1887

Chapter 7 : RNA Processing

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Ebook: Choose a downloadable PDF or ePub file. Chapter is a downloadable PDF file. File must be downloaded within 48 hours of purchase

Buy this Chapter
Digital (?) $15.00

Preview this chapter:
Zoom in
Zoomout

RNA Processing, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555815516/9781555813918_Chap07-1.gif /docserver/preview/fulltext/10.1128/9781555815516/9781555813918_Chap07-2.gif

Abstract:

Most organisms contain between 40 and 50 different transfer RNA (tRNA) molecules that read one or more of the 61 or 62 different sense codons through specific codon-anticodon interactions and position the appropriate amino acid for insertion into the growing polypeptide chain. Additional complexity in the tRNA processing and modification pathway occurs in cases where archaeal tRNA genes contain an intron. The chapter describes introns in archaeal transcripts. The genes for ribosomal RNA (rrn) are located in operons in the archaeal genome and are transcribed to produce multicistronic precursor RNAs. Two early studies used nuclease protection and primer extension assays to define the intermediates generated during processing of the primary rRNA transcript from two canonical rrn operons: the single-rrn operon in and the canonical rrnA operon in . The proportion of modified nucleotides in tRNA can approach 50% or more. The two most frequent modifications in RNA are ribose methylation and the pseudouridylation. In an attempt to distinguish between these two alternatives, actinomycin D was used to inhibit transcription and Northern hybridization was used to follow the decay of the various mRNA fragments. There was a strong correlation between fragment length and stability: the shorter the fragment, the longer the half-life. This correlation was used to argue that the transcript fragments are generated by endonucleotic cleavage rather than premature transcription termination, and that the distal sequences released following cleavage are selectively degraded.

Citation: Klug G, Evguenieva-Hackenberg E, Omer A, Dennis P, Marchfelder A. 2007. RNA Processing, p 158-174. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch7

Key Concept Ranking

Gene Expression and Regulation
0.92052096
Bacteria and Archaea
0.8866921
Bacterial Proteins
0.60935307
Group II Introns
0.43922094
RNA
0.4228792
0.92052096
Highlighted Text: Show | Hide
Loading full text...

Full text loading...

Figures

Image of Figure 1
Figure 1

Maturation of precursor tRNA in Precursor tRNAs are transcribed with 5ʹ-leader and 3ʹ-trailer sequences that have to be removed to yield a functional tRNA. Processing at the 5ʹ end is performed by the ubiquitous enzyme RNase P. The tRNA 3ʹ-end maturation is catalyzed by the endonuclease tRNase Z; after this the 3ʹ-terminal CCA sequence is added by the tRNA nucleotidyltransferase. Some archaeal tRNA precursors contain introns that are removed by the splicing endonuclease, which recognizes the bulge-helix-bulge (BHB) structural motif that forms between the exon/intron and intron/exon boundaries. The two halves of the tRNA that are generated by intron excision are joined by a tRNA ligase activity that has not yet been identified or characterized. In addition to nucleolytic processing, numerous nucleosides in the tRNA are subjected to modification. After all these processing and modification steps, the tRNA is ready for aminoacylation. The order of processing events is not known, and the scheme depicted is not necessarily what occurs in vivo.

Citation: Klug G, Evguenieva-Hackenberg E, Omer A, Dennis P, Marchfelder A. 2007. RNA Processing, p 158-174. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch7
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 2
Figure 2

Structure of the rRNA operons and processing of the ribosomal RNA precursor. (a) The structure of a typical rRNA operon from is shown. 16S, 23S, 5S rRNA, tRNAAla, and tRNACys genes are represented by solid black boxes; inverted repeats flanking the 16S and 23S genes are indicated by hatched boxes. Sequences are not drawn to scale. (b) The rRNA operon is transcribed as a multicistronic precursor molecule and is cleaved at numerous sites by a variety of endonucleases (indicated by black arrows and scissors). The splicing endonuclease (SE) cleaves at the BHB motifs to excise the precursor 16S and precursor 23S rRNA sequences, and RNase P and tRNase Z remove tRNA from the internal transcribed spacer region ( ). The activities responsible for maturation at the 5ʹ and 3ʹ ends of the 16S and 23S rRNAs have not been identified or characterized. There is some evidence to suggest that the 5S sequence is excised from the primary transcript as a precursor (indicated by black arrows upstream and downstream from the 5S rRNA) and trimmed by a few nucleotides at both the 5ʹ and 3ʹ ends to generate the mature 5S sequence ( ). The cleavage site in tRNase Z remove tRNA from the internal transcribed arrow and 3ʹ) was mapped as a 3ʹ-end site and there was no corresponding 5ʹ-end site at the same position ( ). Thus this particular 3ʹ end is either generated by exonucleolytic trimming from the 3ʹ end of the tRNA, or it is generated by an endonucleolytic cleavage in the anticodon loop and the other product containing the tRNA 3ʹ half is degraded. The processing sites for the tRNA have not been mapped experimentally, but tRNACys 5ʹ and 3ʹ processing is very likely to be performed by RNase P and tRNase Z, respectively. The 5ʹ-ETS is located upstream of the 16S rRNA, ITS1 is located between the 16S and the 23S rRNA, ITS2 is located between the 23S and the 5S rRNA, and the 3ʹ-ETS is downstream of the 5S rRNA.

Citation: Klug G, Evguenieva-Hackenberg E, Omer A, Dennis P, Marchfelder A. 2007. RNA Processing, p 158-174. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch7
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 3
Figure 3

Principles of mRNA decay in and and model for mRNA decay by exosomes in . The addition of poly(A) destabilizes transcripts in , and in the nucleus of . Exonucleolytic activity of the exosome has been demonstrated, but the involvement of endonucleases in mRNA turnover is still uncertain. Differential stabilities of mRNA segments can control protein levels in and . Differently shaded bars indicate different ORFs in and , and introns and exons in . Short black bars indicate endonucleolytic cleavage sites in bacterial mRNA. En-doribonucleases are symbolized by scissors, exoribonucleases by “pacmen,” the exosome by multiple “pacmen.” The black hair-pin structures represent stabilizing mRNA secondary structures.

Citation: Klug G, Evguenieva-Hackenberg E, Omer A, Dennis P, Marchfelder A. 2007. RNA Processing, p 158-174. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch7
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 4
Figure 4

RNA-degrading protein complexes in members of the three domains of life. The degradosome of gram-negative bacteria is organized around endoribonuclease E. Association of RNase E with an exoribonuclease and one or more helicases seems to be conserved. The exoribonuclease PNPase consists of a trimer, each of which contains two RNase PH domains, one KH- and one S1 RNA-binding domain. A similar hexameric structure was found for the central ring of the exosome in and , which is composed of six subunits with RNase PH domain. The exosome subunits Rrp4 and Rrp40 show the typical KH- and S1 RNA-binding domains of hydrolytic exoribonucleases. Rrp44 and Csl4, and RNase R comprise the S1 DNA-binding domain. In the exosome core, Rrp41 is catalytically active while Rrp42 is not but contributes to the structuring of the Rrp41 active site.

Citation: Klug G, Evguenieva-Hackenberg E, Omer A, Dennis P, Marchfelder A. 2007. RNA Processing, p 158-174. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch7
Permissions and Reprints Request Permissions
Download as Powerpoint

References

/content/book/10.1128/9781555815516.ch07
1. Aittaleb, M.,, R. Rashid,, Q. Chen,, J. R. Palmer,, C. J. Daniels, and, H. Li. 2003. Structure and function of archaeal box C/D sRNP core proteins. Nat. Struct. Biol. 10:256263.
2. Allmang, C.,, J. Kufel,, G. Chanfreau,, P. Mitchell,, E. Petfalski, and, D. Tollervey. 1999. Functions of the exosome in rRNA, snoRNA and snRNA synthesis. EMBO J. 18:53995410.
3. Allmang, C.,, P. Mitchell,, E. Petfalski, and, D. Tollervey. 2000. Degradation of ribosomal RNA precursors by the exosome. Nucleic Acids Res. 28:16841691.
4. Aloy, P.,, F. D. Ciccarelli,, C. Leutwein,, A. C. Gavin,, G. Superti-Furga,, P. Bork,, B. Bottcher, and, R. B. Russell. 2002. A complex prediction: three-dimensional model of the yeast exosome. EMBO Rep. 3:628635.
5. Apostol, B. L.,, S. K. Westaway,, J. Abelson, and, C. L. Greer. 1991. Deletion analysis of a multifunctional yeast tRNA ligase polypeptide. Identification of essential and dispensable functional domains. J. Biol. Chem. 266:74457455.
6. Aravind, L. 1999. An evolutionary classification of the met-allo-beta-lactamase fold proteins. In Silico Biol. 1:6991.
7. Aravind, L., and, E. V. Koonin. 1999. DNA polymerase betalike nucleotidyltransferase superfamily: identification of three new families, classification and evolutionary history. Nucleic Acids Res. 27:16091618.
8. Baker, D. L.,, O. A. Youssef,, M. I. Chastkofsky,, D. A. Dy,, R. M. Terns, and, M. P. Terns. 2005. RNA-guided RNA modification: functional organization of the archaeal H/ACA RNP. Genes Dev. 19:12381248.
9. Balakin, A. G.,, L. Smith, and, M. J. Fournier. 1996. The RNA world of the nucleolus: two major families of small RNAs defined by different box elements with related functions. Cell 86:823834.
10. Ban, N.,, P. Nissen,, J. Hansen,, P. B. Moore, and, T. A. Steitz. 2000. The complete atomic structure of the large ribosomal subunit at 2.4 A resolution. Science 289:905920.
11. Beelman, C. A., and, R. Parker. 1995. Degradation of mRNA in eukaryotes. Cell 81:179183.
12. Bernstein, J. A.,, A. B. Khodursky,, P. H. Lin,, S. LinChao, and, S. N. Cohen. 2002. Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays. Proc. Natl. Acad. Sci. USA 99:96979702.
13. Bini, E.,, V. Dikshit,, K. Dirksen,, M. Drozda, and, P. Blum. 2002. Stability of mRNA in the hyperthermophilic archaeon Sulfolobus solfataricus. RNA 8:11291136.
14. Björk, G. R. 1995. Biosynthesis and function of modified nucleosides, p. 165–205. In D. Söll and, U. RajBhandary (ed.), tRNA: Structure, Biosynthesis, and Function. ASM Press, Washington, D.C.
15. Blum, E.,, A. J. Carpousis, and, C. F. Higgins. 1999. Poly-adenylation promotes degradation of 3ʹ-structured RNA by the Escherichia coli mRNA degradosome in vitro. J. Biol. Chem. 274:40094016.
16. Blum, E.,, B. Py,, A. J. Carpousis, and, C. F. Higgins. 1997. Polyphosphate kinase is a component of the Escherichia coli RNA degradosome. Mol. Microbiol. 26:387398.
17. Boomershine, W. P.,, C. A. Mclroy,, H. Y. Tsai,, R. C. Wilson,, V. Gopalan, and, M. P. Foster. (2003) Structure of Mth11/Mth Rpp29, an essential protein subunit of archaeal and eukaryotic RNase P. Proc. Natl. Acad. Sci. USA 100:1539815403.
18. Bortolin, M. L.,, J. P. Bachellerie, and, B. Clouet-dʹOrval. 2003. In vitro RNP assembly and methylation guide activity of an unusual box C/D RNA, cis-acting archaeal pre-tRNA(Trp). Nucleic Acids Res. 31:65246535.
19. Bousquet-Antonelli, C.,, Y. Henry,, J. P. GʹElugne,, M. Caizergues-Ferrer, and, T. Kiss. 1997. A small nucleolar RNP protein is required for pseudouridylation of eukaryotic ribosomal RNAs. EMBO J. 16:47704776.
20. Brown, J. W.,, C. J. Daniels, and, J. N. Reeve. 1989. Gene structure, organization, and expression in archaebacteria. Crit. Rev. Microbiol. 16:287338.
21. Brown, J. W., and, J. N. Reeve. 1985. Polyadenylated, non-capped RNA from the archaebacterium Methanococcus vannielii. J. Bacteriol. 162:909917.
22. Brown, J. W., and, J. N. Reeve. 1986. Polyadenylated RNA isolated from the archaebacterium Halobacterium halobium. J. Bacteriol. 166:686688.
23. Burggraf, S.,, N. Larsen,, C. R. Woese, and, K. O. Stetter. 1993. An intron within the 16S ribosomal RNA gene of the archaeon Pyrobaculum aerophilum. Proc. Natl. Acad. Sci. USA 90:25472550.
24. Calvin, K.,, M. D. Hall,, F. Xu,, X. Song, and, H. Li. 2005. Biochemical and structural characterization of the catalytic subunit of a novel RNA splicing endonuclease. J. Mol. Biol. 353:952960.
25. Carpousis, A. J. Carpousis. The Escherichia coli RNA degrado-some: structure, function and relationship in other ribonucleolytic multienzyme complexes. Biochem. Soc. Trans. 30:150155.
26. Cavaille, J.,, M. Nicoloso, and, J. P. Bachellerie. 1996. Targeted ribose methylation of RNA in vivo directed by tailored antisense RNA guides. Nature 383:732735.
27. Cech, T. R. Cech. Self-splicing of group I introns. Annu. Rev. Biochem. 59:543568.
28. Chamberlain, J. R.,, Y. Lee,, W. S. Lane, and, D. R. Engelke. 1998. Purification and characterization of the nuclear RNase P holoenzyme complex reveals extensive subunit overlap with RNase MRP. Genes Dev. 12:16781690.
29. Chant, J., and, P. Dennis. 1986. Archaebacteria: transcription and processing of ribosomal RNA sequences in Halobacterium cutirubrum. EMBO J. 5:10911097.
30. Charette, M., and, M. W. Gray. 2000. Pseudouridine in RNA: what, where, how, and why. IUBMB Life 49:341351.
31. Charpentier, B.,, S. Muller, and, C. Branlant. 2005. Reconstitution of archaeal H/ACA small ribonucleoprotein complexes active in pseudouridylation. Nucleic Acids Res. 33:31333144.
32. Charron, C.,, X. Manival,, A. Clery,, V. Senty-Segault,, B. Charpentier,, N. Marmier Gourrier,, C. Branlant, and, A. Aubry. 2004. The archaeal sRNA binding protein L7Ae has a 3D structure very similar to that of its eukaryal counterpart while having a broader RNA-binding specificity. J. Mol. Biol. 342:757773.
33. Cheng, Z. F., and, M. P. Deutscher. 2002. Purification and characterization of the Escherichia coli exoribonuclease RNase R. Comparison. with RNase II. J. Biol. Chem. 277:2162421629.
34. Cheng, Z. F., and, M. P. Deutscher. 2005. An important role for RNase R in mRNA decay. Mol. Cell 17:313318.
35. Cho, H. D., and, A. M. Weiner. 2004. A single catalytically active subunit in the multimeric Sulfolobus shibatae CCA-adding enzyme can carry out all three steps of CCA addition. J. Biol. Chem. 279:4013040136.
36. Clouet dʹOrval, B.,, M. L. Bortolin,, C. Gaspin, and, J. P. Bachellerie. 2001. Box C/D RNA guides for the ribose methylation of archaeal tRNAs. The tRNATrp intron guides the formation of two ribose-methylated nucleosides in the mature tRNATrp. Nucleic Acids Res. 29:45184529.
37. Cochella, L., and, R. Green. 2005. An active role for tRNA in decoding beyond codon:anticodon pairing. Science 308:11781180.
38. Condon, C., and, H. Putzer. 2002. The phylogenetic distribution of bacterial ribonucleases. Nucleic Acids Res. 30:53395346.
39. Cudny, H.,, J. R. Lupski,, G. N. Godson, and, M. P. Deutscher. 1986. Cloning, sequencing, and species relatedness of the Escherichia coli cca gene encoding the enzyme tRNA nucleo-tidyltransferase. J. Biol. Chem. 261:64446449.
40. Dai, L., and, S. Zimmerly. 2003. ORF-less and reverse-transcriptase-encoding group II introns in archaebacteria, with a pattern of homing into related group II intron ORFs. RNA 9:1419.
41. Dalgaard, J. Z., and, R. A. Garrett. 1992. Protein-coding introns from the 23S rRNA-encoding gene form stable circles in the hyperthermophilic archaeon Pyrobaculum organotro-phum. Gene 121:103110.
42. Daviter, T.,, F. V. T. Murphy, and, V. Ramakrishnan. 2005. Molecular biology. A renewed focus on transfer RNA. Science 308:11231124.
43. Decker, C. J. Decker. The exosome: a versatile RNA processing machine. Curr. Biol. 8:R238R240.
44. Dennis, P. P. Dennis. Multiple promoters for the transcription of the ribosomal RNA gene cluster in Halobacterium cutiru-brum. J. Mol. Biol. 186:457461.
45. Dennis, P. P., and, A. Omer. 2005. Small non-coding RNAs in Archaea. Curr. Opin. Microbiol. 8:685694.
46. Dennis, P. P.,, A. G. Russell, and, M. Moniz De Sa. 1997. Formation of the 5ʹ end pseudoknot in small subunit ribosomal RNA: involvement of U3-like sequences. RNA 3:337343.
47. Dennis, P.P.,, S. Ziesche, and, S. Mylvaganam. 1998. Transcription analysis of two disparate rRNA operons in the halophilic archaeon Haloarcula marismortui. J. Bacteriol. 180:48044813.
48. Deppenmeier, U.,, A. Johann,, T. Hartsch,, R. Merkl,, R. A. Schmitz,, R. Martinez-Arias,, A. Henne,, A. Wiezer,, S. Baumer,, C. Jacobi,, H. Bruggemann,, T. Lienard,, A. Christmann,, M. Bomeke,, S. Steckel,, A. Bhattacharyya,, A. Lykidis,, R. Overbeek,, H. P. Klenk,, R. P. Gunsalus,, H. J. Fritz, and, G. Gottschalk. 2002. The genome of Methanosarcina mazei: evidence for lateral gene transfer between bacteria and archaea. J. Mol. Microbiol. Biotechnol. 4:453461.
49. Deutscher, Deutscher. M. (1995) tRNA processing nucleases, p. 51-65. In D. Söll and, U. RajBhandary (ed.), tRNA: Structure, Biosynthesis, and Function. ASM Press, Washington, D.C.
50. Di Segni, G.,, L. Borghese,, S. Sebastiani, and, G. P. Tocchini-Valentini. 2005. A pre-tRNA carrying intron features typical of Archaea is spliced in yeast. RNA 11:7076.
51. Dragon, F.,, V. Pogacic, and, W. Filipowicz. 2000. In vitro assembly of human H/ACA small nucleolar RNPs reveals unique features of U17 and telomerase RNAs. Mol. Cell. Biol. 20, 30373048.
52. Englert, M., and, H. Beier. 2005. Plant tRNA ligases are multifunctional enzymes that have diverged in sequence and substrate specificity from RNA ligases of other phylogenetic origins. Nucleic Acids Res. 33:388399.
53. Evguenieva-Hackenberg, E.,, P. Walter,, E. Hochleitner,, F. Lottspeich, and, G. Klug. 2003. An exosome-like complex in Sulfolobus solfataricus. EMBO Rep. 4:889893.
54. Fabbri, S.,, P. Fruscoloni,, E. Bufardeci,, E. DiNicola Negri,, M. I. Baldi,, D. G. Attardi,, E. Mattoccia, and, G. P. Tocchini-Valentini. 1998. Conservation of substrate recognition mechanisms by tRNA splicing endonucleases. Science 280:284286.
55. Frank, D. N., and, N. R. Pace. 1998. Ribonuclease P: unity and diversity in a tRNA processing ribozyme. Annu. Rev. Biochem. 67:153180.
56. Franzetti, B.,, B. Sohlberg,, G. Zaccai, and, A. von Gabain. 1997. Biochemical and serological evidence for an RNase E-like activity in halophilic Archaea. J. Bacteriol. 179:11801185.
57. Fruscoloni, P.,, M. I. Baldi, and, G. P. Tocchini-Valentini. 2001. Cleavage of non-tRNA substrates by eukaryal tRNA splicing endonucleases. EMBO Rep. 2:217221.
58. Galagan, J. E.,, C. Nusbaum,, A. Roy,, M. G. Endrizzi,, P. Macdonald,, W FitzHugh,, S. Calvo,, R. Engels,, S. Smirnov,, D. Atnoor,, A. Brown,, N. Allen,, J. Naylor,, N. Stange-Thomann,, K. De-rellano,, R. Johnson,, L. Linton,, P. Mc-wan,, K. Mc-Kernan,, J. Talamas,, A. Tirrell,, W. Ye,, A. Zimmer,, R. D. Barber,, I. Cann,, D. E. Graham,, D. A. Grahame,, A. M. Guss,, R. Hedderich,, C. Ingram-Smith,, H. C. Kuettner,, J. A. Krzycki,, J. A. Leigh,, W. Li,, J. Liu,, B. Mukhopadhyay,, J. N. Reeve,, K. Smith,, T. A. Springer,, L. A. Umayam,, O. White,, R. H. White,, E. Conway de Macario,, J. G. Ferry,, K. F. Jarrell,, H. Jing,, A. J. Macario,, I. Paulsen,, M. Pritchett,, K. R. Sowers,, R. V. Swanson,, S. H. Zinder,, E. Lander,, W W Metcalf, and, B. Birren. 2002. The genome of M. acetivorans reveals extensive metabolic and physiological diversity. Genome Res. 12:532542.
59. Ganot, P.,, M. L. Bortolin, and, T. Kiss. 1997. Site-specific pseudouridine formation in preribosomal RNA is guided by small nucleolar RNAs. Cell 89:799809.
60. Garrett, R. A.,, J. Dalgaard,, N. Larsen,, J. Kjems, and, A. S. Mankin. 1991. Archaeal rRNA operons. Trends Biochem. Sci. 16:2226.
61. Grunberg-Manago, M. 1999. Messenger RNA stability and its role in control of gene expression in bacteria and phages. Annu. Rev. Genet. 33:193227.
62. Guerrier-Takada, C.,, K. Gardiner,, T. Marsh,, N. Pace, and, S. Altman. 1983. The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell 35:849857.
63. Hall, T.A., and, J. W. Brown. 2002. Archaeal RNase P has multiple protein subunits homologous to eukaryotic nuclear RNase P proteins. RNA 8:296306.
64. Hall, T. A., and, J. W. Brown. 2004. Interactions between RNase P protein subunits in archaea. Archaea 1:247254.
65. Hambraeus, G.,, C. von Wachenfeldt, and, L. Hederstedt. 2003. Genome-wide survey of mRNA half-lives in Bacillus subtilis identifies extremely stable mRNAs. Mol. Genet. Genomics 269:706714.
66. Haugel-Nielsen, J.,, E. Hajnsdorf, and, P. Regnier. 1996. The rpsO mRNA of Escherichia coli is polyadenylated at multiple sites resulting from endonucleolytic processing and exonucleolytic degradation. EMBO J. 15:31443152.
67. Hennigan, A. N., and, J. N. Reeve. 1994. mRNAs in the methanogenic archaeon Methanococcus vannielii: numbers, half-lives and processing. Mol. Microbiol. 11:655670.
68. Henras, A.,, Y. Henry,, C. Bousquet-Antonelli,, J. Noaillac-Depeyre,, J. P. Gelugne, and, M. Caizergues-Ferrer. 1998. Nhp2p and Nop10p are essential for the function of H/ACA snoRNPs. EMBO J. 17:70787090.
69. Hong, S. J.,, Q. A. Tran, and, K. C. Keiler. 2005. Cell cycle-regulated degradation of tmRNA is controlled by RNase R and SmpB. Mol. Microbiol. 57:565575.
70. Hopper, A. K. and, E. M. Phizicky. 2003. tRNA transfers to the limelight. Genes Dev. 17:162180.
71. Huang, H.,, J. Liao, and, S. N. Cohen. 1998. Poly(A)- and poly(U)-specific RNA 3ʹ tail shortening by E. coli ribonuclease E. Nature 391:99102.
72. Jacobson, A., and, S. W. Peltz. 1996. Interrelationships of the pathways of mRNA decay and translation in eukaryotic cells. Annu. Rev. Biochem. 65:693739.
73. JSger, A.,, R. Samorski,, F. Pfeifer, and, G. Klug. 2002. Individual gvp transcript segments in Haloferax mediterranei exhibit varying half-lives, which are differentially affected by salt concentration and growth phase. Nucleic Acids Res. 30:54365443.
74. JSger, S.,, O. Fuhrmann,, C. Heck,, M. Hebermehl,, E. Schiltz,, R. Rauhut, and, G. Klug. 2001. An mRNA degrading complex in Rhodobacter capsulatus. Nucleic Acids Res. 29:45814588.
75. Kanai, A.,, H. Oida,, N. Matsuura, and, H. Doi. 2003. Expression cloning and characterization of a novel gene that encodes the RNA-binding protein FAU-1 from Pyrococcus furiosus. Biochem. J. 372:253261.
76. Kiss-Laszlo, Z.,, Y. Henry,, J. P. Bachellerie,, M. Caizergues-Ferrer, and, T. Kiss. 1996. Site-specific ribose methylation of preribosomal RNA: a novel function for small nucleolar RNAs. Cell 85:10771088.
77. Kjems, J., and, R. A. Garrett. 1985. An intron in the 23S ribosomal RNA gene of the archaebacterium Desulfurococcus mobilis. Nature 318:675677.
78. Kjems, J., and, R. A. Garrett. 1988. Novel splicing mechanism for the ribosomal RNA intron in the archaebacterium Desul-furococcus mobilis. Cell 54:693703.
79. Kjems, J., and, R. A. Garrett. 1991. Ribosomal RNA introns in archaea and evidence for RNA conformational changes associated with splicing. Proc. Natl. Acad. Sci. USA 88:439443.
80. Kjems, J.,, H. Leffers,, R. A. Garrett,, G. Wich,, W. Leinfelder, and, A. Bock. 1987. Gene organization, transcription signals and processing of the single ribosomal RNA operon of the archaebacterium Thermoproteus tenax. Nucleic Acids Res. 15:48214835.
81. Klein, D. J.,, T. M. Schmeing,, P. B. Moore, and, T. A. Steitz. 2001. The kink-turn: a new RNA secondary structure motif. EMBO J. 20:42144221.
82. Koonin, Koonin. E. 1996. Pseudouridine synthases: four families of enzymes containing a putative uridine-binding motif also conserved in dUTPases and dCTP deaminases. Nucleic Acids Res. 24:24112415.
83. Koonin, E. V.,, Y. I. Wolf, and, L. Aravind. 2001. Prediction of the archaeal exosome and its connections with the protea-some and the translation and transcription machineries by a comparative-genomic approach. Genome Res. 11:240252.
84. Kouzuma, Y.,, M. Mizoguchi,, H. Takagi,, H. Fukuhara,, M. Tsukamoto,, T. Numata, and, M. Kimura. 2003. Recon-stitution of archaeal ribonuclease P from RNA and four protein components. Biochem. Biophys. Res. Commun. 306:666673.
85. Kowalak, J. A.,, J. J. Dalluge,, J. A. Mcloskey, and, K. O. Stetter. 1994. The role of posttranscriptional modification in stabilization of transfer RNA from hyperthermophiles. Biochemistry 33:78697876.
86. Kuhn, J. F.,, E. J. Tran, and, E. S. Maxwell. 2002. Archaeal ribosomal protein L7 is a functional homolog of the eukaryotic 15.5kD/Snu13p snoRNP core protein. Nucleic Acids Res. 30:931941.
87. Kushner, Kushner. S. 2002. mRNA decay in Escherichia coli comes of age. J. Bacteriol. 184:46584665; discussion, 4657.
88. LaCava, J.,, J. Houseley,, C. Saveanu,, E. Petfalski,, E. Thompson,, A. Jacquier, and, D. Tollervey. 2005. RNA degradation by the exosome is promoted by a nuclear polyadenylation complex. Cell 121:713724.
89. Lafontaine, D. L.,, C. Bousquet-Antonelli,, Y. Henry,, M. Caizergues-Ferrer, and, D. Tollervey. 1998. The box H + ACA snoRNAs carry Cbf5p, the putative rRNA pseudouridine synthase. Genes Dev. 12:527537.
90. Lorentzen, E.,, P. Walter,, S. Fribourg,, E. Evguenieva-Hacken-berg,, G. Klug, and, E. Conti. 2005. The archaeal exosome core is a hexameric ring structure with three catalytic subunits. Nat. Struct. Mol. Biol. 12:575581.
91. Lykke-Andersen, J.,, C. Aagaard,, M. Semionenkov, and, R. A. Garrett. 1997. Archaeal introns: splicing, intercellular mobility and evolution. Trends Biochem. Sci. 22:326331.
92. Mackie, Mackie. G. 1998. Ribonuclease E is a 5ʹ-end-dependent endonuclease. Nature 395:720723.
93. Marck, C., and, H. Grosjean. 2003. Identification of BHB splicing motifs in intron-containing tRNAs from 18 archaea: evolutionary implications. RNA 9:15161531.
94. McCloskey, J. A., and, J. Rozenski. 2005. The Small Subunit rRNA Modification Database. Nucleic Acids Res. 33:D135138.
95. Michel, F., and, J. L. Ferat. 1995. Structure and activities of group II introns. Annu. Rev. Biochem. 64:435461.
96. Minagawa, A.,, H. Takaku,, M. Takagi, and, M. Nashimoto. 2004. A novel endonucleolytic mechanism to generate the CCA 3ʹ termini of tRNA molecules in Thermotoga maritima. J. Biol. Chem. 279:1568815697.
97. Mitchell, P.,, E. Petfalski,, A. Shevchenko,, M. Mann, and, D. Tollervey. 1997. The exosome: a conserved eukaryotic RNA processing complex containing multiple 3ʹX5ʹ exori-bonucleases. Cell 91:457466.
98. Moore, M. J.,, C. C. Query, and, P. A. Sharp. 1993. Splicing of precursors to mRNA by the spliceosome, p. 303-357. In R. F. Gesteland. and, J. F. Atkins. (ed.), The RNA World. Cold Spring Harbor Laboratory Press, Plainview, N.Y.
99. Noon, K. R.,, R. Guymon,, P. F. Crain,, J. A. Mcloskey,, M. Thomm,, J. Lim, and, R. Cavicchioli. 2003. Influence of temperature on tRNA modification in archaea: Methanococcoides burtonii (optimum growth temperature [Topt], 23 degrees C) and Stetteria hydrogenophila (Topt, 95 degrees C). J. Bacteriol. 185:54835490.
100. OʹHara, E. B.,, J. A. Chekanova,, C. A. Ingle,, Z. R. Kushner,, E. Peters, and, S. R. Kushner. 1995. Polyadenylylation helps regulate mRNA decay in Escherichia coli. Proc. Natl. Acad. Sci. USA 92:18071811.
101. Ofengand, J.,, M. Del Campo, and, Y. Kaya. 2001. Mapping pseudouridines in RNA molecules. Methods 25:365373.
102. Ofengand, J., and, M. Fournier. 1998. The pseudouridine residues of rRNA: number, location, biosynthesis and function, p. 229-253. In H. Grosjean. and, R. Benne. (ed.), Modification and Editing of RNA. AMS Press, Washington, D.C.
103. Omer, A. D.,, T. M. Lowe,, A. G. Russell,, H. Ebhardt,, S. R. Eddy, and, P. P. Dennis. (2000) Homologs of small nucleolar RNAs in Archaea. Science 288:517522.
104. Omer, A. D.,, S. Ziesche,, H. Ebhardt, and, P. P. Dennis. 2002. In vitro reconstitution and activity of a C/D box methylation guide ribonucleoprotein complex. Proc. Natl. Acad. Sci. USA 99:52895294.
105. Pace, N. R., and, j. W Brown. 1995. Evolutionary perspective on the structure and function of ribonuclease P, a ribozyme. J. Bacteriol. 177:19191928.
106. Pannucci, J. A.,, E. S. Haas,, T. A. Hall,, J. K. Harris, and, J. W Brown. 1999. RNase P RNAs from some Archaea are cat-alytically active. Proc. Natl. Acad. Sci. USA 96:78037808.
107. Pellegrini, O.,, J. Nezzar,, A. Marchfelder,, H. Putzer, and, C. Condon. 2003. Endonucleolytic processing of CCA-less tRNA precursors by RNase Z in Bacillus subtilis. EMBO J. 22:45344543.
108. Phizicky, E. M., and, C. L. Greer. 1993. Pre-tRNA splicing: variation on a theme or exception to the rule? Trends Biochem. Sci. 18:3134.
109. Phizicky, E. M.,, R. C. Schwartz, and, J. Abelson. 1986. Saccharomyces cerevisiae tRNA ligase. Purification of the protein and isolation of the structural gene. J. Biol. Chem. 261:29782986.
110. Portnoy, V.,, E. Evguenieva-Hackenberg,, F. Klein,, P. Walter,, G. Klug, and, G Schuster. 2005. RNA polyadenylation in Archaea: not observed in Haloferax while the exosome polyadenylates RNA in Sulfolobus. EMBO Rep. 6:11881193.
111. Potter, S.,, P. Durovic,, A. Russell,, X. Wang,, D. de Jong-Wong, and, P. P. Dennis. 1995. Preribosomal RNA processing in archaea: characterization of the RNP endonuclease mediated processing of precursor 16S rRNA in the thermoacidophile Sulfolobus acidocaldarius. Biochem. Cell. Biol. 73:813823.
112. Purusharth, R. I.,, F. Klein,, S. Sulthana,, S. Jager,, M. V. Jagan-nadham,, E. Evguenieva-Hackenberg,, M. K. Ray, and, G. Klug. 2005. Exoribonuclease R interacts with endoribonuclease E and an RNA helicase in the psychrotrophic bacterium Pseudo-monas syringae Lz4W. J. Biol. Chem. 280:1457214578.
113. Raijmakers, R.,, W. V. Egberts,, W. J. van Venrooij, and, G. J. Pruijn. 2002. Protein-protein interactions between human ex-osome components support the assembly of RNase PH-type subunits into a six-membered PNPase-like ring. J. Mol. Biol. 323:653663.
114. Raijmakers, R.,, G. Schilders, and, G. J. Pruijn. 2004. The exosome, a molecular machine for controlled RNA degradation in both nucleus and cytoplasm. Eur. J. Cell. Biol. 83:175183.
115. Randau, L.,, R. Munch,, M. J. Hohn,, D. Jahn, and, D. Soil. 2005. Nanoarchaeum equitans creates functional tRNAs from separate genes for their 5ʹ- and 3ʹ-halves. Nature 433:537541.
116. Rashid, R.,, M. Aittaleb,, Q. Chen,, K. Spiegel,, B. Demeler, and, H. Li. 2003. Functional requirement for symmetric assembly of archaeal box C/D small ribonucleoprotein particles. J. Mol. Biol. 333:295306.
117. Rauhut, R., and, G. Klug. 1999. mRNA degradation in bacteria. FEMS Microbiol. Rev. 23:353370.
118. Renalier, M. H.,, N. Joseph,, C. Gaspin,, P. Thebault, and, A. Mougin. 2005. The Cm56 tRNA modification in archaea is catalyzed either by a specific 2ʹ-O-methylase, or a C/D sRNP. RNA 11:10511063.
119. Röder, R., and, F. Pfeifer. 1996 Influence of salt on the transcription of the gas-vesicle genes of Haloferax mediterranei and identification of the endogenous transcriptional activator gene. Microbiology 142(Pt 7):17151723.
120. Ross, J. 1995. mRNA stability in mammalian cells. Microbiol. Rev. 59:423450.
121. Rozhdestvensky, T. S.,, T. H. Tang,, I. V. Tchirkova,, J. Brosius,, J. P. Bachellerie, and, A. Hiittenhofer. 2003. Binding of L7Ae protein to the K-turn of archaeal snoRNAs: a shared RNA binding motif for C/D and H/ACA box snoRNAs in Archaea. Nucleic Acids Res. 31:869877.
122. Salgia, S. R.,, S. K. Singh,, P. Gurha, and, R. Gupta. 2003. Two reactions of Haloferax volcanii RNA splicing enzymes: joining of exons and circularization of introns. RNA 9:319330.
123. Samaha, R. R.,, R. Green, and, H. F. Noller. 1995. A base pair between tRNA and 23S rRNA in the peptidyl transferase centre of the ribosome. Nature 377:309314.
124. Sarkar, N. 1997. Polyadenylation of mRNA in prokaryotes. Annu. Rev. Biochem. 66:173197.
125. Sawaya, R.,, B. Schwer, and, S. Shuman. 2003. Genetic and biochemical analysis of the functional domains of yeast tRNA ligase. J. Biol. Chem. 278:4392843938.
126. Schierling, K.,, S. Rösch,, R. Rupprecht,, S. Schiffer, and, A. Marchfelder. 2002. tRNA 3ʹ end maturation in archaea has eukaryotic features: the RNase Z from Haloferax volcanii. J. Mol. Biol. 316:895902.
127. Schiffer, S.,, S. Rösch, and, A. Marchfelder. 2002. Assigning a function to a conserved group of proteins: the tRNA 3ʹ-processing enzymes. EMBO J. 21:27692777.
128. Selinger, D. W.,, R. M. Saxena,, K. J. Cheung,, G. M. Church, and, C. Rosenow. 2003. Global RNA half-life analysis in Escherichia coli reveals positional patterns of transcript degradation. Genome Res. 13:216223.
129. Sidrauski, C,, R. Chapman, and, P. Walter. 1998. The unfolded protein response: an intracellular signalling pathway with many surprising features. Trends Cell. Biol. 8:245249.
130. Singh, S. K.,, P. Gurha,, E. J. Tran,, E. S. Maxwell, and, R. Gupta. 2004 Sequential 2ʹ-O-methylation of archaeal pre-tRNATrp nucleotides is guided by the intron-encoded but trans-acting box C/D ribonucleoprotein of pre-tRNA. J. Biol. Chem. 279:4766147671.
131. Steege, Steege. D. 2000. Emerging features of mRNA decay in bacteria. RNA 6:10791090.
132. Symmons, M. F.,, M. G. Williams,, B. F. Luisi,, G. H. Jones, and, A. J. Carpousis. 2002. Running rings around RNA: a super-family of phosphate-dependent RNases. Trends Biochem. Sci. 27:1118.
133. Takayama, K., and, S. Kjelleberg. 2000. The role of RNA stability during bacterial stress responses and starvation. Environ. Microbiol. 2:355365.
134. Tang, T. H.,, N. Polacek,, M. Zywicki,, H. Huber,, K. Brugger,, R. Garrett,, J. P. Bachellerie, and, A. Hiittenhofer. 2005. Identification of novel non-coding RNAs as potential antisense regulators in the archaeon Sulfolobus solfataricus. Mol. Microbiol. 55:469481.
135. Tang, T. H.,, T. S. Rozhdestvensky,, B. C. dʹOrval,, M. L. Bortolin,, H. Huber,, B. Charpentier,, C. Branlant,, J. P. Bachellerie,, J. Brosius, and, A. Hiittenhofer. 2002. RNomics in Archaea reveals a further link between splicing of archaeal introns and rRNA processing. Nucleic Acids Res. 30:921930.
136. Thompson, L. D., and, C. J. Daniels. 1990. Recognition of exon-intron boundaries by the Halobacterium volcanii tRNA intron endonuclease. J. Biol. Chem. 265:1810418111.
137. Tocchini-Valentini, G. D.,, P. Fruscoloni, and, G. P. Tocchini-Valentini. 2005. Structure, function, and evolution of the tRNA endonucleases of Archaea: an example of subfunction-alization. Proc. Natl. Acad. Sci. USA 102:89338938.
138. Tomita, K., and, A. M. Weiner. 2001. Collaboration between CC- and A-adding enzymes to build and repair the 3ʹ-terminal CCA of tRNA in Aquifex aeolicus. Science 294:13341336.
139. Toro, N. 2003. Bacteria and Archaea Group II introns: additional mobile genetic elements in the environment. Environ. Microbiol. 5:143151.
140. Tran, E. J.,, X. Zhang, and, E. S. Maxwell. 2003. Efficient RNA 2ʹ-O-methylation requires juxtaposed and symmetrically assembled archaeal box C/D and C/Dʹ RNPs. EMBO J. 22:39303940.
141. Trotta, C. R.,, F. Miao,, E. A. Arn,, S. W. Stevens,, C. K. Ho,, R. Rauhut, and, J. N. Abelson. 1997. The yeast tRNA splicing endonuclease: a tetrameric enzyme with two active site subunits homologous to the archaeal tRNA endonucleases. Cell 89:849858.
142. van Hoof, A., and, R. Parker. 1999. The exosome: a protea-some for RNA? Cell 99:347350.
143. Vanacova, S.,, J. Wolf,, G. Martin,, D. Blank,, S. Dettwiler,, A. Friedlein,, H. Langen,, G. Keith, and, W. Keller. 2005. A new yeast poly(A) polymerase complex involved in RNA quality control. PLoS Biol. 3:e189.
144. Vogel, A.,, O. Schilling,, B. Späth, and, A. Marchfelder. 2005. The tRNase Z family of proteins. Physiological functions, substrate specificity and structural properties. Biol. Chem. 386:12531264.
145. Volkl, P.,, P. Markiewicz,, C. Baikalov,, S. Fitz-Gibbon,, K. O. Stetter, and, J. H. Miller. 1996. Genomic and cDNA sequence tags of the hyperthermophilic archaeon Pyrobaculum aerophilum. Nucleic Acids Res. 24:43734378.
146. Walsh, A. P.,, M. R. Tock,, M. H. Mallen,, V. R. Kaberdin,, A. von Gabain, and, K. J. Mcowall. 2001. Cleavage of poly(A) tails on the 3ʹ-end of RNA by ribonuclease E of Escherichia coli. Nucleic Acids Res. 29:18641871.
147. Walter, P.,, F. Klein,, E. Lorentzen,, A. Ilchmann,, G. Klug, and, E. Evguenieva-Hackenberg. 2006. Characterization of native and reconstituted exosome complexes from the hyperthermophilic archaeon Sulfolobus solfataricus. Mol. Microbiol. 62:10761089.
148. Wang, Y.,, C. L. Liu,, J. D. Storey,, R. J. Tibshirani,, D. Herschlag, and, P. O. Brown. 2002. Precision and functional specificity in mRNA decay. Proc. Natl. Acad. Sci. USA 99:58605865.
149. Watanabe, Y., and, M. W. Gray. 2000. Evolutionary appearance of genes encoding proteins associated with box H/ACA snoRNAs: cbf5p in Euglena gracilis, an early diverging eu-karyote, and candidate Gar1p and Nop10p homologs in archaebacteria. Nucleic Acids Res. 28:23422352.
150. Watanabe, Y.,, S. Yokobori,, T. Inaba,, A. Yamagishi,, T. Oshima,, Y. Kawarabayasi,, H. Kikuchi, and, K. Kita. 2002. Introns in protein-coding genes in Archaea. FEBS Lett. 510:2730.
151. Watkins, N. J.,, A. Gottschalk,, G. Neubauer,, B. Kastner,, P. Fabrizio,, M. Mann, and, R. Lührmann. 1998. Cbf5p, a potential pseudouridine synthase, and Nhp2p, a putative RNA-binding protein, are present together with Gar1p in all H BOX/ACA-motif snoRNPs and constitute a common bipartite structure. RNA 4:15491568.
152. Watkins, N. J.,, V. Segault,, B. Charpentier,, S. Nottrott,, P. Fabrizio,, A. Bachi,, M. Wilm,, M. Rosbash,, C. Branlant, and, R. Lührmann. 2000. A common core RNP structure shared between the small nucleoar box C/D RNPs and the spliceo-somal U4 snRNP. Cell 103:457466.
153. Xiao, S.,, F. Scott,, C. A. Fierke, and, D. R. Engelke. 2002. Eukaryotic ribonuclease P: a plurality of ribonucleoprotein enzymes. Annu. Rev. Biochem. 71:165189.
154. Xiong, Y., and, T. A. Steitz. 2004. Mechanism of transfer RNA maturation by CCA-adding enzyme without using an oligonucleotide template. Nature 430:640645.
155. Yu, Y. T.,, R. M. Terns, and, M. P. Terns. 2005. Mechanisms and functions of RNA-guided RNA modification, p. 223–262. In Grosjean, H. (ed.), Fine-Tuning of RNA Functions by Modification and Editing, vol. 12. Topics in Current Genetics. Springer Verlag, New York, N.Y.
156. Yue, D.,, N. Maizels, and, A. M. Weiner. 1996. CCA-adding enzymes and poly(A) polymerases are all members of the same nucleotidyltransferase superfamily: characterization of the CCA-adding enzyme from the archaeal hyperthermophile Sulfolobus shibatae. RNA 2:895908.
157. Yue, D.,, A. M. Weiner, and, N. Maizels. 1998. The CCA-adding enzyme has a single active site. J. Biol. Chem. 273:2969329700.
158. Zago, M. A.,, P. P. Dennis, and, A. D. Omer. 2005. The expanding world of small RNAs in the hyperthermophilic archaeon Sulfolobus solfataricus. Mol. Microbiol. 55:18121828.
159. Ziesche, S. M.,, A. D. Omer, and, P. P. Dennis. 2004. RNA-guided nucleotide modification of ribosomal and non-ribosomal RNAs in Archaea. Mol. Microbiol. 54:980993.
160. Zofallova, L.,, Y. Guo, and, R. Gupta. 2000. Junction phosphate is derived from the precursor in the tRNA spliced by the archaeon Haloferax volcanii cell extract. RNA 6:10191030.

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error