Chapter 8 : Translation

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

Translation, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555815516/9781555813918_Chap08-1.gif /docserver/preview/fulltext/10.1128/9781555815516/9781555813918_Chap08-2.gif


The emergence of translation as a process was key to the evolution of modern cellular life. Primitive ‘’life’’ based on self-replicating nucleic acids without translation is conceivable. This chapter describes what is known about the translational apparatus and the protein-synthesis mechanism in archaea. Other essential components of the protein synthesis machinery that are found in all cells are specific sets of proteins known as translation factors. These are necessary to assist the different stages of translation, i.e., initiation, elongation, and termination. In addition, there are genes encoding tRNAs and the accessory proteins that function in translation initiation, elongation, and termination. The four genes encoding the universal initiation factors YciH/SUI1, IF1/IF1A, IF2/IF5B, and EFP/IF5A tend to be unlinked from other translational genes and are likely to be individually transcribed. The gene encoding the putative translation termination factor aRF1 is in general not clustered with other genes encoding components of the protein synthesis apparatus. eIF5A is required to trigger the formation of the first peptide bond. Eucaryal IF2 is an important translation initiation factor, as it specifically interacts with the initiator tRNA (met-tRNAi) and carries it to the 40S ribosomal subunit. The universal protein a(e)IF5A (EFP in bacteria) is usually classed as a translation initiation factors. This protein does little to help the selection of the translation start site and functions as a specialized elongation factor.

Citation: Londei P. 2007. Translation, p 175-197. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch8

Key Concept Ranking

Bacteria and Archaea
Gene Expression and Regulation
Transcription Start Site
Bacterial Proteins
Translation Initiation
Translation Termination
Highlighted Text: Show | Hide
Loading full text...

Full text loading...


Image of Figure 1
Figure 1

Comparison of 16S RNA secondary structure in archaea and bacteria. Secondary structure models are shown for one archaeal 16S rRNA () and one bacterial () 16S RNA. The regions where the structures differ are indicated by arrows. The black lines represent identified tertiary interactions between nucleotides. Data taken from the The details of the database are described in reference .

Citation: Londei P. 2007. Translation, p 175-197. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch8
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 2
Figure 2

The phylogenetic tree of life. Unrooted tree showing the branching of the principal species in the three domains of life. Adapted from Lecompte et al. ( ).

Citation: Londei P. 2007. Translation, p 175-197. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch8
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 3
Figure 3

(.) Organization of the main ribosomal protein gene clusters in archaeal genomes. H-sp sp. NRC1 The last line () shows for comparison the organization of the same genes in that is also present in most bacteria. Genes that are within 50 bp of each other, and may therefore be cotranscribed, are indicated in the same color. Domain-specific genes are underlined.

Citation: Londei P. 2007. Translation, p 175-197. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch8
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 4
Figure 4

The “chalice” structure of the archaeal IF2-like translation initiation factor. The crystal structure of the archaeal translation initiation factor aIF2, homologous to eucaryal eIF5B and bacterial IF2, is shown. The four protein domains are indicated. Data taken from the NCBI structure data bank: PDB: 1G7T viewed with Cn3D 4.1.

Citation: Londei P. 2007. Translation, p 175-197. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch8
Permissions and Reprints Request Permissions
Download as Powerpoint


1. Alix, J. H., and, K. H. Nierhaus. 2003. DnaK-facilitated ribosome assembly in Escherichia coli revisited. RNA 9:787793.
2. Allen, G. S.,, A. Zavialov,, R. Gursky,, M. Ehrenberg, and, J. Frank. 2005. The cryo-EM structure of a translation initiation complex from Escherichia coli. Cell 121:703712.
3. Amils, R., P. Cammarano, and, P. Londei. 1993. Translation in Archaea, p. 393-437. In M. Kates,, D. Kushner, and, A. Matheson (ed.), Biochemistry of Archaea. New Comprehensive Biochemistry Series. Elsevier, Amsterdam, The Netherlands.
4. Anantharaman, V.,, E. V. Koonin, and, L. Aravind. 2002. Comparative genomics and evolution of proteins involved in RNA metabolism. Nucleic Acids Res. 30:14271464.
5. Bachellerie, J. P.,, J. Cavaille, and, A. Huttenhofer. 2002. The expanding snoRNA world. Biochimie 84:775790.
6. Ban, N.,, R Nissen,, J. Hansen,, R B. Moore, and, T. A. Steitz. 2000. The complete atomic structure of the large ribosomal subunit at 2.4 A resolution. Science 289:905920.
7. Bartig. D.,, K. Lemkemeier,, J. Frank,, F. Lottspeich, and, F. Klink. 1992. The archaebacterial hypusine-containing protein. Structural features suggest common ancestry with eu-karyotic translation initiation factor 5A. Eur. J. Biochem. 204:751758.
8. Basu, U.,, K. Si,, H. Deng, and, U. Maitra. 2003. Phosphorylation of mammalian eukaryotic translation initiation factor 6 and its Saccharomyces cerevisiae homologue Tif6p: evidence that phosphorylation of Tif6p regulates its nucleocytoplasmic distribution and is required for yeast cell growth. Mol. Cell Biol. 23:61876199.
9. Basu, U.,, K. Si,, J. R. Warner, and, U. Maitra. 2001. The Saccharomyces cerevisiae TIF6 gene encoding translation initiation factor 6 is required for 60S ribosomal subunit biogenesis. Mol. Cell. Biol. 21:14531462.
10. Battiste, J. L.,, T. V. Pestova,, C. U. Hellen, and, G. Wagner. 2000. The eIF1A solution structure reveals a large RNA-binding surface important for scanning function. Mol. Cell 5:109119.
11. Bell. S. D., and, S. P. Jackson. 1998. Transcription and translation in Archaea: a mosaic of eukaryal and bacterial features. Trends Microbiol. 6:222228.
12. Benelli, D.,, E. Maone, and, P. Londei. 2003. Two different mechanisms for ribosome/mRNA interaction in archaeal translation initiation. Mol. Microbiol. 50:635643.
13. Betlach, M.,, J. Friedman,, H. W. Boyer, and, F. Pfeifer. 1984. Characterization of a halobacterial gene affecting bacterio-opsin gene expression. Nucleic Acids Res. 12:79497959.
14. Bini, E.,, V. Dikshit,, K. Dirksen,, M. Drozda, and, P. Blum. 2002. Stability of mRNA in the hyperthermophilic archaeon Sulfolobus solfataricus. RNA 8:11291136.
15. Boileau, G.,, P. Butler,, J. W. Hershey, and, R. R. Traut. 1983. Direct cross-links between initiation factors 1, 2, and 3 and ri-bosomal proteins promoted by 2-iminothiolane. Biochemistry 22:31623170.
16. Brodersen, D. E.,, W. M. Clemons, Jr.,, A. P. Carter,, B. T. Wimberly, and, V. Ramakrishnan. 2002. Crystal structure of the 30S ribosomal subunit from Thermus thermophilus: structure of the proteins and their interactions with 16S RNA. J. Mol. Biol. 316:725768.
17. Cannone. J. J.,, S. Subramanian,, M. N. Schnare,, J. R. Collett,, L. M. DʹSouza,, Y. Du,, B. Feng,, N. Lin,, L. V. Madabusi,, K. M. Muller,, N. Pande,, Z. Shang,, N. Yu, and, R. R. Gutell. 2002. The Comparative RNA Web (CRW) site: an online database of comparative sequence and structure information for ribo-somal, intron, and other RNAs. BioMed Central Bioinform. 3:15.
18. Castresana, J. 2001. Comparative genomics and bioenergetics. Biochim. Biophys. Acta 1506:147162.
19. Cavaille, J.,, M. Nicoloso, and, J P. Bachellerie. 1996. Targeted ribose methylation of RNA in vivo directed by tailored anti-sense RNA guides. Nature 383:732735.
20. Cech, T. T. 1993. The efficiency and versatility of catalytic RNA: implications for an RNA world. Gene 135:3336.
21. Ceci, M.,, C. Gaviraghi,, C. Gorrini,, L. A. Sala,, N. Offenhauser,, et al 2003. Release of eIF6 (p27BBP) from the 60S subunit allows 80S ribosome assembly. Nature 426:579584.
22. Cobucci-Ponzano, B.,, M. Rossi, and, M. Moracci. 2005. Re-coding in archaea. Mol. Microbiol. 55:339348.
23. Coenye, T., and, P. Vandamme. 2005. Organisation of the S10, spc and alpha ribosomal protein gene clusters in prokaryotic genomes. FEMS Microbiol. Lett. 242:117126.
24. Colthurst, D. R.,, D. G. Campbell, and, C. G. Proud. 1987. Structure and regulation of eukaryotic initiation factor eIF-2. Sequence of the site in the alpha subunit phosphorylated by the haem-controlled repressor and by the double-stranded RNA-activated inhibitor. Eur. J. Biochem. 166:357363.
25. Condo, I.,, A. Ciammaruconi,, D. Benelli,, D. Ruggero, and, P. Londei. 1999. Cis-acting signals controlling translational initiation in the thermophilic archaeon Sulfolobus solfataricus. Mol. Microbiol. 34:377384.
26. Cort, J. R.,, E. V. Koonin,, P. A. Bash, and, M. A. Kennedy. 1999. A phylogenetic approach to target selection for structural genomics: solution structure of YciH. Nucleic Acids Res. 27:40184027.
27. Cui, Y.,, J. D. Dinman,, T. G. Kinzy, and, S. W. Peltz. 1998. The Mof2/Sui1 protein is a general monitor of translational accuracy. Mol. Cell Biol. 18:15061516.
28. Daalgard, J. Z., and, R. A. Garrett. 1993. Archaeal hyperthermophile genes, p. 535–563. In M. Kates,, D. Kushner, and, A. Matheson. (ed.), Biochemistry of Archaea. New Comprehensive Biochemistry Series. Elsevier, Amsterdam. The Netherlands.
29. Das, A.,, M. K. Bagchi,, P. Ghosh-Dastidar, and, N. K. Gupta. 1982. Protein synthesis in rabbit reticulocytes. A study of pep-tide chain initiation using native and beta-subunit-depleted eukaryotic initiation factor 2. J. Biol. Chem. 257:12821288.
30. Dennis, P. P. 1997. Ancient ciphers: translation in Archaea. Cell 89:10071010.
31. Dontsova, M.,, L. Frolova,, J. Vassilieva,, W. Piendl,, L. Kisselev, and, M. Garber. 2000. Translation termination factor aRF1 from the archaeon Methanococcus jannaschii is active with eukaryotic ribosomes. FEBS Lett. 472:213216.
32. Erickson, F. L., and, E. M. Hannig. 1996. Ligand interactions with eukaryotic translation initiation factor 2: role of the gamma-subunit. EMBO J. 15:63116320.
33. Etchegaray, J. P., and, M. Inouye. 1999. Translational enhancement by an element downstream of the initiation codon in Escherichia coli. J. Biol. Chem. 274:1007910085.
34. Fagegaltier, D.,, N. Hubert,, K. Yamada,, T. Mizutani,, P. Carbon, and, A. Krol. 2000. Characterization of mSelB, a novel mammalian elongation factor for selenoprotein translation. EMBO J. 19:47964805.
35. Glick, B. R.,, S. Chladek, and, M. C. Ganoza. 1979. Peptide bond formation stimulated by protein synthesis factor EF-P depends on the aminoacyl moiety of the acceptor. Eur. J. Biochem. 97:2328.
36. Grill, S.,, C. O. Gualerzi,, P. Londei, and, U. Blasi. 2000. Selective stimulation of translation of leaderless mRNA by initiation factor 2: evolutionary implications for translation. EMBO J. 19:41014110.
37. Gualerzi, C., and, C. L. Pon. 1990. Initiation of mRNA translation in prokaryotes. Biochemistry 29:58815889.
38. Guenneugues, M.,, E. Caserta,, L. Brandi,, R. Spurio,, S. Meunier,, et al 2000. Mapping the fMet-tRNA(f)(Met) binding site of initiation factor IF2. EMBO J. 19:52335240.
39. Gutierrez, P.,, M. J. Osborne,, N. Siddiqui,, J. F. Trempe,, C. Arrowsmith, and, K. Gehring. 2004. Structure of the archaeal translation initiation factor aIF2 beta from Methanobacterium thermoautotrophicum: implications for translation initiation. Protein Sci. 13:659667.
40. Hanawa-Suetsugu, K., S. Sekine,, H. Sakai,, C. Hori-Takemoto,, T. Terada,, et al 2004. Crystal structure of elongation factor P from Thermus thermophilus HB8. Proc. Natl. Acad. Sci. USA 101:95959600.
41. Hanner,, M.,, C. Mayer,, C. Kohrer,, G. Golderer,, P. Grobner, and, W. Piendl. 1994. Autogenous translational regulation of the ribosomal MvaL1 operon in the archaebacterium Methanococcus vannielii. J. Bacteriol. 176:409418.
42. Harms, J.,, F. Schluenzen,, R. Zarivach,, A. Bashan,, S. Gat,, et al 2001. High resolution structure of the large ribosomal subunit from a mesophilic eubacterium. Cell 107:679688.
43. Hennigan, A. N., and, J. N. Reeve.. 1994. mRNAs in the methanogenic archaeon Methanococcus vannielii: numbers, half-lives and processing. Mol. Microbiol. 11:655670.
44. Ibba, M., and, D. Soll. 2002. Genetic code: introducing pyrrolysine. Curr. Biol. 12:R464R466.
45. Itoh, T.,, K. Suzuki, and, T. Nakase. 1998. Occurrence of introns in the 16S rRNA genes of members of the genus Ther-moproteus. Arch. Microbiol. 170:155161.
46. Iwabe, N.,, K. Kuma,, M. Hasegawa,, S. Osawa, and, T. Miyata. 1989. Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes. Proc. Natl. Acad. Sci. USA 86:93559359.
47. Joyce, G. F. 2002. The antiquity of RNA-based evolution. Nature 418:214221.
48. Karlin, S.,, J. Mrazek,, J. Ma, and, L. Brocchieri. 2005. Predicted highly expressed genes in archaeal genomes. Proc. Natl. Acad. Sci. USA 102:73037308.
49. Kim, K. K.,, L. W. Hung,, H. Yokota,, R. Kim, and, S. H. Kim. 1998. Crystal structures of eukaryotic translation initiation factor 5A from Methanococcus jannaschii at 1.8 A resolution. Proc. Natl. Acad. Sci. USA 95:1041910424.
50. Kimball, S. R. 1999. Eukaryotic initiation factor eIF2. In t. J. Biochem. Cell. Biol. 31:2529.
51. Kiss, T. 2001. Small nucleolar RNA-guided post-transcriptional modification of cellular RNAs. EMBO J. 20:36173622.
52. Kiss, T. 2002. Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse cellular functions. Cell 109:145148.
53. Kisselev, L.,, M. Ehrenberg, and, L. Frolova. 2003. Termination of translation: interplay of mRNA, rRNAs and release factors?. EMBO J. 22:175182.
54. Kisselev, L. L., and, R. H. Buckingham. 2000. Translational termination comes of age. Trends Biochem. Sci. 25:561566.
55. Kiss-Laszlo, Z.,, Y. Henry, and, T. Kiss. 1998. Sequence and structural elements of methylation guide snoRNAs essential for site-specific ribose methylation of pre-rRNA. EMBO J. 17:797807.
56. Kjems, J., and, R. A. Garrett. 1988. Novel splicing mechanism for the ribosomal RNA intron in the archaebacterium Desul-furococcus mobilis. Cell 54:693703.
57. Koonin, E. V. 2003. Comparative genomics, minimal gene-sets and the last universal common ancestor. Nat. Rev. Microbiol. 1:2736.
58. Kozak, M. 1999. Initiation of translation in prokaryotes and eukaryotes. Gene 234:187208.
59. Kraft, A.,, C. Lutz,, A. Lingenhel,, P. Grobner, and, W. Piendl. 1999. Control of ribosomal protein L1 synthesis in mesophilic and thermophilic archaea. Genetics 152:13631372.
60. Kuhn, J. F.,, E. J. Tran, and, E. S. Maxwell. 2002. Archaeal ri-bosomal protein L7 is a functional homolog of the eukaryotic 15.5kD/Snu13p snoRNP core protein. Nucleic Acids Res. 30:931941.
61. Kyrpides, N.,, R. Overbeek, and, C. Ouzounis. 1999. Universal protein families and the functional content of the last universal common ancestor. J. Mol. Evol. 49:413423.
62. Kyrpides, N. C., and, C. R. Woese. 1998. Archaeal translation initiation revisited: the initiation factor 2 and eukaryotic initiation factor 2B alpha-beta-delta subunit families. Proc. Natl. Acad. Sci. USA 95:37263730.
63. Kyrpides, N. C., and, C. R. Woese. 1998. Universally conserved translation initiation factors. Proc. Natl. Acad. Sci. USA 95:224228.
64. La Teana, A.,, A. Brandi,, M. OʹConnor,, S. Freddi, and, C. L. Pon. 2000. Translation during cold adaptation does not involve mRNA-rRNA base pairing through the downstream box. RNA 6:13931402.
65. Lake, J. A. 1983. Evolving ribosome structure: domains in archaebacteria, eubacteria, and eucaryotes. Cell 33:318319.
66. Lake, J. A. 1985. Evolving ribosome structure: domains in archaebacteria, eubacteria, eocytes and eukaryotes. Annu. Rev. Biochem. 54:507530.
67. Lake, J, A.,, E. Henderson,, M. Oakes, and, M. W. Clark. 1984. Eocytes: a new ribosome structure indicates a kingdom with a close relationship to eukaryotes. Proc. Natl. Acad. Sci. USA 81:37863790.
68. Lamond, A. I., and, T. J. Gibson. 1990. Catalytic RNA and the origin of genetic systems. Trends Genet. 6:145149.
69. Lecompte, O.,, R. Ripp,, J. C. Thierry,, D. Moras, and, O. Poch. 2002. Comparative analysis of ribosomal proteins in complete genomes: an example of reductive evolution at the domain scale. Nucleic Acids Res. 30:53825390.
70. Lee, J. H.,, S. K. Choi,, A. Roll-Mecak,, S. K. Burley, and, T. E. Dever. 1999. Universal conservation in translation initiation revealed by human and archaeal homologs of bacterial translation initiation factor IF2. Proc. Natl. Acad. Sci. USA 96:43424347.
71. Lee, J. H.,, T. V. Pestova,, B. S. Shin,, C. Cao,, S. K. Choi, and, T. E. Dever. 2002. Initiation factor eIF5B catalyzes second GTP-dependent step in eukaryotic translation initiation. Proc. Natl. Acad. Sci. USA 99:1668916694.
72. Leibundgut, M.,, C. Frick,, M. Thanbichler,, A. Bock, and, N. Ban. 2005. Selenocysteine tRNA-specific elongation factor SelB is a structural chimaera of elongation and initiation factors. EMBO J. 24:1122.
73. Li, L., and, C. C. Wang. 2004. Capped mRNA with a single nucleotide leader is optimally translated in a primitive eu-karyote, Giardia lamblia. J. Biol. Chem. 279:1465614664.
74. Londei, P. 2005. Evolution of translational initiation: new insights from the archaea. FEMS Microbiol. Rev. 29:185200.
75. Londei, P.,, A. Teichner,, P. Cammarano,, M. De Rosa, and, A. Gambacorta. 1983. Particle weights and protein composition of the ribosomal subunits of the extremely thermoacidophilic archaebacterium Caldariella acidophila. Biochem. J. 209:461470.
76. Londei, P.,, J. Teixido,, M. Acca,, P. Cammarano, and, R. Amils. 1986. Total reconstitution of active large ribosomal subunits of the thermoacidophilic archaebacterium Sulfolobus solfataricus. Nucleic Acids Res. 14:22692285.
77. Lykke-Andersen, J.,, C. Aagaard,, M. Semionenkov, and, R. A. Garrett. 1997. Archaeal introns: splicing, intercellular mobility and evolution. Trends Biochem. Sci. 22:326331.
78. Mayer, C.,, C. Kohrer,, P. Grobner, and, W. Piendl. 1998. MvaL1 autoregulates the synthesis of the three ribosomal proteins encoded on the MvaL1 operon of the archaeon Methanococcus vannielii by inhibiting its own translation before or at the formation of the first peptide bond. Mol. Microbiol. 27:455468.
79. McCloskey, J. A., and, J. Rozenski. 2005. The Small Subunit rRNA Modification Database. Nucleic Acids Res. 33:D135D138.
80. Merrick, W. C. 1992. Mechanism and regulation of eukary-otic protein synthesis. Microbiol. Rev. 56:291315.
81. Mushegian, A. 2005. Protein content of minimal and ancestral ribosome. RNA 11:14001406.
82. Niewmierzycka, A., and, S. Clarke. 1999. S-Adenosylmethio-nine-dependent methylation in Saccharomyces cerevisiae. Identification of a novel protein arginine methyltransferase. J. Biol. Chem. 274:814824.
83. Nomura, M. 1973. Assembly of bacterial ribosomes. Science 179:864873.
84. Nomura, N.,, Y. Sako, and, A. Uchida. 1998. Molecular characterization and postsplicing fate of three introns within the single rRNA operon of the hyperthermophilic archaeon Aeropyrum pernix K1. J. Bacteriol. 180:36353643.
85. OʹConnor, M.,, T. Asai,, C. L. Squires, and, A. E. Dahlberg. 1999. Enhancement of translation by the downstream box does not involve base pairing of mRNA with the penultimate stem sequence of 16S rRNA. Proc. Natl. Acad. Sci. USA 96:89738978.
86. 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.
87. 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.
88. Orgel, L. E. 2004. Prebiotic chemistry and the origin of the RNA world. Crit. Rev. Biochem. Mol. Biol. 39:99123.
89. Peat, T. S.,, J. Newman,, G. S. Waldo,, J. Berendzen, and, T. C. Terwilliger. 1998. Structure of translation initiation factor 5A from Pyrobaculum aerophilum at 1.75 A resolution. Structure 6:12071214.
90. Pedulla, N.,, R. Palermo,, D. Hasenohrl,, U. Blasi,, P. Cammarano, and, P. Londei. 2005. The archaeal eIF2 homologue: functional properties of an ancient translation initiation factor. Nucleic Acids Res. 33:18041812.
91. Pestova, T. V, and, C. U. Hellen. 2001. Functions of eukary-otic factors in initiation of translation. Cold Spring Harbor Symp. Quant. Biol. 66:389396.
92. Pestova, T. V, and, V. G. Kolupaeva. 2002. The roles of individual eukaryotic translation initiation factors in ribosomal scanning and initiation codon selection. Genes Dev. 16:29062922.
93. Pestova, T. V.,, I. B. Lomakin,, J. H. Lee,, S. K. Choi,, T. E. Dever, and, C. U. Hellen. 2000. The joining of ribosomal subunits in eukaryotes requires eIF5B. Nature 403:332335.
94. Ramirez, C, A., K. E. Kopke,, D.-C. Yang,, T. Boeckh, and, A. T. Matheson. 1993. The structure, function and evolution of archaeal ribosomes, p. 439–466. In M. Kates,, D. Kushner, and, A. Matheson. (ed.), Biochemistry of Archaea. New Comprehensive Biochemistry Series, Elsevier, Amsterdam, The Netherlands.
95. Ringquist, S.,, D. Schneider,, T. Gibson,, C. Baron,, A. Bock, and, L. Gold. 1994. Recognition of the mRNA selenocysteine insertion sequence by the specialized translational elongation factor SELB. Genes Dev. 8:376385.
96. Rivera, M. C, and, J. A. Lake. 1992. Evidence that eukaryotes and eocyte prokaryotes are immediate relatives. Science 257:7476.
97. Roll-Mecak, A.,, P. Alone,, C. Cao,, T. E. Dever, and, S. K. Burley. 2004. X-ray structure of translation initiation factor eIF2gamma: implications for tRNA and eIF2alpha binding. J. Biol. Chem 279:1063410642.
98. Roll-Mecak, A.,, C. Cao,, T. E. Dever, and, S. K. Burley. 2000. X-Ray structures of the universal translation initiation factor IF2/eIF5B: conformational changes on GDP and GTP binding. Cell 103:781792.
99. Rother, M.,, A. Resch,, W. L. Gardner,, W. B. Whitman, and, A. Bock. 2001. Heterologous expression of archaeal seleno-protein genes directed by the SECIS element located in the 3ʹ non-translated region. Mol. Microbiol. 40:900908.
100. Rother, M.,, R. Wilting,, S. Commans, and, A. Bock.. 2000. Identification and characterisation of the selenocysteine-specific translation factor SelB from the archaeon Methanococcus jannaschi i. J. Mol. Biol. 299:351358.
101. Sanchez, M. E.,, P. Londei, and, R. Amils. 1996. Total reconstitution of active small ribosomal subunits of the extreme halophilic archaeon Haloferax mediterranei.. Biochim. Bio-phys. Acta 1292:140144.
102. Sanchez, M. E.,, D. Urena,, R. Amils, and, P. Londei. 1990. In vitro reassembly of active large ribosomal subunits of the halophilic archaebacterium Haloferax mediterranei. Biochemistry 29:92569261.
103. Sartorius-Neef, S., and, F. Pfeifer. 2004. In vivo studies on putative Shine-Dalgarno sequences of the halophilic archaeon Halobacterium salinarum. Mol. Microbiol. 51:579588.
104. Schmitt, E.,, S. Blanquet, and, Y. Mechulam. 2002. The large subunit of initiation factor aIF2 is a close structural homologue of elongation factors. EMBO J. 21:18211832.
105. Sensen, C. W.,, H. P. Klenk,, R. K. Singh,, G. Allard,, C. C. Chan,, et al 1996. Organizational characteristics and information content of an archaeal genome: 156 kb of sequence from Sulfolobus solfataricus P2. Mol. Microbiol. 22:175191.
106. Sette, M.,, P. van Tilborg,, R. Spurio,, R. Kaptein,, M. Paci,, et al 1997. The structure of the translational initiation factor IF1 from E. coli contains an oligomer-binding motif. EMBO J. 16:14361643.
107. Shean, C. S., and, M. E. Gottesman. 1992. Translation of the prophage lambda cl transcript. Cell 70:513522.
108. Si, K., and, U. Maitra. 1999. The Saccharomyces cerevisiae homologue of mammalian translation initiation factor 6 does not function as a translation initiation factor. Mol. Cell. Biol. 19:14161426.
109. Slupska, M. M.,, A. G. King,, S. Fitz-Gibbon,, J. Besemer,, M. Borodovsky, and, J. H. Miller. 2001. Leaderless transcripts of the crenarchaeal hyperthermophile Pyrobaculum aerophilum. J. Mol. Biol. 309:347360.
110. Song, H.,, P. Mugnier,, A. K. Das,, H. M. Webb,, D. R. Evans,, et al 2000. The crystal structure of human eukaryotic release factor eRF1—mechanism of stop codon recognition and pep-tidyl-tRNA hydrolysis. Cell 100:311321.
111. Tahara, M.,, A. Ohsawa,, S. Saito, and, M. Kimura. 2004. In vitro phosphorylation of initiation factor 2 alpha (aIF2 alpha) from hyperthermophilic archaeon Pyrococcus horikoshii OT3. J. Biochem. (Tokyo) 135:479485.
112. Teichner, A.,, P. Londei, and, P. Cammarano. 1986. Intralineage diversity of archaebacterial ribosomes. A dichotomy of ribosome features separates methanococcaceae and sulfur-dependent thermophiles from other archaebacterial taxa. J. Mol. Evol. 23:343353.
113. Tollervey, D. 1996. Small nucleolar RNAs guide ribosomal RNA methylation. Science 273:10561057.
114. Tolstrup, N.,, C. W. Sensen,, R. A. Garrett, and, I. G. Clausen. 2000. Two different and highly organized mechanisms of translation initiation in the archaeon Sulfolobus solfataricus. Extremophiles 4:175179.
115. Torarinsson, E.,, H. P. Klenk, and, R. A. Garrett. 2005. Divergent transcriptional and translational signals in Archaea. Environ. Microbiol. 7:4754.
116. Udagawa, T.,, Y. Shimizu, and, T. Ueda. 2004. Evidence for the translation initiation of leaderless mRNAs by the intact 70 S ribosome without its dissociation into subunits in eubacteria. J. Biol. Chem. 279:85398546.
117. Wang, H.,, D. Boisvert,, K. K. Kim,, R. Kim, and, S. H. Kim. 2000. Crystal structure of a fibrillarin homologue from Methanococcus jannaschii, a hyperthermophile, at 1.6 A resolution. EMBO J. 19:317323.
118. Woese, Woese. C. 2001. Translation: in retrospect and prospect. RNA 7:10551167.
119. Woese, C. R.,, O. Kandler, and, M. L. Wheelis. 1990. Towards a natural system of organisms: proposal for the domains Ar-chaea, Bacteria, and Eucarya. Proc. Natl. Acad. Sci. USA 87:45764579.
120. Woese, C. R.,, L. J. Magrum, and, G. E. Fox. 1978. Archaebacteria. J. Mol. Evol. 11:245251.
121. Yang, W., and, A. G. Hinnebusch. 1996. Identification of a regulatory subcomplex in the guanine nucleotide exchange factor eIF2B that mediates inhibition by phosphorylated eIF2. Mol. Cell. Biol. 16:66036616.
122. Yao, M.,, A. Ohsawa,, S. Kikukawa,, I. Tanaka, and, M. Kimura. 2003. Crystal structure of hyperthermophilic archaeal initiation factor 5A: a homologue of eukaryotic initiation factor 5A (eIF-5A). J. Biochem. (Tokyo) 133:7581.
123. Yatime, L.,, E. Schmitt,, S. Blanquet, and, Y. Mechulam. 2004. Functional molecular mapping of archaeal translation initiation factor 2. J. Biol. Chem. 279:1598415993.
124. Yatime, L.,, E. Schmitt,, S. Blanquet, and, Y. Mechulam. 2005. Structure-function relationships of the intact aIF2alpha subunit from the archaeon Pyrococcus abyssi. Biochemistry 44:87498756.
125. Yoshizawa, S.,, L. Rasubala,, T. Ose,, D. Kohda,, D. Fourmy, and, K. Maenaka. 2005. Structural basis for mRNA recognition by elongation factor SelB. Nat. Struct. Mol. Biol. 12:198203.
126. 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.
127. Zavialov, A. V.,, L. Mora,, R. H. Buckingham, and, M. Ehrenberg. 2002. Release of peptide promoted by the GGQ motif of class 1 release factors regulates the GTPase activity of RF3. Mol. Cell 10:789798.
128. Zhang, Y.,, P. V. Baranov,, J. F. Atkins, and, V. N. Gladyshev. 2005. Pyrrolysine and selenocysteine use dissimilar decoding strategies. J. Biol. Chem. 280:2074020751.
129. 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.


Generic image for table
Table 1.

Size and number of genes for ribosomal RNAs in

Citation: Londei P. 2007. Translation, p 175-197. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch8
Generic image for table
Table 2.

Differential protein composition of archaeal ribosomes

Citation: Londei P. 2007. Translation, p 175-197. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch8
Generic image for table
Table 3.

Translation initiation factors in

Citation: Londei P. 2007. Translation, p 175-197. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch8

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