The Ribosome: Some Hard Facts about Its Structure and Hot Air about Its Evolution

Abstract

Ribosomes from all species consist of approximately two-thirds RNA and one-third protein.Ribosomes from mammalian mitochondria are an exception, with the ratio of protein and RNA reversed (see Sharma et al. 2003).All ribosomes consist of two subunits, termed 50S and 30S in bacteria or 60S and 40S in eukaryotes.Together, they comprise the 70S ribosome in bacteria or the 80S ribosome in eukaryotes (Fig. 1A).The mRNA containing the genetic template binds in a cleft in the small subunit.The amino acids themselves are brought into the ribosome by aminoac ylated tRNA substrates.The ribosome has three binding sites for tRNA: the A (aminoacyl) site that brings the new aminoacyl tRNA, the P (peptidyl) site that holds the nascent peptide chain, and the E (exit) site to which the deacylated P-site tRNA moves after peptide bond formation (Fig. 1B).Translation in all species can be divided into three stages (Fig. 2) (for review, see Schmeing and Ram a krishnan 2009).During initiation, the small subunit of the ribosome binds mRNA at the start site of the coding sequence, in a precise manner that puts the start codon in the P site.This requires three initiation factors and a special initiator tRNA that binds to the P site.Initiation is followed by the elongation cycle, which consists of three important steps: decoding, peptidyl transfer, and translocation.During decoding, the correct aminoacyl tRNA, which is delivered to the A site of the ribosome as a ternary complex with elongation factor Tu (EF-Tu) and GTP, is selected based on the codon on the mRNA in the A site.Selection of the tRNA leads to hydrolysis of GTP by EF-Tu and release of the factor from the ribosome.The aminoacyl end of the selected tRNA then swings into the peptidyl transferase center (PTC) in the 50S subunit of the ribosome, where peptide bond formation occurs rapidly and spontaneously.*The title is a paraphrase of one by the late eminent crystallographer David M. Blow: "Hard facts on structure: Hot air about mobility" (Nature [1982] 297: 454-455).