Domains two and three of Escherichia coli ribosomal S1 protein confers 30S subunits a high affinity for downstream A/U-rich mRNAs

S1, a multi-domain ribosomal protein associated with the 30S subunit, is essential for translation initiation. S1 binds with high affinity to single-stranded mRNA containing A/U-rich patches upstream of the start codon. It was previously reported that domains 1-3 of S1 protein play a role in the docking and unfolding of structured mRNAs to the ribosome. Moreover, S1-deficient 30S subunits are still able to bind to low structured mRNAs. However, mRNAs containing A/U-rich patches in the early base positions after start codon enhance protein synthesis and mRNA binding to the ribosome, which suggests that S1 is also able to interact with these A/U-rich regions. To evaluate the essentiality of S1 domains in the binding to low structured mRNAs containing A/U/G nucleotides after the start codon as well as their role in translation and cell viability, S1 protein deletion variants were generated. We show that S1 domain 3 is necessary to discriminate these mRNAs according to the nucleotide nature since its absence abrogated S1 binding to A/U-rich mRNAs and allowed binding to G-rich mRNAs. Interestingly, domains 2 and 3 were required for the binding of mRNAs containing A/U-rich sequences after the start codon to 30S, in vitro translation and cell viability.