Dominic ^a,b   Théberge Julien, Gabriel ^a   Brakier Gingras, Léa ^a   Heveker, Nikolaus ^a,b  

^a UNIVERSITÉ DE MONTRÉAL   (Canada)

^b UNIVERSITY OF MONTREAL   (Canada)

Author keywords

HIV 1 programmed 1 ribosomal frameshift; Peptide library

Indexed keywords

ARGININE; CHLORAMPHENICOL; GREEN FLUORESCENT PROTEIN; PEPTIDE LIBRARY; RED FLUORESCENT PROTEIN; THIOREDOXIN; PEPTIDE; PHOTOPROTEIN; RECOMBINANT PROTEIN; VIRUS RNA;

AMINO ACID SEQUENCE; ARTICLE; BACTERIUM ISOLATION; CONTROLLED STUDY; ESCHERICHIA COLI; EUKARYOTE; FLUORESCENCE; FLUORESCENCE ACTIVATED CELL SORTER; GENE EXPRESSION; GENETIC SCREENING; HUMAN; HUMAN CELL; HUMAN IMMUNODEFICIENCY VIRUS 1; MOLECULAR CLONING; NONHUMAN; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN SYNTHESIS; PROTEIN TARGETING; QUANTITATIVE ANALYSIS; REPORTER GENE; RIBOSOMAL FRAMESHIFTING; RIBOSOME; RNA BINDING; RNA TRANSLATION; SEQUENCE ANALYSIS; SIGNAL TRANSDUCTION; CHEMISTRY; CONFORMATION; DRUG EFFECT; GENETICS; METABOLISM; NUCLEOTIDE SEQUENCE; PLASMID;

ESCHERICHIA COLI; EUKARYOTA; HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1;

AMINO ACID SEQUENCE; BASE SEQUENCE; ESCHERICHIA COLI; FRAMESHIFTING, RIBOSOMAL; GENES, REPORTER; GREEN FLUORESCENT PROTEINS; HIV-1; LUMINESCENT PROTEINS; NUCLEIC ACID CONFORMATION; PEPTIDE LIBRARY; PEPTIDES; PLASMIDS; PROTEIN BIOSYNTHESIS; RECOMBINANT PROTEINS; RNA, VIRAL;

EID: 42449084551     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.887008     Document Type: Article

References (42)

1. Baril, M., Dulude, D., Steinberg, S.V., and Brakier-Gingras, L. 2003. The frameshift stimulatory signal of human immunodeficiency virus type 1 group O is a pseudoknot. J. Mol. Biol. 331: 571-583.
2. Belanger, F., Leger, M., Saraiya, A.A., Cunningham, P.R., and Brakier-Gingras, L. 2002. Functional studies of the 900 tetraloop capping helix 27 of 16S ribosomal RNA. J. Mol. Biol. 320: 979-989.
3. Bevis, B.J. and Glick, B.S. 2002. Rapidly maturing variants of the Discosoma red fluorescent protein (DsRed). Nat. Biotechnol. 20: 83-87.
4. Biswas, P., Jiang, X., Pacchia, A.L., Dougherty, J.P., and Peltz, S.W. 2004. The human immunodeficiency virus type 1 ribosomal frameshifting site is an invariant sequence determinant and an important target for antiviral therapy. J. Virol. 78: 2082-2087.
5. Brierley, I. and Dos Ramos, F.J. 2006. Programmed ribosomal frameshifting in HIV-1 and the SARS-CoV. Virus Res. 119: 29-42.
6. Brierley, I. and Pennell, S. 2001. Structure and function of the stimulatory RNAs involved in programmed eukaryotic-1 ribosomal frameshifting. Cold Spring Harb. Symp. Quant. Biol. 66: 233-248.
7. Corey, M.J. and Corey, E. 1996. On the failure of de novo-designed peptides as biocatalysts. Proc. Natl. Acad. Sci. 93: 11428-11434.
8. Dinman, J.D. and Kinzy, T.G. 1997. Translational misreading: Mutations in translation elongation factor 1α differentially affect programmed ribosomal frameshifting and drug sensitivity. RNA 3: 870-881.
9. Dinman, J.D., Ruiz-Echevarria, M.J., Czaplinski, K., and Peltz, S.W. 1997. Peptidyl-transferase inhibitors have antiviral properties by altering programmed -1 ribosomal frameshifting efficiencies: Development of model systems. Proc. Natl. Acad. Sci. 94: 6606-6611.
10. Dulude, D., Baril, M., and Brakier-Gingras, L. 2002. Characterization of the frameshift stimulatory signal controlling a programmed -1 ribosomal frameshift in the human immunodeficiency virus type 1. Nucleic Acids Res. 30: 5094-5102. doi: 10.1093/nar/gkf657.
11. Dulude, D., Berchiche, Y.A., Gendron, K., Brakier-Gingras, L., and Heveker, N. 2006. Decreasing the frameshift efficiency translates into an equivalent reduction of the replication of the human immunodeficiency virus type 1. Virology 345: 127-136.
12. Gaudin, C., Mazauric, M.H., Traikia, M., Guittet, E., Yoshizawa, S., and Fourmy, D. 2005. Structure of the RNA signal essential for translational frameshifting in HIV-1. J. Mol. Biol. 349: 1024-1035.
13. Grentzmann, G., Ingram, J.A., Kelly, P.J., Gesteland, R.F., and Atkins, J.F. 1998. A dual-luciferase reporter system for studying recoding signals. RNA 4: 479-486.
14. Harada, K., Martin, S.S., and Frankel, A.D. 1996. Selection of RNA-binding peptides in vivo. Nature 380: 175-179.
15. Harada, K., Martin, S.S., Tan, R., and Frankel, A.D. 1997. Molding a peptide into an RNA site by in vivo peptide evolution. Proc. Natl. Acad. Sci. 94: 11887-11892.
16. Hung, M., Patel, P., Davis, S., and Green, S.R. 1998. Importance of ribosomal frameshifting for human immunodeficiency virus type 1 particle assembly and replication. J. Virol. 72: 4819-4824.
17. Jacks, T., Madhani, H.D., Masiarz, F.R., and Varmus, H.E. 1988. Signals for ribosomal frameshifting in the Rous sarcoma virus gagpol region. Cell 55: 447-458.
18. Karacostas, V., Wolffe, E.J., Nagashima, K., Gonda, M.A., and Moss, B. 1993. Overexpression of the HIV-1 gag-pol polyprotein results in intracellular activation of HIV-1 protease and inhibition of assembly and budding of virus-like particles. Virology 193: 661-671.
19. Kollmus, H., Hentze, M.W., and Hauser, H. 1996. Regulated ribosomal frameshifting by an RNA-protein interaction. RNA 2: 316-323.
20. Laursen, B.S., Sorensen, H.P., Mortensen, K.K., and Sperling-Petersen, H.U. 2005. Initiation of protein synthesis in bacteria. Microbiol. Mol. Biol. Rev. 69: 101-123.
21. LaVallie, E.R., DiBlasio, E.A., Kovacic, S., Grant, K.L., Schendel, P.F., and McCoy, J.M. 1993. A thioredoxin gene fusion expression system that circumvents inclusion body formation in the E. coli cytoplasm. Biotechnology 11: 187-193.
22. Lee, K., Holland-Staley, C.A., and Cunningham, P.R. 1996. Genetic analysis of the Shine-Dalgarno interaction: Selection of alternative functional mRNA-rRNA combinations. RNA 2: 1270-1285.
23. Lee, K., Varma, S., SantaLucia Jr., J., and Cunningham, P.R. 1997. In vivo determination of RNA structure-function relationships: Analysis of the 790 loop in ribosomal RNA. J. Mol. Biol. 269: 732-743.
24. Léger, M., Sidani, S., and Brakier-Gingras, L. 2004. A reassessment of the response of the bacterial ribosome to the frameshift stimulatory signal of the human immunodeficiency virus type 1. RNA 10: 1225-1235.
25. Léger, M., Dulude, D., Steinberg, S.V., and Brakier-Gingras, L. 2007. The three transfer RNAs occupying the A, P, and E sites on the ribosome are involved in viral programmed -1 ribosomal frameshift. Nucleic Acids Res. 35: 5581-5592. doi: 10.1093/nar/gkm578.
26. Lu, Z., Tripp, B.C., and McCoy, J.M. 1998. Displaying libraries of conformationally constrained peptides on the surface of Escherichia coli as flagellin fusions. Methods Mol. Biol. 87: 265-280.
27. McNaughton, BR, Gareiss, PC, and Miller, BL 2007. Identification of a selective small-molecule ligand for HIV-1 frameshift-inducing stem-loop RNA from an 11,325 member resin bound dynamic combinatorial library. J. Am. Chem. Soc. 129: 11306-11307.
28. Namy, O., Moran, S.J., Stuart, D.I., Gilbert, R.J., and Brierley, I. 2006. A mechanical explanation of RNA pseudoknot function in programmed ribosomal frameshifting. Nature 441: 244-247.
29. Park, J. and Morrow, C.D. 1991. Overexpression of the gag-pol precursor from human immunodeficiency virus type 1 proviral genomes results in efficient proteolytic processing in the absence of virion production. J. Virol. 65: 5111-5117.
30. Plant, E.P. and Dinman, J.D. 2006. Comparative study of the effects of heptameric slippery site composition on -1 frameshifting among different eukaryotic systems. RNA 12: 666-673.
31. Plant, E.P., Jacobs, K.L., Harger, J.W., Meskauskas, A., Jacobs, J.L., Baxter, J.L., Petrov, A.N., and Dinman, J.D. 2003. The 9-A solution: How mRNA pseudoknots promote efficient programmed -1 ribosomal frameshifting. RNA 9: 168-174.
32. Serrano, M., Lin, A.W., McCurrach, M.E., Beach, D., and Lowe, S.W. 1997. Oncogenic ras provokes premature senescence associated with accumulation of p53 and p16ink4a. Cell 88: 593-602.
33. Shehu-Xhilaga, M., Crowe, S.M., and Mak, J. 2001. Maintenance of the Gag/Gag-Pol ratio is important for human immunodeficiency virus type 1 RNA dimerization and viral infectivity. J. Virol. 75: 1834-1841.
34. Spahn, C.M., Jan, E., Mulder, A., Grassucci, R.A., Sarnow, P., and Frank, J. 2004. Cryo-EM visualization of a viral internal ribosome entry site bound to human ribosomes: The IRES functions as an RNA-based translation factor. Cell 118: 465-475.
35. Staple, D.W. and Butcher, S.E. 2005. Solution structure and thermodynamic investigation of the HIV-1 frameshift inducing element. J. Mol. Biol. 349: 1011-1023.
36. Takyar, S., Hickerson, R.P., and Noller, H.F. 2005. mRNA helicase activity of the ribosome. Cell 120: 49-58.
37. Telenti, A., Martinez, R., Munoz, M., Bleiber, G., Greub, G., Sanglard, D., and Peters, S. 2002. Analysis of natural variants of the human immunodeficiency virus type 1 gag-pol frameshift stem-loop structure. J. Virol. 76: 7868-7873.
38. Thompson, J., O'Connor, M., Mills, J.A., and Dahlberg, A.E. 2002. The protein synthesis inhibitors, oxazolidinones and chloramphenicol, cause extensive translational inaccuracy in vivo. J. Mol. Biol. 322: 273-279.
39. Weiss, M.A. and Narayana, N. 1998. RNA recognition by arginine-rich peptide motifs. Biopolymers 48: 167-180.
40. Weiss, R.B., Dunn, D.M., Shuh, M., Atkins, J.F., and Gesteland, R.F. 1989. E. coli ribosomes re-phase on retroviral frameshift signals at rates ranging from 2 to 50 percent. New Biol. 1: 159-169.
41. Xu, X., Leo, C., Jang, Y., Chan, E., Padilla, D., Huang, B.C., Lin, T., Gururaja, T., Hitoshi, Y., Lorens, J.B., et al. 2001. Dominant effector genetics in mammalian cells. Nat. Genet. 27: 23-29.
42. Yusupova, G.Z., Yusupov, M.M., Cate, J.H., and Noller, H.F. 2001. The path of messenger RNA through the ribosome. Cell 106: 233-241.