Unraveling new roles for minor components of the E. coli RNA degradosome

RNA Biology

Volumn 6, Issue 4, 2009, Pages

  Kaberdin, Vladimir R ^a   Lin Chao, Sue ^a  

^a INSTITUTE OF MOLECULAR BIOLOGY   (Taiwan)

Author keywords

Bacterial stress responses; Post transcriptional control; RNA decay and processing; RNase E

Indexed keywords

EID: 85011939098     PISSN: 15476286     EISSN: 15558584     Source Type: Journal    
DOI: 10.4161/rna.6.4.9320     Document Type: Review

References (30)

1. Carpousis AJ, Van Houwe G, Ehretsmann C, Krisch HM. Copurification of E. coli RNase E and PNPase: evidence for a specific association between two enzymes important in RNA processing and degradation. Cell 1994; 76:889-900.
2. Miczak A, Kaberdin VR, Wei CL, Lin-Chao S. Proteins associated with RNase E in a multicomponent ribonucleolytic complex. Proc Natl Acad Sci USA 1996; 93:3865-3869 (Pubitemid 26144213)
3. Py B, Causton H, Mudd EA, Higgins CF. A protein complex mediating mRNA degradation in Escherichia coli. Mol Microbiol 1994; 14:717-729
4. Py B, Higgins CF, Krisch HM, Carpousis AJ. A DEAD-box RNA helicase in the Escherichia coli RNA degradosome. Nature 1996; 381:169-172
5. Carpousis AJ. The RNA degradosome of Escherichia coli: an mRNA-degrading machine assembled on RNase E. Annu Rev Microbiol 2007; 61:71-87.
6. Régnier P, Arraiano CM. Degradation of mRNA in bacteria: emergence of ubiquitous features. Bioessays 2000; 22:235-244 (Pubitemid 30144416)
7. Bernstein JA, Lin PH, Cohen SN, Lin-Chao S. Global analysis of Escherichia coli RNA degradosome function using DNA microarrays. Proc Natl Acad Sci USA 2004; 101:2758-2763
8. Khemici V, Carpousis AJ. The RNA degradosome and poly(A) polymerase of Escherichia coli are required in vivo for the degradation of small mRNA decay intermediates containing REP-stabilizers. Mol Microbiol 2004; 51:777-790
9. Khemici V, Poljak L, Toesca I, Carpousis AJ. 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 2005; 102:6913-6918 (Pubitemid 40675416)
10. Kaberdin VR, Miczak A, Jakobsen JS, Lin-Chao S, McDowall KJ, von Gabain A. The endoribonucleolytic N-terminal half of Escherichia coli RNase E is evolutionarily conserved in Synechocystis sp. and other bacteria but not the C-terminal half, which is sufficient for degradosome assembly. Proc Natl Acad Sci USA 1998; 95:11637-11642
11. Vanzo NF, Li YS, Py B, Blum E, Higgins CF, Raynal LC, et al. Ribonuclease E organizes the protein interactions in the Escherichia coli RNA degradosome. Genes Dev 1998; 12:2770-2781
12. Callaghan AJ, Marcaida MJ, Stead JA, McDowall KJ, Scott WG, Luisi BF. Structure of Escherichia coli RNase E catalytic domain and implications for RNA turnover. Nature 2005; 437:1187-1191
13. Callaghan AJ, Aurikko JP, Ilag LL, Gunter Grossmann J, Chandran V, Kuhnel K, et al. Studies of the RNA degradosome-organizing domain of the Escherichia coli ribonuclease RNase E. J Mol Biol 2004; 340:965-979
14. Tompa P. The interplay between structure and function in intrinsically unstructured proteins. FEBS Lett 2005; 579:3346-3354 (Pubitemid 40804685)
15. Prud'homme-Genereux A, Beran RK, Iost I, Ramey CS, Mackie GA, Simons RW. Physical and functional interactions among RNase E, polynucleotide phosphorylase and the cold-shock protein, CsdA: evidence for a 'cold shock degradosome'. Mol Microbiol 2004; 54:1409-1421
16. Khemici V, Toesca I, Poljak L, Vanzo NF, Carpousis AJ. 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 2004; 54:1422-1430
17. Gao J, Lee K, Zhao M, Qiu J, Zhan X, Saxena A, et al. Differential modulation of E. coli mRNA abundance by inhibitory proteins that alter the composition of the degradosome. Mol Microbiol 2006; 61:394-406.
18. Lee K, Zhan X, Gao J, Qiu J, Feng Y, Meganathan R, et al. RraA. a protein inhibitor of RNase E activity that globally modulates RNA abundance in E. coli. Cell 2003; 114:623-634 (Pubitemid 37159258)
19. Jager S, Hebermehl M, Schiltz E, Klug G. Composition and activity of the Rhodobacter capsulatus degradosome vary under different oxygen concentrations. J Mol Microbiol Biotechnol 2004; 7:148-154
20. Kaberdin VR, Bläsi U. Translation initiation and the fate of bacterial mRNAs. FEMS Microbiol Reviews 2006; 30:967-979 (Pubitemid 44583798)
21. Valentin-Hansen P, Eriksen M, Udesen C. The bacterial Sm-like protein Hfq: a key player in RNA transactions. Mol Microbiol 2004; 51:1525-1533 (Pubitemid 38406529)
22. Aiba H. Mechanism of RNA silencing by Hfq-binding small RNAs. Curr Opin Microbiol 2007; 10:134-139 (Pubitemid 46590050)
23. Worrall JA, Gorna M, Crump NT, Phillips LG, Tuck AC, Price AJ, et al. Reconstitution and analysis of the multienzyme Escherichia coli RNA degradosome. J Mol Biol 2008; 382:870-883
24. Singh D, Chang SJ, Lin PH, Averina OV, Kaberdin VR, Lin-Chao S. Regulation of ribonuclease E activity by the L4 ribosomal protein of Escherichia coli. Proc Natl Acad Sci USA 2009; 106:864-869
25. Kaplan R, Apirion D. Decay of ribosomal ribonucleic acid in Escherichia coli cells starved for various nutrients. J Biol Chem 1975; 250:3174-3178
26. Khemici V, Poljak L, Luisi BF, Carpousis AJ. The RNase E of Escherichia coli is a membrane-binding protein. Mol Microbiol 2008; 70:799-813.
27. Liou GG, Jane WN, Cohen SN, Lin NS, 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 2001; 98:63-68
28. Blum E, Py B, Carpousis AJ, Higgins CF. Polyphosphate kinase is a component of the Escherichia coli RNA degradosome. Mol Microbiol 1997; 26:387-398
29. Regonesi ME, Del Favero M, Basilico F, Briani F, Benazzi L, Tortora P, et al. Analysis of the Escherichia coli RNA degradosome composition by a proteomic approach. Biochimie 2006; 88:151-161
30. Morita T, Maki K, Aiba H. RNase E-based ribonucleoprotein complexes: mechanical basis of mRNA destabilization mediated by bacterial noncoding RNAs. Genes Dev 2005; 19:2176-2186 (Pubitemid 41330319)