Chapter 4 Co-immunopurification of Multiprotein Complexes Containing RNA-Degrading Enzymes

Methods in Enzymology

Volumn 447, Issue , 2008, Pages 65-82

  Carpousis, Agamemnon J ^a   Khemici, Vanessa ^a   Aït Bara, Soraya ^a   Poljak, Leonora ^a  

^a UMR   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIBODY; BUFFER; ENZYME; IMMUNOGLOBULIN G; MESSENGER RNA; MULTIPROTEIN COMPLEX; POLYCLONAL ANTIBODY; PROTEIN A; RABBIT ANTISERUM; RIBONUCLEASE E; SEPHAROSE; EXORIBONUCLEASE; PNPT1 PROTEIN, HUMAN; RIBONUCLEASE; RNA;

BACTERIUM; CROSS LINKING; ESCHERICHIA COLI; GENETIC ENGINEERING; LABORATORY TEST; NONHUMAN; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; PROTEIN PURIFICATION; PSEUDOALTEROMONAS; PSEUDOALTEROMONAS HALOPLANKTIS; REVIEW; RNA DEGRADATION; RNA PROCESSING; AFFINITY CHROMATOGRAPHY; ARTICLE; ENZYMOLOGY; ISOLATION AND PURIFICATION; METABOLISM; METHODOLOGY; POLYACRYLAMIDE GEL ELECTROPHORESIS;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; ORYCTOLAGUS CUNICULUS; PSEUDOALTEROMONAS HALOPLANKTIS;

ANTIBODIES; CHROMATOGRAPHY, AFFINITY; ELECTROPHORESIS, POLYACRYLAMIDE GEL; ENDORIBONUCLEASES; ESCHERICHIA COLI; EXORIBONUCLEASES; RNA;

EID: 58249084639     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0076-6879(08)02204-0     Document Type: Review

References (41)

1. Babitzke P., and Kushner S.R. The AMS (altered mRNA stability) protein and ribonuclease E are encoded by the same structural gene of Escherichia coli. Proc. Natl. Acad. Sci. USA 88 (1991) 1-5
2. Butland G., Peregrin-Alvarez J.M., Li J., Yang W., Yang X., Canadien V., Starostine A., Richards D., Beattie B., Krogan N., Davey M., Parkinson J., Greenblatt J., and Emili A. Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433 (2005) 531-537
3. Callaghan A.J., Aurikko J.P., Ilag L.L., Gunter Grossmann J., Chandran V., Kuhnel K., Poljak L., Carpousis A.J., Robinson C.V., Symmons M.F., and Luisi B.F. Studies of the RNA degradosome-organizing domain of the Escherichia coli ribonuclease RNase E. J. Mol. Biol. 340 (2004) 965-979
4. Callaghan A.J., Marcaida M.J., Stead J.A., McDowall K.J., Scott W.G., and Luisi B.F. Structure of Escherichia coli RNase E catalytic domain and implications for RNA turnover. Nature 437 (2005) 1187-1191
5. Callaghan A.J., Redko Y., Murphy L.M., Grossmann J.G., Yates D., Garman E., Ilag L.L., Robinson C.V., Symmons M.F., McDowall K.J., and Luisi B.F. "Zn-link": A metal-sharing interface that organizes the quaternary structure and catalytic site of the endoribonuclease, RNase E. Biochemistry 44 (2005) 4667-4675
6. Carpousis A.J. The Escherichia coli RNA degradosome: Structure, function and relationship to other ribonucleolytic multienzyme complexes. Biochem. Soc. Trans. 30 (2002) 150-155
7. Carpousis A.J. Degradation of targeted mRNAs in Escherichia coli: Regulation by a small antisense RNA. Genes Dev. 17 (2003) 2351-2355
8. Carpousis A.J. The RNA degradosome of Escherichia coli: An mRNA-degrading machine assembled on RNase E. Annu. Rev. Microbiol. 61 (2007) 71-87
9. Carpousis A.J., Leroy A., Vanzo N., and Khemici V. Escherichia coli RNA degradosome. Methods Enzymol. 342 (2001) 333-345
10. Carpousis A.J., Van Houwe G., Ehretsmann C., and Krisch H.M. Copurification of E. coli RNAase E and PNPase: Evidence for a specific association between two enzymes important in RNA processing and degradation. Cell 76 (1994) 889-900
11. Carpousis A.J., Vanzo N.F., and Raynal L.C. mRNA degradation: A tale of poly(A) and multiprotein machines. Trends Genet. 15 (1999) 24-28
12. Celesnik H., Deana A., and Belasco J.G. Initiation of RNA decay in Escherichia coli by 5′-pyrophosphate removal. Mol. Cell 27 (2007) 79-90
13. Chandran V., and Luisi B.F. Recognition of enolase in the Escherichia coli RNA degradosome. J. Mol. Biol. 358 (2006) 8-15
14. Chandran V., Poljak L., Vanzo N.F., Leroy A., Miguel R.N., Fernandez-Recio J., Parkinson J., Burns C., Carpousis A.J., and Luisi B.F. Recognition and cooperation between the ATP-dependent RNA helicase RhlB and ribonuclease RNase E. J. Mol. Biol. 367 (2007) 113-132
15. Coburn G.A., and Mackie G.A. Degradation of mRNA in Escherichia coli: An old problem with some new twists. Prog. Nucleic Acid Res. Mol. Biol. 62 (1999) 55-108
16. Condon C., and Putzer H. The phylogenetic distribution of bacterial ribonucleases. Nucleic Acids Res. 30 (2002) 5339-5346
17. Ehretsmann C.P., Carpousis A.J., and Krisch H.M. Specificity of Escherichia coli endoribonuclease RNase E: In vivo and in vitro analysis of mutants in a bacteriophage T4 mRNA processing site. Genes Dev. 6 (1992) 149-159
18. Gao J., Lee K., Zhao M., Qiu J., Zhan X., Saxena A., Moore C.J., Cohen S.N., and Georgiou G. Differential modulation of E. coli mRNA abundance by inhibitory proteins that alter the composition of the degradosome. Mol. Microbiol. 61 (2006) 394-406
19. Grunberg-Manago M. Messenger RNA stability and its role in control of gene expression in bacteria and phages. Annu. Rev. Genet. 33 (1999) 193-227
20. Iost I., and Dreyfus M. DEAD-box RNA helicases in Escherichia coli. Nucleic Acids Res. 34 (2006) 4189-4197
21. Jager S., Fuhrmann O., Heck C., Hebermehl M., Schiltz E., Rauhut R., and Klug G. An mRNA degrading complex in Rhodobacter capsulatus. Nucleic Acids Res. 29 (2001) 4581-4588
22. Khemici V., Poljak L., Toesca I., and Carpousis A.J. Evidence in vivo that the DEAD-box RNA helicase RhlB facilitates the degradation of ribosome-free mRNA by RNase E. Proc. Natl. Acad. Sci. USA 102 (2005) 6913-6918
23. Khemici V., Toesca I., Poljak L., Vanzo N.F., and Carpousis A.J. The RNase E of Escherichia coli has at least two binding sites for DEAD-box RNA helicases: Functional replacement of RhlB by RhlE. Mol. Microbiol. 54 (2004) 1422-1430
24. Kushner S.R. mRNA decay in Escherichia coli comes of age. J. Bacteriol. 184 (2002) 4658-4665
25. Lee K., and Cohen S.N. A Streptomyces coelicolor functional orthologue of Escherichia coli RNase E shows shuffling of catalytic and PNPase-binding domains. Mol. Microbiol. 48 (2003) 349-360
26. Lee K., Zhan X., Gao J., Qiu J., Feng Y., Meganathan R., Cohen S.N., and Georgiou G. RraA. a protein inhibitor of RNase E activity that globally modulates RNA abundance in E. coli. Cell 114 (2003) 623-634
27. Liou G.G., Jane W.N., Cohen S.N., Lin N.S., and Lin-Chao S. RNA degradosomes exist in vivo in Escherichia coli as multicomponent complexes associated with the cytoplasmic membrane via the N-terminal region of ribonuclease E. Proc. Natl. Acad. Sci. USA 98 (2001) 63-68
28. Marcaida M.J., DePristo M.A., Chandran V., Carpousis A.J., and Luisi B.F. The RNA degradosome: Life in the fast lane of adaptive molecular evolution. Trends Biochem. Sci. 31 (2006) 359-365
29. Masse E., Escorcia F.E., and Gottesman S. Coupled degradation of a small regulatory RNA and its mRNA targets in Escherichia coli. Genes Dev. 17 (2003) 2374-2383
30. Medigue C., Krin E., Pascal G., Barbe V., Bernsel A., Bertin P.N., Cheung F., Cruveiller S., D'Amico S., Duilio A., Fang G., Feller G., et al. Coping with cold: The genome of the versatile marine Antarctica bacterium Pseudoalteromonas haloplanktis TAC125. Genome. Res. 15 (2005) 1325-1335
31. Miczak A., Kaberdin V.R., Wei C.L., and Lin-Chao S. Proteins associated with RNase E in a multicomponent ribonucleolytic complex. Proc. Natl. Acad. Sci. USA 93 (1996) 3865-3869
32. Morita T., Maki K., and Aiba H. RNase E-based ribonucleoprotein complexes: Mechanical basis of mRNA destabilization mediated by bacterial noncoding RNAs. Genes Dev. 19 (2005) 2176-2186
33. Mudd E.A., Krisch H.M., and Higgins C.F. RNase E, an endoribonuclease, has a general role in the chemical decay of Escherichia coli mRNA: Evidence that rne and ams are the same genetic locus. Mol. Microbiol. 4 (1990) 2127-2135
34. Ow M.C., and Kushner S.R. Initiation of tRNA maturation by RNase E is essential for cell viability in E. coli. Genes Dev. 16 (2002) 1102-1115
35. Prud'homme-Genereux A., Beran R.K., Iost I., Ramey C.S., Mackie G.A., and Simons R.W. Physical and functional interactions among RNase E, polynucleotide phosphorylase and the cold-shock protein, CsdA: Evidence for a "cold shock degradosome.". Mol. Microbiol. 54 (2004) 1409-1421
36. Purusharth R.I., Klein F., Sulthana S., Jager S., Jagannadham M.V., Evguenieva-Hackenberg E., Ray M.K., and Klug G. Exoribonuclease R interacts with endoribonuclease E and an RNA helicase in the psychrotrophic bacterium Pseudomonas syringaeLz4W. J. Biol. Chem. 280 (2005) 14572-14578
37. Py B., Causton H., Mudd E.A., and Higgins C.F. A protein complex mediating mRNA degradation in Escherichia coli. Mol. Microbiol. 14 (1994) 717-729
38. Py B., Higgins C.F., Krisch H.M., and Carpousis A.J. A DEAD-box RNA helicase in the Escherichia coli RNA degradosome. Nature 381 (1996) 169-172
39. Taghbalout A., and Rothfield L. RNaseE and the other constituents of the RNA degradosome are components of the bacterial cytoskeleton. Proc. Natl. Acad. Sci. USA 104 (2007) 1667-1672
40. Taraseviciene L., Miczak A., and Apirion D. The gene specifying RNase E (rne) and a gene affecting mRNA stability (ams) are the same gene. Mol. Microbiol. 5 (1991) 851-855
41. Vanzo N.F., Li Y.S., Py B., Blum E., Higgins C.F., Raynal L.C., Krisch H.M., and Carpousis A.J. Ribonuclease E organizes the protein interactions in the Escherichia coli RNA degradosome. Genes Dev. 12 (1998) 2770-2781