Initiation of mRNA translation in bacteria: structural and dynamic aspects

Abstract

Initiation of mRNA translation is a major checkpoint for regulating level and fidelity of protein synthesis. Being rate limiting in protein synthesis, translation initiation also represents the target of many post-transcriptional mechanisms regulating gene expression. The process begins with the formation of an unstable 30S pre-initiation complex (30S pre-IC) containing initiation factors (IFs) IF1, IF2 and IF3, the translation initiation region of an mRNA and initiator fMet-tRNA whose codon and anticodon pair in the P-site following a first-order rearrangement of the 30S pre-IC produces a locked 30S initiation complex (30SIC); this is docked by the 50S subunit to form a 70S complex that, following several conformational changes, positional readjustments of its ligands and ejection of the IFs, becomes a 70S initiation complex productive in initiation dipeptide formation. The first EF-G-dependent translocation marks the beginning of the elongation phase of translation. Here, we review structural, mechanistic and dynamical aspects of this process.

Eukaryotic aspects of translation initiation brought into focus

“…Owing to the large investment of energy involved in translation, this entire process is tightly regulated at the stage of initiation, reducing the wasteful expenditure of resources. In eubacteria, translation initiation is facilitated by two universally conserved factors, IFs (initiation factors) 1 (note that this homologue of eubacterial IF1 in eukaryotes is named eIF1A: eIF1 is a separate factor) and 2, and a region of rRNA dubbed the anti-Shine-Dalgarno sequence [1,2]. The position of the first codon within the decoding site is established by base pairing between the Shine-Dalgarno sequence, located upstream of the first codon within the mRNA, and its complement within the ribosomal rRNA [2].…”

“…IF1 binds within the A-site, preventing its premature occupation by a further tRNA and favouring mRNA association, while IF2 stabilizes recruited formyl-methionyl-tRNAi within the P-site and remains bound, blocking the initiation process from continuing until the large subunit joins the small subunit. The selection of cognate tRNAi and formation of the proper codon-anticodon interaction are kinetically favoured, but reversible, occurring stochastically [1]. Joining of the large subunit leads to the only irreversible step in eubacterial translation initiation, GTP hydrolysis by IF2, releasing GDP and Pi; the factors then depart, allowing translation elongation to begin [1].…”

“…The selection of cognate tRNAi and formation of the proper codon-anticodon interaction are kinetically favoured, but reversible, occurring stochastically [1]. Joining of the large subunit leads to the only irreversible step in eubacterial translation initiation, GTP hydrolysis by IF2, releasing GDP and Pi; the factors then depart, allowing translation elongation to begin [1].…”

Four translation initiation pathways employed by the leaderless mRNA in eukaryotes

“…IF2 is known to stabilize both the initiator tRNA and mRNA binding to the bacterial ribosome1617. According to kinetic studies, IF2 and Met-tRNA Met f association usually precedes mRNA binding to the 30 S subunit, although the precise order is thought to depend on a particular mRNA species16.…”

Noncanonical Translation Initiation Comes of Age

“…This mode of initiation, where the SD is a major component of the ribosome binding site (RBS), is widespread in bacteria and archaea and has until recently been inferred to be the dominant initiation pathway. The model posits that the SD-aSD interaction increases the local concentration of 30S ribosomal subunits in the vicinity of the initiation codon, facilitating subsequent events in initiation complex formation (1). Systematic approaches in Escherichia coli have demonstrated the influence of SD length and its distance from the initiation codon (2).…”