The leucine zipper domains of the transcription factors GCN4 and c-Jun have Ribonuclease Activity

PLoS ONE

Volumn 5, Issue 5, 2010, Pages

  Nikolaev, Yaroslav ^a,b   Deillon, Christine ^a   Hoffmann, Stefan R K ^a   Bigler, Laurent ^a   Friess, Sebastian ^c   Zenobi, Renato ^c   Pervushin, Konstantin ^b   Hunziker, Peter ^d   Gutte, Bernd ^a  

^a UNIVERSITY OF ZURICH   (Switzerland)

^b UNIVERSITY OF BASEL   (Switzerland)

^c ETH ZURICH   (Switzerland)

^d FUNCTIONAL GENOMICS CENTER ZURICH   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

3',5' CYCLIC NUCLEOTIDE PHOSPHODIESTERASE; ADENOSINE 2',3' PHOSPHATE; ENZYME INHIBITOR; LEUCINE ZIPPER PROTEIN; MUTANT PROTEIN; PROTEIN C JUN; RIBONUCLEASE; RIBONUCLEASE A; RNA 18S; SYNTHETIC PEPTIDE; TRANSCRIPTION FACTOR GCN4;

AMINO ACID SEQUENCE; ARTICLE; CHEMICAL BOND; CONTROLLED STUDY; ELECTROSPRAY MASS SPECTROMETRY; ENHANCER REGION; ENZYME ACTIVITY; ENZYME INACTIVATION; ENZYME MECHANISM; ENZYME REPRESSION; ENZYME SPECIFICITY; GENE MUTATION; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; HUMAN; IN VIVO STUDY; NONHUMAN; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN FUNCTION; RNA CLEAVAGE; RNA DEGRADATION; TRANSCRIPTION INITIATION;

AMINO ACID SEQUENCE; BASIC-LEUCINE ZIPPER TRANSCRIPTION FACTORS; CHROMATOGRAPHY, HIGH PRESSURE LIQUID; ENZYME ASSAYS; ENZYME INHIBITORS; HUMANS; KINETICS; LEUCINE ZIPPERS; MOLECULAR SEQUENCE DATA; MOLECULAR WEIGHT; MUTANT PROTEINS; PEPTIDES; PROTEIN STRUCTURE, TERTIARY; PROTO-ONCOGENE PROTEINS C-JUN; RIBONUCLEASES; RNA STABILITY; SACCHAROMYCES CEREVISIAE PROTEINS; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION;

EID: 77956527819     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0010765     Document Type: Article

References (54)

1. Landschulz WH, Johnson PF, McKnight SL (1988) The leucine zipper: a hypothetical structure common to a new class of DNA binding proteins. Science 240: 1759-1764.
2. Lupas AN, Gruber M (2005) The structure of alpha-helical coiled coils. Adv Protein Chem 70: 37-78.
3. Tupler R, Perini G, Green MR (2001) Expressing the human genome. Nature 409: 832-833.
4. Amoutzias GD, Robertson DL, Van de Peer Y, Oliver SG (2008) Choose your partners: dimerization in eukaryotic transcription factors. Trends Biochem Sci 33: 220-229.
5. Liu N, Caderas G, Gutte B, Thomas RM (1997) An artificial HIV enhancerbinding peptide is dimerized by the addition of a leucine zipper. Eur Biophys J 25: 399-403.
6. Rieker JD, Hu JC (2000) Molecular applications of fusions to leucine zippers. Meth Enzymol 328: 282-296.
7. Liu N, Caderas G, Deillon C, Hoffmann S, Klauser S, et al. (2001) Fusion proteins from artificial and natural structural modules. Curr Protein Pept Sci 2: 107-121.
8. Liu J, Zheng Q, Deng Y, Cheng CS, Kallenbach NR, et al. (2006) A seven-helix coiled coil. Proc Natl Acad Sci U S A 104: 15457-15462.
9. Mittl PR, Deillon C, Sargent D, Liu N, Klauser S, et al. (2000) The retro-GCN4 leucine zipper sequence forms a stable three-dimensional structure. Proc Natl Acad Sci U S A 97: 2562-2566.
10. Richards FM, Wyckoff HW (1971) Bovine pancreatic ribonuclease. In: Boyer PD, ed. The Enzymes, 3rd ed, Vol IV, Academic Press, New York. pp 647-806.
11. Jeffery CJ (2003) Moonlighting proteins: old proteins learning new tricks. Trends Genet 19: 415-417.
12. Lima WF, Crooke ST (1999) Highly efficient endonucleolytic cleavage of RNA by a Cys(2)His(2) zinc-finger peptide. Proc Natl Acad Sci U S A 96: 10010-10015.
13. Lei G, Arany I, Tyring SK, Brysk H, Brysk MM (1998) Zinc-alpha 2- glycoprotein has ribonuclease activity. Arch Biochem Biophys 355: 160-164.
14. Nakamura T, Sugita M (2008) A conserved DYW domain of the pentatricopeptide repeat protein possesses a novel endoribonuclease activity. FEBS Lett 582: 4163-4168.
15. Small ID, Peeters N (2000) The PPR motif - a TPR-related motif prevalent in plant organellar proteins. Trends Biochem Sci 25: 46-47.
16. O'Toole N, Hattori M, Andres C, Iida K, Lurin C, et al. (2008) On the expansion of the pentatricopeptide repeat gene family in plants. Mol Biol Evol 25: 1120-1128.
17. Michels WJ, Jr., Pyle AM (1995) Conversion of a group II intron into a new multiple-turnover ribozyme that selectively cleaves oligonucleotides: elucidation of reaction mechanism and structure/function relationships. Biochemistry 34: 2965-2977.
18. Scheffer U, Strick A, Ludwig V, Peter S, Kalden E, et al. (2005) Metal-free catalysts for the hydrolysis of RNA derived from guanidines, 2-aminopyridines, and 2-aminobenzimidazoles. J Am Chem Soc 127: 2211-2217.
19. Breslow R, Doherty JB, Guillot G, Lipsey C (1978) Beta-Cyclodextrinylbisimidazole, a Model for Ribonuclease. J Am Chem Soc 100: 3227-3229.
20. Fouace S, Gaudin C, Picard S, Corvaisier S, Renault J, et al. (2004) Polyamine derivatives as selective RNaseA mimics. Nucleic Acids Res 32: 151-157.
21. Gnaccarini C, Peter S, Scheffer U, Vonhoff S, Klussmann S, et al. (2006) Sitespecific cleavage of RNA by a metal-free artificial nuclease attached to antisense oligonucleotides. J Am Chem Soc 128: 8063-8067.
22. Niittymäki T, Lönnberg H (2006) Artificial ribonucleases. Org Biomol Chem 4: 15-25.
23. Perreault DM, Cabell LA, Anslyn EV (1997) Using guanidinium groups for the recognition of RNA and as catalysts for the hydrolysis of RNA. Bioorg Med Chem 5: 1209-1220.
24. Bibillo A, Figlerowicz M, Kierzek R (1999) The non-enzymatic hydrolysis of oligoribonucleotides VI. The role of biogenic polyamines. Nucleic Acids Res 27: 3931-3937.
25. Bashkin JK, Frolova EI, Sampath US (1994) Sequence-Specific Cleavage of HIV Messenger-RNA by a Ribozyme Mimic. J Am Chem Soc 116: 5981-5982.
26. Brittain IJ, Huang X, Long EC (1998) Selective recognition and cleavage of RNA loop structures by Ni(II).Xaa-Gly-His metallopeptides. Biochemistry 37: 12113-12120.
27. Koroleva LS, Serpokrylova IY, Vlassov VV, Silnikov VN (2007) Design and synthesis of metal-free artificial ribonucleases. Protein Pept Lett 14: 151-163.
28. Barbier B, Brack A (1992) Conformation-Controlled Hydrolysis of Polyribonucleotides by Sequential Basic Polypeptides. J Am Chem Soc 114: 3511-3515.
29. Fasken MB, Corbett AH (2005) Process or perish: quality control in mRNA biogenesis. Nat Struct Mol Biol 12: 482-488.
30. Mata J, Marguerat S, Bahler J (2005) Post-transcriptional control of gene expression: a genome-wide perspective. Trends Biochem Sci 30: 506-514.
31. Moore MJ (2002) Nuclear RNA turnover. Cell 108: 431-434.
32. Doma MK, Parker R (2007) RNA quality control in eukaryotes. Cell 131: 660-668.
33. Struhl K (2007) Transcriptional noise and the fidelity of initiation by RNA polymerase II. Nat Struct Mol Biol 14: 103-105.
34. Hehlgans T, Stolz M, Klauser S, Cui T, Salgam P, et al. (1993) The DNAbinding properties of an artificial 42-residue polypeptide derived from a natural repressor. FEBS Lett 315: 51-55.
35. Städler K, Liu N, Trotman L, Hiltpold A, Caderas G, et al. (1995) Design, synthesis, and characterization of HIV-1 enhancer-binding polypeptides derived from bacteriophage 434 repressor. Int J Pept Protein Res 46: 333-340.
36. Caderas G, Klauser S, Liu N, Bienz A, Gutte B (1999) Inhibition of HIV-1 enhancer-controlled transcription by artificial enhancer-binding peptides derived from bacteriophage 434 repressor. Eur J Biochem 266: 599-607.
37. Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31: 3406-3415.
38. Todd AE, Orengo CA, Thornton JM (2002) Plasticity of enzyme active sites. Trends Biochem Sci 27: 419-426.
39. Dickson KA, Haigis MC, Raines RT (2005) Ribonuclease inhibitor: structure and function. Prog Nucleic Acid Res Mol Biol 80: 349-374.
40. O'Shea EK, Klemm JD, Kim PS, Alber T (1991) X-ray structure of the GCN4 leucine zipper, a two-stranded, parallel coiled coil. Science 254: 539-544.
41. Pitsch S, Scheffer U, Hey M, Strick A, Gobel MW (2003) On facts and artefacts: The difficulty to evaluate an artificial nuclease. Helv Chim Acta 86: 3740-3752.
42. Zitzewitz JA, Bilsel O, Luo J, Jones BE, Matthews CR (1995) Probing the folding mechanism of a leucine zipper peptide by stopped-flow circular dichroism spectroscopy. Biochemistry 34: 12812-12819.
43. Liu N, Deillon C, Klauser S, Gutte B, Thomas RM (1998) Synthesis, physicochemical characterization, and crystallization of a putative retro-coiled coil. Protein Sci 7: 1214-1220.
44. d'Avignon DA, Bretthorst GL, Holtzer ME, Schwarz KA, Angeletti RH, et al. (2006) Site-specific experiments on folding/unfolding of Jun coiled coils: thermodynamic and kinetic parameters from spin inversion transfer nuclear magnetic resonance at leucine-18. Biopolymers 83: 255-267.
45. Steyaert J, Hallenga K, Wyns L, Stanssens P (1990) Histidine-40 of ribonuclease T1 acts as base catalyst when the true catalytic base, glutamic acid-58, is replaced by alanine. Biochemistry 29: 9064-9072.
46. Landt O, Tholke J, Grunert HP, Saenger W, Hahn U (1997) Ribonuclease T1 is active when both catalytic histidines are replaced by aspartate. Biol Chem 378: 553-558.
47. Nikolaev Y, Pervushin K (2007) NMR Spin State Exchange Spectroscopy Reveals Equilibrium of Two Distinct Conformations of Leucine Zipper GCN4 in Solution. J Am Chem Soc 129: 6461-6469.
48. Schiene-Fischer C, Habazettl J, Schmid FX, Fischer G (2002) The hsp70 chaperone DnaK is a secondary amide peptide bond cis-trans isomerase. Nat Struct Biol 9: 419-424.
49. Wentworth AD, Jones LH, Wentworth P, Jr., Janda KD, Lerner RA (2000) Antibodies have the intrinsic capacity to destroy antigens. Proc Natl Acad Sci U S A 97: 10930-10935.
50. Wentworth P, Jr., McDunn JE, Wentworth AD, Takeuchi C, Nieva J, et al. (2002) Evidence for antibody-catalyzed ozone formation in bacterial killing and inflammation. Science 298: 2195-2199.
51. Hu S, Xie Z, Onishi A, Yu X, Jiang L, et al. (2009) Profiling the human protein- DNA interactome reveals ERK2 as a transcriptional repressor of interferon signaling. Cell 139: 610-622.
52. Merrifield RB (1963) Solid Phase Peptide Synthesis.1.Synthesis of a Tetrapeptide. J Am Chem Soc 85: 2149-2154.
53. Merrifield RB (1995) Solid-phase peptide synthesis. In: Gutte B, ed. Peptides: Synthesis, structures, and applications: Academic Press, New York. pp 93-169.
54. Carpino LA, Han GY (1970) The 9-Fluorenylmethoxycarbonyl Function, a New Base-Sensitive Amino-Protecting Group. J Am Chem Soc 92: 5748-5749.