Ribosomes are the universal cellular ribozymes (RNA enzymes) responsible for the translation of the genetic code into proteins. Their structures have become available during the last decade by X-ray crystallography using synchrotron radiation. Digging into these structures has revealed a remnant of a prebiotic machine for chemical bonding that is still functioning within all contemporary ribosomes. These multi-component riboprotein assemblies are of molecular weights of 2.5 MDa and 4 MDa (for prokaryotic and eukaryotic sources, respectively). Even in bacteria they contain over 4500 RNA nucleotides and 52 different proteins. Structure analysis accompanied by biochemical assays indicated that, despite the size difference, the ribosome functional regions, namely the decoding centre and the active site (peptidyl transferase centre, PTC), are composed of ribosomal RNA (rRNA), and are highly conserved across all domains of life.

In the contemporary ribosome, the PTC is situated in the centre of a universal semi-symmetrical substructure composed of 180 nucleotides, an unusual feature of the otherwise asymmetric ribosome. The architecture of this structural element positions the ribosome’s substrates in favourable stereochemistry for peptide bond formation and nascent protein elongation as well as for substrate-mediated catalysis. It thus provides all of the ribosome’s catalytic contributions for peptide bond formation and confines the void required for the motions involved in substrate translocation within the PTC.

This internal symmetry substructure exists in all known ribosome high-resolution structures and its exceptionally high sequence conservation (over 95%) indicates its ancient origin. This entity has a pocket-shape structure that seems to be a relic of an ancient ribozyme, which was capable of catalysing various reactions, including peptide bond formation and non-coded amino acid polymerisation. This dimeric RNA assembly could be formed from two self-folded RNA chains of identical, similar or different sequences, spontaneously or by gene duplication or gene fusion. Based on the presumed capability of the prebiotic ‘pocket-like’ construct to accommodate substrates with stereochemistry enabling peptide bond formation, it is suggested that the semi-symmetrical region of the contemporary ribosome originated from a semi symmetrical entity, which we named 'proto-ribosome'.

The fold of each half of this semi-symmetrical region is similar to motifs that have been identified in various natural ribozymes (e.g.gene regulators, riboswitches, RNA polymerases, ribozymes catalysing phosphodiester cleavage, RNA processing and RNA modification). Some of these ribozymes are believed to be relics from the prebiotic world and hence are supposed to be sufficiently stable to survive environmental alterations and evolution stresses.

Dimerisation in a symmetrical manner could have occurred by utilising chemical complementarity obtained by tertiary interactions (e.g. the common GNRA system that includes the abundant and ubiquitous ‘A-minor’ structural motif), or assisted by other molecules acting as small chaperones that offer stabilisation. Additional structural support could be obtained from short peptides that have high affinity to RNA, or from oligo peptides that could form structural arrangements similar to protein/RNA interactions within the contemporary ribosome. These short peptides could have been produced without carrying coded sequences. According to this suggestion, a proto-ribosome that produced peptides with amino acid composition that was sufficiently biased in order to fulfil simple tasks was provided with better fitness, thus had higher probability to be retained.

We are assessing the feasibility of a dimeric proto-ribosome capable of the formation of chemical bonds according to the following scheme. We are first testing the tendency of various RNA chains to dimerise. These are tested for their ability to bind small molecules, nucleotides and amino acids conjugated with short nucleotides, and then to form chemical bonds between them. Among the various RNA segments that have been constructed, several, albeit not all, chains with sequences resembling those observed in the current ribosome, are capable of forming dimers that may adopt a ‘pocket-like’ structure. Specifically, a marked preference was detected for the dimerisation of sequences resembling the P-region, including those that underwent mutational alterations by in vitro site-directed mutagenesis. This noticeable preference may indicate a higher stability of this portion of the symmetrical region, or its higher significance in nascent chain elongation. This is in accord with the contemporary accommodation of the initial tRNA at the P-site of the PTC, in which each half hosts a slightly different substrate.

The emergence of coded translation that includes the growing complexity of the ribosome into the size and shape allowing programmed translation occurred after those oligopeptides that were produced accidentally but found useful in the RNA world, survived and formed some kind of replication machinery. Co-evolution of the proto-ribosome into the modern complex molecular machine dictated the production of carriers that could decode this code while bound to the cognate amino acid, namely the tRNA molecules.

 

Principal publication and authors

M.J. Belousoff (a), C. Davidovich (a), E. Zimmerman (a), Y. Caspi (a,b), I. Wekselman (a), L. Rozenszajn (a,c), T. Shapira (a), O. Sade-Falk (a,d), L. Taha (a,d), A. Bashan (a), M.S. Weiss (e) and A. Yonath (a), Biochemical Society Transactions 38, 422–427 (2010).
(a) The Department of Structural Biology, Weizmann Institute, Rehovot (Israel)
(b) Present address: Harvard FAS Center for Systems Biology, Cambridge, MA (USA)
(c) Present address: University of Toronto, Ontario (Canada)
(d) Present address: Hebrew University of Jerusalem (Israel)
(e) EMBL Hamburg Outstation, c/o DESY, Hamburg (Germany)