S1 Ribosomal Protein Functions in Translation Initiation and Ribonuclease RegB Activation Are Mediated by Similar RNA-Protein Interactions

Abstract

The ribosomal protein S1, in Escherichia coli, is necessary for the recognition by the ribosome of the translation initiation codon of most messenger RNAs. It also participates in other functions. In particular, it stimulates the T4 endoribonuclease RegB, which inactivates some of the phage mRNAs, when their translation is no longer required, by cleaving them in the middle of their Shine-Dalgarno sequence. In each function, S1 seems to target very different RNAs, which led to the hypothesis that it possesses different RNA-binding sites. We previously demonstrated that the ability of S1 to activate RegB is carried by a fragment of the protein formed of three consecutive domains (domains D3, D4, and D5). The same fragment plays a central role in all other functions. We analyzed its structural organization and its interactions with three RNAs: two RegB substrates and a translation initiation region. We show that these three RNAs bind the same area of the protein through a set of systematic (common to the three RNAs) and specific (RNA-dependent) interactions. We also show that, in the absence of RNA, the D4 and D5 domains are associated, whereas the D3 and D4 domains are in equilibrium between open (noninteracting) and closed (weakly interacting) forms and that RNA binding induces a structural reorganization of the fragment. All of these results suggest that the ability of S1 to recognize different RNAs results from a high adaptability of both its structure and its binding surface.

Ribosomal protein S1 unwinds double-stranded RNA in multiple steps

“…Consistent with this assignment, NMR studies on truncated S1 with only D3-5 showed that even in the absence of RNA, D4 and D5 are tightly associated, whereas D3 is loosely connected to D4 (40). When binding to RNA, there is a conformational change of the linker between D3 and D4, and all three domains bind to the RNA with similar RNA-protein interactions (40). Based on the results described above, we propose a minimum model for S1 interaction with RNA secondary structures (Fig.…”

“…To complete a 10 nt total binding size, the hidden step would be from binding of another single RNA-binding domain. Consistent with this assignment, NMR studies on truncated S1 with only D3-5 showed that even in the absence of RNA, D4 and D5 are tightly associated, whereas D3 is loosely connected to D4 (40). When binding to RNA, there is a conformational change of the linker between D3 and D4, and all three domains bind to the RNA with similar RNA-protein interactions (40).…”

Downregulation of Chloroplast RPS1 Negatively Modulates Nuclear Heat-Responsive Expression of HsfA2 and Its Target Genes in Arabidopsis

“…The modern chloroplast maintains a circular genome and transcription and translation machinery similar to that of its evolutionary precursor [74], [75]. In E. coli , ribosomal protein S1 contains six S1 domains that are essential for RNA binding and is an essential protein required for the translation of most transcripts [57], [59], [60]. Based on the molecular diversity analysis, RPS1s in prokaryotes have been classified into four types depending on their functional reliability of translation initiation [58].…”

“…In this study, we have identified chloroplast ribosomal protein S1 (RPS1) as a heat-responsive protein through proteomic screening of heat-responsive proteins. In Escherichia coli , RPS1, the largest ribosomal protein, is involved in the process of mRNA recognition and binding by the 30S ribosomal subunit to the translation initiation site [57]–[59]. The RPS1 in E. coli consists of six repetitions of a conserved structural domain, called S1 domain, which is found in many other proteins involved in RNA metabolism in all organisms [57], [58].…”

“…In Escherichia coli , RPS1, the largest ribosomal protein, is involved in the process of mRNA recognition and binding by the 30S ribosomal subunit to the translation initiation site [57]–[59]. The RPS1 in E. coli consists of six repetitions of a conserved structural domain, called S1 domain, which is found in many other proteins involved in RNA metabolism in all organisms [57], [58]. In bacteria, RPS1 is believed to facilitate the binding of the 30S small ribosomal subunit near the initiation codon of the transcripts [59], [60].…”