The canonical translation initiation mechanism involves base pairing between the mRNA and 16S rRNA. However, a variety of identified mechanisms deviate from this conventional route. Beck and Janssen (J Bacteriol 199:e00091-17, 2017, https://doi.org/10.1128/JB.00091-17) have recently described another noncanonical mode of translation initiation. Here, we describe how this process differs from previously reported mechanisms, with the hope that it will foster increased awareness of the diversity of regulatory mechanisms that await discovery.
The standard model for initiation of translation in bacteria involves base pairing between a Shine-Dalgarno (SD) sequence upstream of the start codon and the complementary anti-SD (aSD) sequence at the 3= end of 16S rRNA in a 30S ribosomal subunit. 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). In general, longer SD elements support increased expression; however, the relationship is nonlinear, and binding affinity alone does not fully explain the observed protein expression levels. Weaker SD sequences are particularly susceptible to the effects of mRNA decay and transcription termination (3), while extended (8-to 10-nucleotide [nt]) SD sequences inhibit translation, presumably since such sequences trap the ribosome on the RBS (4). Among E. coli genes, the average SD length is 6.3 nt (5), and the average spacing between the SD and initiation codon is 4.4 nt (4). The SD sequences from Bacillus subtilis, in general, are longer than their E. coli counterparts (6), a property that may be linked to the absence of a large ribosomal protein bS1 in many Gram-positive organisms (7).30S subunit binding and effective initiation is heavily influenced by the mRNA structure surrounding the RBS. Many of the gene regulatory mechanisms that target initiation operate by altering the local RNA structure encompassing SD sequences. These mechanisms include translational coupling, where translation of an upstream open reading frame (uORF) disrupts the RNA structure surrounding the downstream RBS. The binding of small regulatory RNAs or RNA binding proteins, metabolites (in riboswitches), or increases in temperature (in thermosensors) can all influence the local RNA structure, with corresponding effects on initiation. An additional model is required to explain how certain mRNAs with RBSs sequestered in stable structures can be translated effectively. The "standby binding" model posits that 30S subunits bind first to single-stranded RNA flanking the structured, RBS-containing element. The bou...