메뉴 건너뛰기




Volumn 26, Issue 6, 2013, Pages 286-296

Randomized codon mutagenesis reveals that the HIV Rev arginine-rich motif is robust to substitutions and that double substitution of two critical residues alters specificity

Author keywords

arginine rich motif; HIV rev; neutral evolution; Protein RNA recognition; Rev aptamer I; Rev response element

Indexed keywords

ARGININE; REV PROTEIN;

EID: 84876465842     PISSN: 09523499     EISSN: 10991352     Source Type: Journal    
DOI: 10.1002/jmr.2272     Document Type: Article
Times cited : (8)

References (56)
  • 1
    • 0026045893 scopus 로고
    • HIV-1 Rev regulation involves recognition of non-Watson-Crick base pairs in viral RNA
    • Bartel DP, Zapp ML, Green MR, Szostak JW,. 1991. HIV-1 Rev regulation involves recognition of non-Watson-Crick base pairs in viral RNA. Cell 67: 529-536.
    • (1991) Cell , vol.67 , pp. 529-536
    • Bartel, D.P.1    Zapp, M.L.2    Green, M.R.3    Szostak, J.W.4
  • 3
    • 0028268016 scopus 로고
    • Binding of an HIV Rev peptide to Rev responsive element RNA induces formation of purine-purine base pairs
    • Battiste JL, Tan R, Frankel AD, Williamson JR,. 1994. Binding of an HIV Rev peptide to Rev responsive element RNA induces formation of purine-purine base pairs. Biochemistry 33: 2741-2747.
    • (1994) Biochemistry , vol.33 , pp. 2741-2747
    • Battiste, J.L.1    Tan, R.2    Frankel, A.D.3    Williamson, J.R.4
  • 4
    • 28344450939 scopus 로고    scopus 로고
    • Arginine-rich motifs present multiple interfaces for specific binding by RNA
    • Bayer TS, Booth LN, Knudsen SM, Ellington AD,. 2005. Arginine-rich motifs present multiple interfaces for specific binding by RNA. RNA 11: 1848-1857.
    • (2005) RNA , vol.11 , pp. 1848-1857
    • Bayer, T.S.1    Booth, L.N.2    Knudsen, S.M.3    Ellington, A.D.4
  • 7
    • 0038813728 scopus 로고    scopus 로고
    • Structural mimicry in the phage phi21 N peptide-boxB RNA complex
    • Cilley CD, Williamson JR,. 2003. Structural mimicry in the phage phi21 N peptide-boxB RNA complex. RNA 9: 663-676.
    • (2003) RNA , vol.9 , pp. 663-676
    • Cilley, C.D.1    Williamson, J.R.2
  • 8
    • 18444383371 scopus 로고    scopus 로고
    • Protein families and RNA recognition
    • Chen Y, Varani G,. 2005. Protein families and RNA recognition. FEBS J. 272: 2088-2097.
    • (2005) FEBS J. , vol.272 , pp. 2088-2097
    • Chen, Y.1    Varani, G.2
  • 9
    • 44949184659 scopus 로고    scopus 로고
    • Bacteriophage P22 antitermination boxB sequence requirements are complex and overlap with those of lambda
    • DOI: 10.1128/JB.00059-08
    • Cocozaki AI, Ghattas IR, Smith CA,. 2008a. Bacteriophage P22 antitermination boxB sequence requirements are complex and overlap with those of lambda. J. Bacteriol. 190: 4263-4271. DOI: 10.1128/JB.00059-08.
    • (2008) J. Bacteriol. , vol.190 , pp. 4263-4271
    • Cocozaki, A.I.1    Ghattas, I.R.2    Smith, C.A.3
  • 10
    • 57349103145 scopus 로고    scopus 로고
    • The RNA-binding domain of bacteriophage P22 N protein is highly mutable and a single mutation relaxes specificity toward λ
    • DOI: 10.1128/JB.00997-08
    • Cocozaki AI, Ghattas IR, Smith CA,. 2008b. The RNA-binding domain of bacteriophage P22 N protein is highly mutable and a single mutation relaxes specificity toward λ. J. Bacteriol. 190: 7699-7708. DOI: 10.1128/JB.00997-08.
    • (2008) J. Bacteriol. , vol.190 , pp. 7699-7708
    • Cocozaki, A.I.1    Ghattas, I.R.2    Smith, C.A.3
  • 11
    • 0042337396 scopus 로고    scopus 로고
    • Sequence and structure space of RNA-binding peptides
    • Das C, Frankel AD,. 2003. Sequence and structure space of RNA-binding peptides. Biopolymers 70: 80-85.
    • (2003) Biopolymers , vol.70 , pp. 80-85
    • Das, C.1    Frankel, A.D.2
  • 12
    • 52049106911 scopus 로고    scopus 로고
    • A solution to limited genomic capacity: Using adaptable binding surfaces to assemble the functional HIV Rev oligomer on RNA
    • DOI: 10.1016/j.molcel.2008.07.016
    • Daugherty MD, D'Orso I, Frankel AD,. 2008. A solution to limited genomic capacity: using adaptable binding surfaces to assemble the functional HIV Rev oligomer on RNA. Mol. Cell 31: 824-834. DOI: 10.1016/j.molcel.2008.07.016.
    • (2008) Mol. Cell , vol.31 , pp. 824-834
    • Daugherty, M.D.1    D'Orso, I.2    Frankel, A.D.3
  • 13
    • 78549248443 scopus 로고    scopus 로고
    • Structural basis for cooperative RNA binding and export complex assembly by HIV Rev
    • DOI: 10.1038/nsmb.1902
    • Daugherty MD, Liu B, Frankel AD,. 2010. Structural basis for cooperative RNA binding and export complex assembly by HIV Rev. Nat. Struct. Mol. Biol. 17: 1337-1342. DOI: 10.1038/nsmb.1902.
    • (2010) Nat. Struct. Mol. Biol. , vol.17 , pp. 1337-1342
    • Daugherty, M.D.1    Liu, B.2    Frankel, A.D.3
  • 14
    • 0032727991 scopus 로고    scopus 로고
    • Themes in RNA-protein recognition
    • Draper DE,. 1999. Themes in RNA-protein recognition. J. Mol. Biol. 293: 255-270.
    • (1999) J. Mol. Biol. , vol.293 , pp. 255-270
    • Draper, D.E.1
  • 15
    • 0036903361 scopus 로고    scopus 로고
    • Modelling 'evo-devo' with RNA
    • Fontana W., 2002. Modelling 'evo-devo' with RNA. Bioessays 24: 1164-1177.
    • (2002) Bioessays , vol.24 , pp. 1164-1177
    • Fontana, W.1
  • 16
    • 0027288664 scopus 로고
    • Clustered arginine residues of bacteriophage lambda N protein are essential to antitermination of transcription, but their locale cannot compensate for boxB loop defects
    • Franklin NC,. 1993. Clustered arginine residues of bacteriophage lambda N protein are essential to antitermination of transcription, but their locale cannot compensate for boxB loop defects. J. Mol. Biol. 231: 343-360
    • (1993) J. Mol. Biol. , vol.231 , pp. 343-360
    • Franklin, N.C.1
  • 17
    • 0024671716 scopus 로고
    • Overexpression of N antitermination proteins of bacteriophages lambda, 21, and P22: Loss of N protein specificity
    • Franklin NC, Doelling JH,. 1989. Overexpression of N antitermination proteins of bacteriophages lambda, 21, and P22: loss of N protein specificity. J. Bacteriol. 171: 2513-2522.
    • (1989) J. Bacteriol. , vol.171 , pp. 2513-2522
    • Franklin, N.C.1    Doelling, J.H.2
  • 19
    • 3042681604 scopus 로고    scopus 로고
    • Protein tolerance to random amino acid change
    • DOI: 10.1073/pnas.0403255101
    • Guo HH, Choe J, Loeb LA,. 2004. Protein tolerance to random amino acid change. Proc. Natl. Acad. Sci. U. S. A. 101: 9205-9210. DOI: 10.1073/pnas.0403255101.
    • (2004) Proc. Natl. Acad. Sci. U. S. A. , vol.101 , pp. 9205-9210
    • Guo, H.H.1    Choe, J.2    Loeb, L.A.3
  • 20
    • 0029868515 scopus 로고    scopus 로고
    • Selection of RNA-binding peptides in vivo
    • Harada K, Martin SS, Frankel AD,. 1996. Selection of RNA-binding peptides in vivo. Nature 380: 175-179.
    • (1996) Nature , vol.380 , pp. 175-179
    • Harada, K.1    Martin, S.S.2    Frankel, A.D.3
  • 22
    • 0025166385 scopus 로고
    • HIV-1 regulator of virion expression (Rev) protein binds to an RNA stem-loop structure located within the Rev response element
    • Heaphy S, Dingwall C, Ernberg I, Gait MJ, Green SM, Karn J, Lowe AD, Singh M, Skinner MA,. 1990. HIV-1 regulator of virion expression (Rev) protein binds to an RNA stem-loop structure located within the Rev response element. Cell 60: 685-693.
    • (1990) Cell , vol.60 , pp. 685-693
    • Heaphy, S.1    Dingwall, C.2    Ernberg, I.3    Gait, M.J.4    Green, S.M.5    Karn, J.6    Lowe, A.D.7    Singh, M.8    Skinner, M.A.9
  • 23
    • 0025149054 scopus 로고
    • Mutational analysis of the human immunodeficiency virus type 1 Rev transactivator: Essential residues near the amino terminus
    • Hope TJ, McDonald D, Huang XJ, Low J, Parslow TG,. 1990. Mutational analysis of the human immunodeficiency virus type 1 Rev transactivator: essential residues near the amino terminus. J. Virol. 64: 5360-5366.
    • (1990) J. Virol. , vol.64 , pp. 5360-5366
    • Hope, T.J.1    McDonald, D.2    Huang, X.J.3    Low, J.4    Parslow, T.G.5
  • 24
    • 24044528558 scopus 로고    scopus 로고
    • Evolvability of the mode of peptide binding by an RNA
    • Iwazaki T, Li X, Harada K,. 2005. Evolvability of the mode of peptide binding by an RNA. RNA 11: 1364-1373
    • (2005) RNA , vol.11 , pp. 1364-1373
    • Iwazaki, T.1    Li, X.2    Harada, K.3
  • 25
    • 0025780933 scopus 로고
    • The neutral theory of molecular evolution: A review of recent evidence
    • Kimura M., 1991. The neutral theory of molecular evolution: a review of recent evidence. Jpn J Genet 66: 367-386.
    • (1991) Jpn J Genet , vol.66 , pp. 367-386
    • Kimura, M.1
  • 26
    • 0026540537 scopus 로고
    • Specific binding of a basic peptide from HIV-1 Rev
    • Kjems J, Calnan BJ, Frankel AD, Sharp PA,. 1992. Specific binding of a basic peptide from HIV-1 Rev. EMBO J. 11: 1119-1129.
    • (1992) EMBO J. , vol.11 , pp. 1119-1129
    • Kjems, J.1    Calnan, B.J.2    Frankel, A.D.3    Sharp, P.A.4
  • 28
    • 0032540286 scopus 로고    scopus 로고
    • NMR structure of the bacteriophage lambda N peptide/boxB RNA complex: Recognition of a GNRA fold by an arginine-rich motif
    • Legault P, Li J, Mogridge J, Kay LE, Greenblatt J,. 1998. NMR structure of the bacteriophage lambda N peptide/boxB RNA complex: recognition of a GNRA fold by an arginine-rich motif. Cell 93: 289-299.
    • (1998) Cell , vol.93 , pp. 289-299
    • Legault, P.1    Li, J.2    Mogridge, J.3    Kay, L.E.4    Greenblatt, J.5
  • 29
    • 0035838382 scopus 로고    scopus 로고
    • Current topics in RNA-protein recognition: Control of specificity and biological function through induced fit and conformational capture
    • Leulliot N, Varani G,. 2001. Current topics in RNA-protein recognition: control of specificity and biological function through induced fit and conformational capture. Biochemistry 40: 7947-7956.
    • (2001) Biochemistry , vol.40 , pp. 7947-7956
    • Leulliot, N.1    Varani, G.2
  • 30
    • 0029014899 scopus 로고
    • Interaction of human immunodeficiency virus type 1 Tat-derived peptides with TAR RNA
    • Long KS, Crothers DM,. 1995. Interaction of human immunodeficiency virus type 1 Tat-derived peptides with TAR RNA. Biochemistry 34: 8885-8895.
    • (1995) Biochemistry , vol.34 , pp. 8885-8895
    • Long, K.S.1    Crothers, D.M.2
  • 31
    • 0024518918 scopus 로고
    • The HIV-1 rev trans-activator acts through a structured target sequence to activate nuclear export of unspliced viral mRNA
    • Malim MH, Hauber J, Le SY, Maizel JV, Cullen BR,. 1989. The HIV-1 rev trans-activator acts through a structured target sequence to activate nuclear export of unspliced viral mRNA. Nature 338: 254-257.
    • (1989) Nature , vol.338 , pp. 254-257
    • Malim, M.H.1    Hauber, J.2    Le, S.Y.3    Maizel, J.V.4    Cullen, B.R.5
  • 33
    • 0029865623 scopus 로고    scopus 로고
    • Context-dependent secondary structure formation of a designed protein sequence
    • Minor DL Jr, Kim PS,. 1996. Context-dependent secondary structure formation of a designed protein sequence. Nature 380: 730-734.
    • (1996) Nature , vol.380 , pp. 730-734
    • Minor, Jr.D.L.1    Kim, P.S.2
  • 34
    • 0037058932 scopus 로고    scopus 로고
    • Near-neutrality in evolution of genes and gene regulation
    • Ohta T., 2002. Near-neutrality in evolution of genes and gene regulation. Proc. Natl. Acad. Sci. U. S. A. 99: 16134-16137.
    • (2002) Proc. Natl. Acad. Sci. U. S. A. , vol.99 , pp. 16134-16137
    • Ohta, T.1
  • 35
    • 81755180766 scopus 로고    scopus 로고
    • The control of HIV transcription: Keeping RNA polymerase II on track
    • DOI: 10.1016/j.chom.2011.11.002
    • Ott M, Geyer M, Zhou Q,. 2011. The control of HIV transcription: keeping RNA polymerase II on track. Cell Host Microbe 10: 426-435. DOI: 10.1016/j.chom.2011.11.002.
    • (2011) Cell Host Microbe , vol.10 , pp. 426-435
    • Ott, M.1    Geyer, M.2    Zhou, Q.3
  • 36
    • 0037321040 scopus 로고    scopus 로고
    • Selection of RRE RNA binding peptides using a kanamycin antitermination assay
    • Peled-Zehavi H, Horiya S, Das C, Harada K, Frankel AD,. 2003. Selection of RRE RNA binding peptides using a kanamycin antitermination assay. RNA 9: 252-261.
    • (2003) RNA , vol.9 , pp. 252-261
    • Peled-Zehavi, H.1    Horiya, S.2    Das, C.3    Harada, K.4    Frankel, A.D.5
  • 37
    • 0028858599 scopus 로고
    • Solution structure of a bovine immunodeficiency virus Tat-TAR peptide-RNA complex
    • Puglisi JD, Chen L, Blanchard S, Frankel AD,. 1995. Solution structure of a bovine immunodeficiency virus Tat-TAR peptide-RNA complex. Science 270: 1200-1203.
    • (1995) Science , vol.270 , pp. 1200-1203
    • Puglisi, J.D.1    Chen, L.2    Blanchard, S.3    Frankel, A.D.4
  • 38
    • 0000641399 scopus 로고    scopus 로고
    • Antitermination in bacteriophage lambda. The structure of the N36 peptide-boxB RNA complex
    • Schärpf M, Sticht H, Schweimer K, Boehm M, Hoffmann S, Rösch P,. 2000. Antitermination in bacteriophage lambda. The structure of the N36 peptide-boxB RNA complex. Eur. J. Biochem. 267: 2397-2408.
    • (2000) Eur. J. Biochem. , vol.267 , pp. 2397-2408
    • Schärpf, M.1    Sticht, H.2    Schweimer, K.3    Boehm, M.4    Hoffmann, S.5    Rösch, P.6
  • 39
    • 0034698298 scopus 로고    scopus 로고
    • One sequence, two ribozymes: Implications for the emergence of new ribozyme folds
    • Schultes EA, Bartel DP,. 2000. One sequence, two ribozymes: implications for the emergence of new ribozyme folds. Science 289: 448-452.
    • (2000) Science , vol.289 , pp. 448-452
    • Schultes, E.A.1    Bartel, D.P.2
  • 41
    • 0032575334 scopus 로고    scopus 로고
    • Altering the context of an RNA bulge switches the binding specificities of two viral Tat proteins
    • Smith CA, Crotty S, Harada Y, Frankel AD,. 1998. Altering the context of an RNA bulge switches the binding specificities of two viral Tat proteins. Biochemistry 37: 10808-10814.
    • (1998) Biochemistry , vol.37 , pp. 10808-10814
    • Smith, C.A.1    Crotty, S.2    Harada, Y.3    Frankel, A.D.4
  • 42
    • 45849141267 scopus 로고    scopus 로고
    • Tailoring the peptide-binding specificity of an RNA by combinations of specificity-altering mutations
    • DOI: 10.1080/15257770801944493
    • Sugaya M, Nishimura F, Katoh A, Harada K,. 2008a. Tailoring the peptide-binding specificity of an RNA by combinations of specificity-altering mutations. Nucleosides Nucleotides Nucleic Acids 27: 534-545. DOI: 10.1080/15257770801944493.
    • (2008) Nucleosides Nucleotides Nucleic Acids , vol.27 , pp. 534-545
    • Sugaya, M.1    Nishimura, F.2    Katoh, A.3    Harada, K.4
  • 43
    • 45849109378 scopus 로고    scopus 로고
    • Amino acid requirement for the high affinity binding of a selected arginine-rich peptide with the HIV Rev-response element RNA
    • DOI: 10.1002/psc.1027
    • Sugaya M, Nishino N, Katoh A, Harada K,. 2008b. Amino acid requirement for the high affinity binding of a selected arginine-rich peptide with the HIV Rev-response element RNA. J. Pept. Sci. 14: 924-935. DOI: 10.1002/psc.1027.
    • (2008) J. Pept. Sci. , vol.14 , pp. 924-935
    • Sugaya, M.1    Nishino, N.2    Katoh, A.3    Harada, K.4
  • 44
    • 0029655644 scopus 로고    scopus 로고
    • RNA aptamers selected to bind human immunodeficiency virus type 1 Rev in vitro are Rev responsive in vivo
    • Symensma TL, Giver L, Zapp M, Takle GB, Ellington AD,. 1996. RNA aptamers selected to bind human immunodeficiency virus type 1 Rev in vitro are Rev responsive in vivo. J. Virol. 70: 179-187.
    • (1996) J. Virol. , vol.70 , pp. 179-187
    • Symensma, T.L.1    Giver, L.2    Zapp, M.3    Takle, G.B.4    Ellington, A.D.5
  • 46
    • 0028596537 scopus 로고
    • Costabilization of peptide and RNA structure in an HIV Rev peptide-RRE complex
    • Tan R, Frankel AD,. 1994. Costabilization of peptide and RNA structure in an HIV Rev peptide-RRE complex. Biochemistry 33: 14579-14585.
    • (1994) Biochemistry , vol.33 , pp. 14579-14585
    • Tan, R.1    Frankel, A.D.2
  • 47
    • 0032516079 scopus 로고    scopus 로고
    • A novel glutamine-RNA interaction identified by screening libraries in mammalian cells
    • Tan R, Frankel AD,. 1998. A novel glutamine-RNA interaction identified by screening libraries in mammalian cells. Proc. Natl. Acad. Sci. U. S. A. 95: 4247-4252.
    • (1998) Proc. Natl. Acad. Sci. U. S. A. , vol.95 , pp. 4247-4252
    • Tan, R.1    Frankel, A.D.2
  • 48
    • 64849101493 scopus 로고    scopus 로고
    • Protein dynamism and evolvability
    • DOI: 10.1126/science.1169375
    • Tokuriki N, Tawfik DS,. 2009. Protein dynamism and evolvability. Science 324: 203-207. DOI: 10.1126/science.1169375.
    • (2009) Science , vol.324 , pp. 203-207
    • Tokuriki, N.1    Tawfik, D.S.2
  • 49
    • 0037469371 scopus 로고    scopus 로고
    • Evolution of mutational robustness
    • Wilke CO, Adami C,. 2003. Evolution of mutational robustness. Mutat. Res. 522: 3-11.
    • (2003) Mutat. Res. , vol.522 , pp. 3-11
    • Wilke, C.O.1    Adami, C.2
  • 50
    • 11144259344 scopus 로고    scopus 로고
    • Retention of conformational flexibility in HIV-1 Rev-RNA complexes
    • Wilkinson TA, Zhu L, Hu W, Chen Y,. 2004. Retention of conformational flexibility in HIV-1 Rev-RNA complexes. Biochemistry 43: 16153-16160.
    • (2004) Biochemistry , vol.43 , pp. 16153-16160
    • Wilkinson, T.A.1    Zhu, L.2    Hu, W.3    Chen, Y.4
  • 51
    • 0033784534 scopus 로고    scopus 로고
    • Induced fit in RNA-protein recognition
    • Williamson JR,. 2000. Induced fit in RNA-protein recognition. Nat. Struct. Biol. 7: 834-837.
    • (2000) Nat. Struct. Biol. , vol.7 , pp. 834-837
    • Williamson, J.R.1
  • 52
    • 0029847929 scopus 로고    scopus 로고
    • Anti-peptide aptamers recognize amino acid sequence and bind a protein epitope
    • Xu W, Ellington AD,. 1996. Anti-peptide aptamers recognize amino acid sequence and bind a protein epitope. Proc. Natl. Acad. Sci. U. S. A. 93: 7475-7480.
    • (1996) Proc. Natl. Acad. Sci. U. S. A. , vol.93 , pp. 7475-7480
    • Xu, W.1    Ellington, A.D.2
  • 53
    • 0030475417 scopus 로고    scopus 로고
    • Deep penetration of an α-helix into a widened RNA major groove in the HIV-1 Rev peptide-RNA aptamer complex
    • Ye X, Gorin A, Ellington AD, Patel DJ,. 1996. Deep penetration of an α-helix into a widened RNA major groove in the HIV-1 Rev peptide-RNA aptamer complex. Nat. Struct. Biol. 3: 1026-1033
    • (1996) Nat. Struct. Biol. , vol.3 , pp. 1026-1033
    • Ye, X.1    Gorin, A.2    Ellington, A.D.3    Patel, D.J.4
  • 55
    • 0024310483 scopus 로고
    • Sequence-specific RNA binding by the HIV-1 Rev protein
    • Zapp ML, Green MR,. 1989. Sequence-specific RNA binding by the HIV-1 Rev protein. Nature 342: 714-716.
    • (1989) Nature , vol.342 , pp. 714-716
    • Zapp, M.L.1    Green, M.R.2
  • 56
    • 0025917131 scopus 로고
    • Oligomerization and RNA binding domains of the type 1 human immunodeficiency virus Rev protein: A dual function for an arginine-rich binding motif
    • Zapp M L, Hope T J, Parslow T G, Green M R,. 1991. 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. 88: 7734-7738.
    • (1991) Proc. Natl. Acad. Sci. U. S. A. , vol.88 , pp. 7734-7738
    • Zapp, M.L.1    Hope, T.J.2    Parslow, T.G.3    Green, M.R.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.