Archaeal Ribosomes

Abstract

Ribosomes, the essential cellular organelles carrying out protein synthesis, have a basic design that is fundamentally conserved in all three kingdoms of life (Archaea, Bacteria and Eukarya). Nevertheless, there are ribosomal features specific of each kingdom. Archaeal ribosomes have a size and composition similar to those of their bacterial counterparts: they contain three ribonucleic acid (RNA) molecules, 16S, 23S and 5S RNA and 50–70 proteins depending on the species. However, the primary structures of both archaeal ribosomal RNA and r‐proteins are closer to those of eukaryotes. As many Archaea have adapted to function under conditions of extreme salt or temperature, their ribosomal components are highly resistant to such adverse conditions, and the overall ribosome structure often has an higher rigidity than that of mesophilic microorganisms. This makes archaeal ribosomes optimally suited for crystallographic studies, and in fact, high‐resolution three‐dimensional structures have been obtained with ribosomal crystals from halophilic and thermophilic Archaea. These studies pioneered the resolution at the atomic level of ribosome architecture, a feat that won the 2009 Nobel Prize in Chemistry to Ada Yonath, Thomas Steitz and Venki Ramakrishnan.

Key Concepts:

  • Ribosome structure is very well conserved in all cells. In Archaea, the small ribosomal subunits have certain structural features (‘bill’ and ‘lobes’) also seen in Eukarya but not in Bacteria.

  • Archaeal ribosomes are composed of 30S and 50S subunits that join to make a 70S particle. They contain 3 rRNA molecules (16S, 23S and 5S) and up to 68 ribosomal proteins.

  • The primary sequences of both archaeal rRNA and r‐proteins are closer to those of eukaryotes than to those of bacteria. All of the archaeal r‐proteins are represented in eukaryotes, whereas no r‐proteins are shared by Archaea and Bacteria only.

  • Archaeal ribosomes have a heterogeneous protein composition. Early branching Archaea (Crenarchaeota) tend to have protein‐richer ribosomes, whereas late‐branching species (halobacteriales, Thermoplasmatales) tend to have protein‐poorer ribosomes.

  • The ribosomes of the extremophilic Archaea show specific adaptations to harsh environmental conditions. In general, they have a more rigid structure than mesophilic ribosomes. Halophilic ribosomes increase their hydration capacity by having acidic instead of basic ribosomal proteins.

Keywords: Archaea; ribosomes; r‐proteins; rRNAs; adaptation to extreme environments

Figure 1.

(a) Large, and (b) small ribosomal subunits, illustrating some distinguishing features seen by electron microscopy. (c) Small ribosomal subunits from different kingdoms have the same overall structure, but with slight perceived variations.

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References

Amann G, Stetter KO, Llobet‐Brossa E, Amann R and Antón J (2000) Direct proof for the presence and expression of two 5% different 16S rRNA genes in individual cells of Haloarcula marismortui. Extremophiles 4: 373–376.

Amils R, Cammarano P and Londei P (1993) Translation in Archaea. Amsterdam: Elsevier.

Bachellerie JP, Cavaille J and Huttenhofer A (2002) The expanding snoRNA world. Biochimie 84: 775–790.

Ban N, Nissen P, Hansen J, Moore PB and Steitz TA (2000) The complete atomic structure of the large ribosomal subunit at 2.4 A resolution. Science 289: 905–920.

Briganti G, Giordano R, Londei P and Pedone F (1998) Small angle neutron scattering analysis of thermal stability of 23S rRNA and the intact 50S subunits of Sulfolobus solfataricus. Biochimica et Biophysica Acta 1379: 297–301.

Cammarano P, Mazzei F, Londei P et al. (1983) Secondary structure features of ribosomal RNA species within intact ribosomal subunits and efficiency of RNA‐protein interactions in thermoacidophilic (Caldariella acidophila, Bacillus acidocaldarius) and mesophilic (Escherichia coli) bacteria. Biochimica et Biophysica Acta 740: 300–312.

Cui HL, Zhou PJ, Oren A and Liu SJ (2009) Intraspecific polymorphism of 16S rRNA genes in two halophilic archaeal genera, Haloarcula and Halomicrobium. Extremophiles 13: 31–37.

Garrett RA, Dalgaard J, Larsen N, Kjems J and Mankin AS (1991) Archaeal rRNA operons. Trends in Biochemical Sciences 16: 22–26.

Green R and Noller HF (1997) Ribosomes and translation. Annual Review of Biochemistry 66: 679–716.

Kiss T (2001) Small nucleolar RNA‐guided post‐transcriptional modification of cellular RNAs. EMBO Journal 20: 3617–3622.

Kiss T (2002) Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse cellular functions. Cell 109: 145–148.

Kjems J and Garrett RA (1991) Ribosomal RNA introns in archaea and evidence for RNA conformational changes associated with splicing. Proceedings of the National Academy of Sciences of the USA 88: 439–443.

Lake JA (1983) Ribosome evolution: the structural bases of protein synthesis in archaebacteria, eubacteria, and eukaryotes. Progress in Nucleic Acid Research and Molecular Biology 30: 163–194.

Lake JA, Henderson E, Clark MW and Matheson AT (1982) Mapping evolution with ribosome structure: intralineage constancy and interlineage variation. Proceedings of the National Academy of Sciences of the USA 79: 5948–5952.

Lecompte O, Ripp R, Thierry JC, Moras D and Poch O (2002) Comparative analysis of ribosomal proteins in complete genomes: an example of reductive evolution at the domain scale. Nucleic Acids Research 30: 5382–5390.

Londei P, Teichner A, Cammarano P, De Rosa M and Gambacorta A (1983) Particle weights and protein composition of the ribosomal subunits of the extremely thermoacidophilic archaebacterium Caldariella acidophila. Biochemical Journal 209: 461–470.

McCloskey JA and Rozenski J (2005) The small subunit rRNA modification database. Nucleic Acids Research 33: D135–D138.

Mushegian A (2005) Protein content of minimal and ancestral ribosome. RNA 11: 1400–1406.

Rivera MC and Lake JA (1992) Evidence that eukaryotes and eocyte prokaryotes are immediate relatives. Science 257: 74–76.

Tollervey D (1996) Small nucleolar RNAs guide ribosomal RNA methylation. Science 273: 1056–1057.

Woese CR and Fox GE (1977) Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proceedings of the National Academy of Sciences of the USA 74: 5088–5090.

Woese CR, Kandler O and Wheelis ML (1990) Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proceedings of the National Academy of Sciences of the USA 87: 4576–4579.

Further Reading

Cavicchioli R (ed.) (2007) Archaea: Molecular Cell Biology. Washington, DC: ASM Press.

Garrett RA and Klenk H‐P (eds) (2006) Archaea : Physiology, Molecular Biology and Evolution. Malden, MA; Oxford, UK; Carlton, Australia: Blackwell Publishing.

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How to Cite close
Londei, Paola(Dec 2010) Archaeal Ribosomes. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0000293.pub2]