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Chapter 8 : Translation
Category: Microbial Genetics and Molecular Biology; Environmental Microbiology
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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.
Comparison of 16S RNA secondary structure in archaea and bacteria. Secondary structure models are shown for one archaeal 16S rRNA (S. solfataricus) and one bacterial (E. coli) 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 http://www.rna.icmb.utexas.edu/. The details of the database are described in reference 17 .
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. ( 69 ).
(See the separate color insert for the color version of this illustration.) Organization of the main ribosomal protein gene clusters in archaeal genomes. SSO, Sulfolobus solfataricus; STO, Sulfolobus tokodaii; AFU, Archaeoglobus fulgidus; APE, Aeropyrum pernix; PFU, Pyrococcus furiosus; PHO, Pyrococcus horikoshii; PAB, Pyrococcus abyssi; TKO, Thermococcus kodakaraensis; PAE, Pyrobaculum aerophylum; MKA, Methanopyrus kandleri; MMA, Methanosarcina mazei; MAC, Methanosarcina acetivorans; MTH, Methanothermobacter thermautotrophicus; MJA, Methanococcus jannaschii; MMP, Methanococcus maripaludis; HMA, Haloarcula marismortui; H-sp, Halobacterium sp. NRC1; TAC, Thermoplasma acidophilum; TVO, Thermoplasma volcanii. The last line (ECO) shows for comparison the organization of the same genes in E. coli 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.
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.
Sizea and numberb of genes for ribosomal RNAs in Archaea
Differential protein composition of archaeal ribosomes
Translation initiation factors in Archaea