Functional analysis of mRNA scavenger decapping enzymes

RNA

Volumn 10, Issue 9, 2004, Pages 1412-1422

  Liu, Shin Wu ^a   Jiao, Xinfu ^a   Liu, Hudan ^a   Gu, Meigang ^b   Lima, Christopher D ^b   Kiledjian, Megerditch ^a  

^a RUTGERS UNIVERSITY   (United States)

^b NEW YORK STRUCTURAL BIOLOGY CENTER   (United States)

Author keywords

Cytoplasmic foci; HIT motif; mRNA decapping; mRNA decay

Indexed keywords

EXORIBONUCLEASE; HISTIDINE DERIVATIVE; MESSENGER RNA; NUCLEAR PROTEIN; PROTEIN; PROTEIN DCP2; PROTEIN DCPS; SCAVENGER; UNCLASSIFIED DRUG;

ARTICLE; CATALYSIS; CATALYST; EUKARYOTIC CELL; HYDROLYSIS; IMMUNOFLUORESCENCE MICROSCOPY; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN DEGRADATION; PROTEIN FOLDING; PROTEIN MOTIF; PROTEIN STRUCTURE; RNA DEGRADATION;

BASE PAIRING; BASE SEQUENCE; CELL NUCLEUS; CYTOPLASM; ELECTROPHORETIC MOBILITY SHIFT ASSAY; ENDORIBONUCLEASES; EUKARYOTIC INITIATION FACTOR-4E; HUMANS; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; RECOMBINANT PROTEINS; RNA CAPS; RNA, MESSENGER;

EUKARYOTA;

EID: 4344641442     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1261/rna.7660804     Document Type: Article

References (36)

1. Bessman, M.J., Frick, D.N., and O'Handley, S.F. 1996. The MutT proteins or "Nudix" hydrolases, a family of versatile, widely distributed, "housecleaning" enzymes. J. Biol. Chem. 271: 25059-25062.
2. Brenner, C. 2002. Hint, Fhit, and GalT: function, structure, evolution, and mechanism of three branches of the histidine triad superfamily of nucleotide hydrolases and transferases. Biochemistry 41: 9003-9014.
3. Brenner, C., Garrison, P., Gilmour, J., Peisach, D., Ringe, D., Petsko, G.A., and Lowenstein, J.M. 1997. Crystal structures of HINT demonstrate that histidine triad proteins are GalT-related nucleotide-binding proteins. Nat. Struct. Biol. 4: 231-238.
4. Brenner, C., Bieganowski, P., Pace, H.C., and Huebner, K. 1999. The histidine triad superfamily of nucleotide-binding proteins. J. Cell. Physiol. 181: 179-187.
5. Dehlin, E., Wormington, M., Korner, C.G., and Wahle, E. 2000. Cap-dependent deadenylation of mRNA. EMBO J. 19: 1079-1086.
6. Dunckley, T. and Parker, R. 1999. The DCP2 protein is required for mRNA decapping in Saccharomyces cerevisiae and contains a functional MutT motif. EMBO J. 18: 5411-5422.
7. Gao, M., Fritz, D.T., Ford, L.P., and Wilusz, J. 2000. Interaction between a poly(A)-specific ribonuclease and the 5′ cap influences mRNA deadenylation rates in vitro. Mol. Cell 5: 479-488.
8. Ghosh, T., Peterson, B., Tomasevic, N., and Peculis, B.A. 2004. Xenopus U8 snoRNA binding protein is a conserved nuclear decapping enzyme. Mol. Cell 13: 817-828.
9. Gu, M., Fabrega, C., Liu, S.W., Liu, H., Kiledjian, M., and Lima, C.D. 2004. Insights into the structure, mechanism, and regulation of scavenger mRNA decapping activity. Mol. Cell 14: 67-80.
10. Ingelfinger, D., Arndt-Jovin, D.J., Luhrmann, R., and Achsel, T. 2002. The human Lsm1-7 proteins colocalize with the mRNA-degrading enzymes Dcp1/2 and Xrnl in distinct cytoplasmic foci. RNA 8: 1489-1501.
11. Jiao, X., Trifillis, P., and Kiledjian, M. 2002. Identification of target messenger RNA substrates for the murine deleted in Azoospermia-like RNA-binding protein. Biol. Reprod. 66: 475-485.
12. Khanna, R. and Kiledjian, M. 2004. Poly(A)-binding-protein-mediated regulation of hDcp2 decapping in vitro. EMBO J. 23: 1968-1976.
13. Koonin, E.V. 1993. A highly conserved sequence motif defining the family of MutT-related proteins from eubacteria, eukaryotes and viruses. Nucleic Acids Res. 21: 4847.
14. Kwasnicka, D.A., Krakowiak, A., Thacker, C., Brenner, C., and Vincent, S.R. 2003. Coordinate expression of NADPH-dependent flavin reductase, Fre-1, and Hint-related 7meGMP-directed hydrolase, DCS-1. J. Biol. Chem. 278: 39051-39058.
15. Lima, C.D., Klein, M.G., and Hendrickson, W.A. 1997. Structure-based analysis of catalysis and substrate definition in the HIT protein family. Science 278: 286-290.
16. Liu, H., Rodgers, N.D., Jiao, X., and Kiledjian, M. 2002. The scavenger mRNA decapping enzyme DcpS is a member of the HIT family of pyrophosphatases. EMBO J. 21: 4699-4708.
17. Lykke-Andersen, J. 2002. Identification of a human decapping complex associated with hUpf proteins in nonsense-mediated decay. Mol Cell Biol 22: 8114-8121.
18. Martinez, J., Ren, Y.G., Thuresson, A.C., Hellman, U., Astiom, J., and Virtanen, A. 2000. A 54-kDa fragment of the Poly(A)-specific ribonuclease is an oligomeric, processive, and cap-interacting Poly(A)-specific 3′ exonuclease. J. Biol. Chem. 275: 24222-24230.
19. Mejean, V., Salles, C., Bullions, L.C., Bessman, M.J., and Claverys, J.P. 1994. Characterization of the mutX gene of Streptococcus pneumoniae as a homologue of Escherichia coli mutT, and tentative definition of a catalytic domain of the dGTP pyrophosphohydrolases. Mol. Microbiol. 11: 323-330.
20. Mossessova, E. and Lima, C.D. 2000. Ulp1-SUMO crystal structure and genetic analysis reveal conserved interactions and a regulatory element essential for cell growth in yeast. Mol. Cell 5: 865-876.
21. Niedzwiecka, A., Marcotrigiano, J., Stepinski, J., Jankowska-Anyszka, M., Wyslouch-Cieszynska, A., Dadlez, M., Gingras, A.C., Mak, P., Darzynkiewicz, E., Sonenberg, N., et al. 2002. Biophysical studies of eIF4E cap-binding protein: recognition of mRNA 5′ cap structure and synthetic fragments of eIF4G and 4E-BP1 proteins. J. Mol. Biol. 319: 615-635.
22. Nuss, D.L. and Furuichi, Y. 1977. Characterization of the m7G(5′)pppN-pyrophosphatase activity from HeLa cells. J. Biol. Chem. 252: 2815-2821.
23. Nuss, D.L., Furuichi, Y., Koch, G., and Shatkin, A.J. 1975. Detection in HeLa cell extracts of a 7-methyl guanosine specific enzyme activity that cleaves m7GpppNm. Cell 6: 21-27.
24. Pace, H.C., Garrison, P.N., Robinson, A.K., Barnes, L.D., Draganescu, A., Rosler, A., Blackburn, G.M., Siprashvili, Z., Croce, C.M., Huebner, K., et al. 1998. Genetic, biochemical, and crystallographic characterization of Fhit- substrate complexes as the active signaling form of Fhit. Proc. Natl. Acad. Sci. 95: 5484-5489.
25. Parker, R. and Song, H. 2004. The enzymes and control of eukaryotic mRNA turnover. Nat. Struct. Mol. Biol. 11: 121-127.
26. Piccirillo, C., Khanna, R., and Kiledjian, M. 2003. Functional characterization of the mammalian mRNA decapping enzyme hDcp2. RNA 9: 1138-1147.
27. Rodgers, N.D., Wang, Z., and Kiledjian, M. 2002. Regulated α-globin mRNA decay is a cytoplasmic event proceeding through 3′-to-5′ exosome-dependent decapping. RNA 8: 1526-1537.
28. Salehi, Z., Geffers, L., Vilela, C., Birkenhager, R., Ptushkina, M., Berthelot, K., Ferro, M., Gaskell, S., Hagan, I., Stapley, B., and McCarthy, J.E. 2002. A nuclear protein in Schizosaccharomyces pombe with homology to the human tumour suppressor Fhit has decapping activity. Mol. Microbiol. 46: 49-62.
29. Seraphin, B. 1992. The HIT protein family: a new family of proteins present in prokaryotes, yeast and mammals. DNA Seq. 3: 177-179.
30. Steiger, M., Carr-Schmid, A., Schwartz, D.C., Kiledjian, M., and Parker, R. 2003. Analysis of recombinant yeast decapping enzyme. RNA 9: 231-238.
31. van Dijk, E., Cougot, N., Meyer, S., Babajko, S., Wahle, E., and Seraphin, B. 2002. Human Dcp2: A catalytically active mRNA decapping enzyme located in specific cytoplasmic structures. EMBO J. 21: 6915-6924.
32. Wang, Z. and Kiledjian, M. 2001. Functional link between the mammalian exosome and mRNA decapping. Cell 107: 751-762.
33. Wang, Z., Day, N., Trifillis, P., and Kiledjian, M. 1999. An mRNA stability complex functions with poly (A)-binding protein to stabilize mRNA in vitro. Mol. Cell. Biol. 19: 4552-4560.
34. Wang, Z., Jiao, X., Carr-Schmid, A., and Kiledjian, M. 2002. The hDcp2 protein is a mammalian mRNA decapping enzyme. Proc. Natl. Acad. Sci. 99: 12663-12668.
35. Wilson, G.M. and Brewer, G. 1999. Identification and characterization of proteins binding A + U-rich elements. Methods 17: 74-83.
36. Zuberek, J., Jemielity, J., Niedzwiecka, A., Stepinski, J., Wyslouch-Cieszynska, A., Stolarski, R., and Darzynkiewicz, E. 2003. Influence of the length of the phosphate chain in mRNA 5′ cap analogues on their interaction with eukaryotic initiation factor 4E. Nucleosides Nucleotides Nucleic Acids 22: 1707-1710.