A fluorescence-based assay suitable for quantitative analysis of deadenylase enzyme activity

Nucleic Acids Research

Volumn 42, Issue 5, 2014, Pages

  Maryati, Maryati ^a   Kaur, Ishwinder ^a   Jadhav, Gopal P ^a   Olotu Umoren, Loyin ^a   Oveh, Blessing ^a   Hashmi, Lubna ^a   Fischer, Peter M ^a   Winkler, G Sebastiaan ^a  

^a UNIVERSITY OF NOTTINGHAM   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

EXONUCLEASE;

ADENYLATION; ARTICLE; DNA PROBE; ENZYME ACTIVITY; ENZYME ASSAY; ENZYME DEGRADATION; ENZYME KINETICS; ENZYME MECHANISM; ENZYME PURIFICATION; ENZYME STRUCTURE; ENZYME SUBSTRATE; FLUORESCENCE; FLUORESCENCE RESONANCE ENERGY TRANSFER; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS;

ENZYME ASSAYS; ENZYME INHIBITORS; EXORIBONUCLEASES; FLUORESCENCE; HELA CELLS; HUMANS; RIBONUCLEASES; SMALL MOLECULE LIBRARIES; TRANSCRIPTION FACTORS;

EID: 84892402977     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt972     Document Type: Article

References (44)

1. Garneau, N.L., Wilusz, J. and Wilusz, C.J. (2007) The highways and byways of mRNA decay. Nat. Rev. Mol. Cell Biol., 8, 113-126.
2. Goldstrohm, A.C. and Wickens, M. (2008) Multifunctional deadenylase complexes diversify mRNA control. Nat. Rev. Mol Cell Biol., 9, 337-344.
3. Parker, R. and Song, H. (2004) The enzymes and control of eukaryotic mRNA turnover. Nat. Struct. Mol. Biol., 11, 121-127.
4. Wahle, E. and Winkler, G.S. (2013) RNA decay machines: Deadenylation by the Ccr4-Not and Pan2-Pan3 complexes. Biochim. Biophys. Acta, 1829, 561-570.
5. Godwin, A.R., Kojima, S., Green, C.B. and Wilusz, J. (2013) Kiss your tail goodbye: The role of PARN, Nocturnin, and Angel deadenylases in mRNA biology. Biochim. Biophys. Acta, 1829, 571-579.
6. Lackner, D.H., Beilharz, T.H., Marguerat, S., Mata, J., Watt, S., Schubert, F., Preiss, T. and Bahler, J. (2007) A network of multiple regulatory layers shapes gene expression in fission yeast. Mol. Cell, 26, 145-155.
7. Munroe, D. and Jacobson, A. (1990) mRNA poly(A) tail, a 30 enhancer of translational initiation. Mol. Cell Biol., 10, 3441-3455.
8. Baggs, J.E. and Green, C.B. (2003) Nocturnin, a deadenylase in Xenopus laevis retina: A mechanism for posttranscriptional control of circadian-related mRNA. Curr. Biol., 13, 189-198.
9. Rorbach, J., Nicholls, T.J. and Minczuk, M. (2011) PDE12 removes mitochondrial RNA poly(A) tails and controls translation in human mitochondria. Nucleic Acids Res., 39, 7750-7763.
10. Virtanen, A., Henriksson, N., Nilsson, P. and Nissbeck, M. (2013) Poly(A)-specific ribonuclease (PARN): An allosterically regulated, processive and mRNA cap-interacting deadenylase. Crit. Rev. Biochem. Mol. Biol., 48, 192-209.
11. Dehlin, E., Wormington, M., Korner, C.G. and Wahle, E. (2000) Cap-dependent deadenylation of mRNA. EMBO J., 19, 1079-1086. (Pubitemid 30119832
12. Gao, M., Wilusz, C.J., Peltz, S.W. and Wilusz, J. (2001) A novel mRNA-decapping activity in HeLa cytoplasmic extracts is regulated by AU-rich elements. EMBO J., 20, 1134-1143. (Pubitemid 32186803
13. Martinez, J., Ren, Y.G., Nilsson, P., Ehrenberg, M. and Virtanen, A. (2001) The mRNA cap structure stimulates rate of poly(A) removal and amplifies processivity of degradation. J. Biol. Chem., 276, 27923-27929.
14. Brown, C.E., Tarun, Jr. S.Z. Boeck, R. and Sachs, A.B. (1996) PAN3 encodes a subunit of the Pab1p-dependent poly(A) nuclease in Saccharomyces cerevisiae. Mol. Cell Biol., 16, 5744-5753.
15. Uchida, N., Hoshino, S. and Katada, T. (2004) Identification of a human cytoplasmic poly(A) nuclease complex stimulated by poly(A)-binding protein. J. Biol. Chem., 279, 1383-1391.
16. Tucker, M., Valencia-Sanchez, M.A., Staples, R.R., Chen, J., Denis, C.L. and Parker, R. (2001) The transcription factor associated Ccr4 and Caf1 proteins are components of the major cytoplasmic mRNA deadenylase in Saccharomyces cerevisiae. Cell, 104, 377-386. (Pubitemid 32206458
17. Yamashita, A., Chang, T.C., Yamashita, Y., Zhu, W., Zhong, Z., Chen, C.Y. and Shyu, A.B. (2005) Concerted action of poly(A) nucleases and decapping enzyme in mammalian mRNA turnover. Nat. Struct. Mol. Biol., 12, 1054-1063.
18. Temme, C., Zaessinger, S., Meyer, S., Simonelig, M. and Wahle, E. (2004) A complex containing the CCR4 and CAF1 proteins is involved in mRNA deadenylation in Drosophila. EMBO J., 23, 2862-2871. (Pubitemid 39013558
19. Temme, C., Zhang, L., Kremmer, E., Ihling, C., Chartier, A., Sinz, A., Simonelig, M. and Wahle, E. (2010) Subunits of the Drosophila CCR4-NOT complex and their roles in mRNA deadenylation. RNA, 16, 1356-1370.
20. Bartlam, M. and Yamamoto, T. (2010) The structural basis for deadenylation by the CCR4-NOT complex. Protein Cell, 1, 443-452.
21. Collart, M.A. and Panasenko, O.O. (2012) The Ccr4-not complex. Gene, 492, 42-53.
22. Horiuchi, M., Takeuchi, K., Noda, N., Muroya, N., Suzuki, T., Nakamura, T., Kawamura-Tsuzuku, J., Takahasi, K., Yamamoto, T. and Inagaki, F. (2009) Structural basis for the antiproliferative activity of the Tob-hCaf1 complex. J. Biol. Chem., 284, 13244-13255.
23. Wang, H., Morita, M., Yang, X., Suzuki, T., Yang, W., Wang, J., Ito, K., Wang, Q., Zhao, C., Bartlam, M. et al. (2010) Crystal structure of the human CNOT6L nuclease domain reveals strict poly(A) substrate specificity. EMBO J., 29, 2566-2576.
24. Basquin, J., Roudko, V.V., Rode, M., Basquin, C., Seraphin, B. and Conti, E. (2012) Architecture of the nuclease module of the yeast Ccr4-not complex: The Not1-Caf1-Ccr4 interaction. Mol. Cell, 48, 207-218.
25. Petit, A.P., Wohlbold, L., Bawankar, P., Huntzinger, E., Schmidt, S., Izaurralde, E. and Weichenrieder, O. (2012) The structural basis for the interaction between the CAF1 nuclease and the NOT1 scaffold of the human CCR4-NOT deadenylase complex. Nucleic Acids Res., 40, 11058-11072.
26. Albert, T.K., Lemaire, M., van Berkum, N.L., Gentz, R., Collart, M.A. and Timmers, H.T. (2000) Isolation and characterization of human orthologs of yeast CCR4-NOT complex subunits. Nucleic Acids Res., 28, 809-817. (Pubitemid 30068266
27. Draper, M.P., Salvadore, C. and Denis, C.L. (1995) Identification of a mouse protein whose homolog in Saccharomyces cerevisiae is a component of the CCR4 transcriptional regulatory complex. Mol. Cell Biol., 15, 3487-3495.
28. Dupressoir, A., Morel, A.P., Barbot, W., Loireau, M.P., Corbo, L. and Heidmann, T. (2001) Identification of four families of yCCR4-And Mg2+-dependent endonuclease-related proteins in higher eukaryotes, and characterization of orthologs of yCCR4 with a conserved leucine-rich repeat essential for hCAF1/hPOP2 binding. BMC Genomics, 2, 9.
29. Aslam, A., Mittal, S., Koch, F., Andrau, J.C. and Winkler, G.S. (2009) The Ccr4-Not Deadenylase Subunits CNOT7 and CNOT8 Have Overlapping Roles and Modulate Cell Proliferation. Mol. Biol. Cell, 20, 3840-3850.
30. Mittal, S., Aslam, A., Doidge, R., Medica, R. and Winkler, G.S. (2011) The Ccr4a (CNOT6) and Ccr4b (CNOT6L) deadenylase subunits of the human Ccr4-Not complex contribute to the prevention of cell death and senescence. Mol. Biol. Cell, 22, 748-758.
31. Morita, M., Suzuki, T., Nakamura, T., Yokoyama, K., Miyasaka, T. and Yamamoto, T. (2007) Depletion of mammalian CCR4b deadenylase triggers elevation of the p27Kip1 mRNA level and impairs cell growth. Mol. Cell Biol., 27, 4980-4990.
32. Cheng, Y., Liu, W.F., Yan, Y.B. and Zhou, H.M. (2006) A nonradioactive assay for poly(a)-specific ribonuclease activity by methylene blue colorimetry. Protein Pept. Lett., 13, 125-128.
33. Greiner-Stoeffele, T., Grunow, M. and Hahn, U. (1996) A general ribonuclease assay using methylene blue. Anal. Biochem., 240, 24-28.
34. He, G.J. and Yan, Y.B. (2012) A deadenylase assay by sizeexclusion chromatography. PLoS One, 7, e33700.
35. Nilsson, P. and Virtanen, A. (2006) Expression and purification of recombinant poly(A)-specific ribonuclease (PARN) Int. J. Biol. Macromol., 39, 95-99.
36. Sherman, W., Day, T., Jacobson, M.P., Friesner, R.A. and Farid, R. (2006) Novel procedure for modeling ligand/receptor induced fit effects. J. Med. Chem., 49, 534-553.
37. Verdonk, M.L., Cole, J.C., Hartshorn, M.J., Murray, C.W. and Taylor, R.D. (2003) Improved protein-ligand docking using GOLD. Proteins, 52, 609-623. (Pubitemid 37034158
38. Andersen, K.R., Jonstrup, A.T., Van, L.B. and Brodersen, D.E. (2009) The activity and selectivity of fission yeast Pop2p are affected by a high affinity for Zn2+and Mn2+in the active site. RNA, 15, 850-861.
39. Jonstrup, A.T., Andersen, K.R., Van, L.B. and Brodersen, D.E. (2007) The 1.4-A crystal structure of the S. pombe Pop2p deadenylase subunit unveils the configuration of an active enzyme. Nucleic Acids Res., 35, 3153-3164. (Pubitemid 47073652
40. Liu, W.F. and Yan, Y.B. (2008) Biophysical and biochemical characterization of recombinant human Pop2 deadenylase. Protein Expr. Purif., 60, 46-52.
41. Astrom, J., Astrom, A. and Virtanen, A. (1991) In vitro deadenylation of mammalian mRNA by a HeLa cell 30 exonuclease. EMBO J., 10, 3067-3071.
42. Korner, C.G. and Wahle, E. (1997) Poly(A) tail shortening by a mammalian poly(A)-specific 30-exoribonuclease. J. Biol. Chem., 272, 10448-10456.
43. Balatsos, N., Vlachakis, D., Chatzigeorgiou, V., Manta, S., Komiotis, D., Vlassi, M. and Stathopoulos, C. (2012) Kinetic and in silico analysis of the slow-binding inhibition of human poly(A)-specific ribonuclease (PARN) by novel nucleoside analogues. Biochimie, 94, 214-221.
44. Balatsos, N.A., Vlachakis, D., Maragozidis, P., Manta, S., Anastasakis, D., Kyritsis, A., Vlassi, M., Komiotis, D. and Stathopoulos, C. (2009) Competitive inhibition of human poly(A)-specific ribonuclease (PARN) by synthetic fluoro-pyranosyl nucleosides. Biochemistry, 48, 6044-6051.