The archaeal exosome

Advances in Experimental Medicine and Biology

Volumn 702, Issue , 2010, Pages 29-38

  Evguenieva Hackenberg, Elena ^a  

^a JUSTUS LIEBIG UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL ENZYME; BACTERIAL PROTEIN; DINUCLEOSIDE PHOSPHATE; POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE; RIBONUCLEOTIDE; ARCHAEAL PROTEIN; ARCHAEAL RNA; RNA;

ARCHAEBACTERIUM; ARTICLE; CATALYSIS; CELL ACTIVITY; CELL FUNCTION; CELL STRUCTURE; COMPLEX FORMATION; CRYSTAL STRUCTURE; CRYSTALLOGRAPHY; ENZYME ACTIVE SITE; ENZYME ACTIVITY; EUKARYOTE; EXOSOME; GENE SEQUENCE; IN VIVO STUDY; METHANOTHERMOBACTER THERMAUTOTROPHICUS; NONHUMAN; ORTHOLOGY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DEPLETION; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN INTERACTION; PROTEIN PHOSPHORYLATION; PROTEIN PROCESSING; PROTEIN PURIFICATION; PROTEIN STRUCTURE; PROTEIN SYNTHESIS; RNA BINDING; RNA DEGRADATION; RNA PROCESSING; RNA SYNTHESIS; SEQUENCE ANALYSIS; SULFOLOBUS SOLFATARICUS; CHEMISTRY; METABOLISM; RNA STABILITY;

ARCHAEA; ARCHAEAL PROTEINS; EXORIBONUCLEASES; EXOSOMES; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEIN SUBUNITS; RNA, ARCHAEAL; RNA; RNA STABILITY; SULFOLOBUS SOLFATARICUS;

ARCHAEA; BACTERIA (MICROORGANISMS); EUKARYOTA;

EID: 79960679359     PISSN: 00652598     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4419-7841-7_3     Document Type: Article

References (43)

1. Woese CR, Fox GE. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci USA 1977; 74:5088-5090. (Pubitemid 8241042)
2. Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms:proposal for the domains Archaea, Bacteria and Eucarya. Proc Natl Acad Sci USA 1990; 87:4576-4579.
3. Kletzin A. General characteristics and important model organisms. In: Cavicchioli R., ed. Archaea-Molecular and Cellular Biology, Washington, DC: ASM Press 2007:14-92.
4. Barry ER, Bell SD. DNA replication in the archaea. Microbiol Mol Biol Rev 2006; 70:876-887. (Pubitemid 44958259)
5. Werner F, Weinzierl RO. A recombinant RNA polymerase II-like enzyme capable of promoter-specíc transcription. Mol Cell 2002; 10:635-646. (Pubitemid 35284179)
6. Anantharaman V, Koonin EV, Aravind L. Comparative genomics and evolution of proteins involved in RNA metabolism. Nucleic Acids Res 2002; 30:1427-1464. (Pubitemid 34679722)
7. Koonin EV, Wolf YI, Aravind L. Prediction of the archaeal exosome and its connections with the proteasome and the translation and transcription machineries by a comparative-genomic approach. Genome Res 2001; 11:240-252. (Pubitemid 32166533)
8. Evguenieva-Hackenberg E, Walter P, Hochleitner E, et al. An exosome-like complex in Sulfolobus solfataricus. EMBO Rep 2003; 4:889-893. (Pubitemid 37309279)
9. Lorentzen E, Walter P, Fribourg S, et al. The archaeal exosome core is a hexameric ring structure with three catalytic subunits. Nat Struct Mol Biol 2005; 12:575-581. (Pubitemid 40980806)
10. Büttner K, Wenig K, Hopfner KP. Structural framework for the mechanism of archaeal exosomes in RNA processing. Mol Cell 2005; 20:461-471. (Pubitemid 41572302)
11. Portnoy V, Evguenieva-Hackenberg E, Klein F, et al. RNA polyadenylation in Archaea: not observed in Haloferax while the exosome polynucleotidylates RNA in Sulfolobus. EMBO Rep 2005; 6:1188-1193. (Pubitemid 41741704)
12. Walter P, Klein F, Lorentzen E, et al. Characterization of native and reconstituted exosome complexes from the hyperthermophilic archaeon Sulfolobus solfataricus. Mol Microbiol 2006; 62:1076-1089. (Pubitemid 44655319)
13. Ramos CR, Oliveira CL, Torriani IL, et al. The Pyrococcus exosome complex: structural and functional characterization. J Biol Chem 2006; 281:6751-6759. (Pubitemid 43847611)
14. Evguenieva-Hackenberg E, Roppelt V, Finsterseifer P, et al. Rrp4 and Csl4 are needed for effcient degradation but not for polyadenylation of synthetic and natural RNA by the archaeal exosome. Biochemistry 2008; 47:13158-13168.
15. Mohanty BK, Kushner SR. Polynucleotide phosphorylase functions both as a 3′ right-arrow 5′ exonuclease and a poly(A) polymerase in Escherichia coli. Proc Natl Acad Sci USA 2000; 97:11966-11971.
16. Rott R, Zipor G, Portnoy V, et al. RNA polyadenylation and degradation in cyanobacteria are similar to the chloroplast but different from Escherichia coli. J Biol Chem 2003; 278:15771-15777. (Pubitemid 36799690)
17. Farhoud MH, Wessels HJ, Steenbakkers PJ, et al. Protein complexes in the archaeon Methanothermobacter thermautotrophicus analyzed by blue native/SDS-PAGE and mass spectrometry. Mol Cell Proteomics 2005; 4:1653-1663. (Pubitemid 41749259)
18. Lorentzen E, Dziembowski A, Lindner D, et al. RNA channelling by the archaeal exosome. EMBO Rep 2007; 8:470-476. (Pubitemid 46696517)
19. Liu Q, Greimann JC, Lima CD. Reconstitution, activities and structure of the eukaryotic RNA exosome. Cell 2006; 127:1223-1237. Erratum in: Cell 2007; 131:188-189. (Pubitemid 44894519)
20. Symmons MF, Jones GH, Luisi BF. A duplicated fold is the structural basis for polynucleotide phosphorylase catalytic activity, processivity and regulation. Structure 2000; 8:1215-1226. (Pubitemid 32667486)
21. Walter P. Aufklärung von Struktur und Funktion des archaealen Exosoms durch Charakterisierung nativer und rekonstituierter Proteinkomplexe aus Sulfolobus solfataricus. Dissertation, 2007: Universität Giessen, Germany.
22. Mitchell P, Petfalski E, Shevchenko A, et al. The exosome: a conserved eukaryotic RNA processing complex containing multiple 3′ → 5′ exoribonucleases. Cell 1997; 91:457-466. (Pubitemid 27508235)
23. Chekanova JA, Dutko JA, Mian IS, et al. Arabidopsis thaliana exosome subunit AtRrp4p is a hydrolytic 3′ → 5′ exonuclease containing S1 and KH RNA-binding domains. Nucleic Acids Res 2002; 30:695-700. (Pubitemid 34679634)
24. Oddone A, Lorentzen E, Basquin J, et al. Structural and biochemical characterization of the yeast exosome component Rrp40. EMBO Rep 2007; 8:63-69. (Pubitemid 46043802)
25. Navarro MV, Oliveira CC, Zanchin NI, et al. Insights into the mechanism of progressive RNA degradation by the archaeal exosome. J Biol Chem 2008; 283:14120-14131.
26. Lu C, Ding F, Ke A. Crystal structure of the S. solfataricus archaeal exosome reveals conformational exibility in the RNA-binding ring. PLoS One 2010; 5:e8739.
27. Lorentzen E, Conti E. Structural basis of 3′ end RNA recognition and exoribonucleolytic cleavage by an exosome RNase PH core. Mol Cell 2005; 20:473-481. (Pubitemid 41572303)
28. Nurmohamed S, Vaidialingam B, Callaghan AJ, et al. Crystal structure of Escherichia coli polynucleotide phosphorylase core bound to RNase E, RNA and manganese: implications for catalytic mechanism and RNA degradosome assembly. J Mol Biol 2009; 389:17-33.
29. Shi Z, Yang WZ, Lin-Chao S, et al. Crystal structure of Escherichia coli PNPase: central channel residues are involved in processive RNA degradation. RNA 2008; 14:2361-2371.
30. van Hoof A, Staples RR, Baker RE, et al. Function of the ski4p (Csl4p) and Ski7p proteins in 3′-to-5′ degradation of mRNA. Mol Cell Biol 2000; 20:8230-8243.
31. Raijmakers R, Noordman YE, van Venrooij WJ, et al. Protein-protein interactions of hCsl4p with other human exosome subunits. J Mol Biol 2002; 315:809-818. (Pubitemid 34729328)
32. Haile S, Estevez AM, Clayton C. A role for the exosome in the in vivo degradation of unstable mRNAs. RNA 2003; 9:1491-1501. (Pubitemid 37463475)
33. Bonneau F, Basquin J, Ebert J, et al. The yeast exosome functions as a macromolecular cage to channel RNA substrates for degradation. Cell 2009; 139(3):547-59.
34. Evguenieva-Hackenberg E, Klug G. RNA degradation in Archaea and Gram-negative bacteria different from Escherichia coli. Prog Mol Biol Transl Sci 2009; 85:275-317.
35. Portnoy V, Schuster G. RNA polyadenylation and degradation in different Archaea; roles of the exosome and RNase R. Nucleic Acids Res 2006; 34:5923-5931. (Pubitemid 44941171)
36. Hartung S, Hopfner KP. Lessons from structural and biochemical studies on the archaeal exosome. Biochem Soc Trans 2009; 37:83-87.
37. Dziembowski A, Lorentzen E, Conti E, et al. A single subunit, Dis3, is essentially responsible for yeast exosome core activity. Nat Struct Mol Biol 2007; 14:15-22. (Pubitemid 46067418)
38. Wang HW, Wang J, Ding F, et al. Architecture of the yeast Rrp44 exosome complex suggests routes of RNA recruitment for 3′ end processing. Proc Natl Acad Sci USA 2007; 104:16844-16849. (Pubitemid 350210953)
39. LaCava J, Houseley J, Saveanu C, et al. RNA degradation by the exosome is promoted by a nuclear polyadenylation complex. Cell 2005; 121:713-724. (Pubitemid 40797594)
40. Vanácová S, Wolf J, Martin G, et al. A new yeast poly(A) polymerase complex involved in RNA quality control. PLoS Biol 2005; 3:e189.
41. Liou GG, Jane WN, Cohen SN, et al. 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. (Pubitemid 32095864)
42. Taghbalout A, Rothield L. RNase E and RNA helicase B play central roles in the cytosceletal organization of the RNA degradosome. J Biol Chem 2008; 283:13850-13855.
43. Commichau FM, Rothe FM, Herzberg C, et al. Novel activities of glycolytic enzymes in Bacillus subtilis: interactions with essential proteins involved in mRNA processing. Mol Cell Proteomics 2009; 8:1350-1360.