The structure of a ribosomal protein S8/<i>spc</i> operon mRNA complex

Merianos, Helen J.; Wang, Jimin; Moore, Peter B.

doi:10.1261/rna.7030704

Cited by 58 publications

(51 citation statements)

References 37 publications

(63 reference statements)

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“…Like the example here, the RNAs interacting with both L1 and L10 are believed to act through mimicry of the rRNA binding sites (Nevskaya et al 2005;Iben and Draper 2008). Although there are narrowly distributed r-protein mRNA binding sites that are obvious mimics of the rRNA (e.g., that interacting S8) (Merianos et al 2004), most r-protein binding motifs showing obvious mimicry are broadly distributed.…”

Section: Discussionmentioning

confidence: 80%

“…Several of the mRNA structures form secondary or tertiary structures that appear to mimic the rRNA binding sites of their protein interaction partners. For example, the mRNA structures interacting with L1, L10(L12) 4 complex, S8, and L20 each bear striking resemblance to the rRNA binding sites for these proteins (Merianos et al 2004;Guillier et al 2005;Nevskaya et al 2005;Iben and Draper 2008). In other cases there is no clear resemblance between the mRNA and rRNA binding sites (Tang and Draper 1989;Mathy et al 2004).…”

Section: Introductionmentioning

confidence: 99%

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Bacterial RNA motif in the 5′ UTR of rpsF interacts with an S6:S18 complex

Deiorio-Haggar

Soo

et al. 2013

RNA

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Approximately half the transcripts encoding ribosomal proteins in Escherichia coli include a structured RNA motif that interacts with a specific ribosomal protein to inhibit gene expression, thus allowing stoichiometric production of ribosome components. However, many of these RNA structures are not widely distributed across bacterial phyla. It is increasingly common for RNA motifs associated with ribosomal protein genes to be identified using comparative genomic methods, yet these are rarely experimentally validated. In this work, we characterize one such motif that precedes operons containing rpsF and rpsR, which encode ribosomal proteins S6 and S18. This RNA structure is widely distributed across many phyla of bacteria despite differences within the downstream operon, and examples are present in both E. coli and Bacillus subtilis. We demonstrate a direct interaction between an example of the RNA from B. subtilis and an S6:S18 complex using in vitro binding assays, verify our predicted secondary structure, and identify a putative protein-binding site. The proposed binding site bears a strong resemblance to the S18 binding site within the 16S rRNA, suggesting molecular mimicry. This interaction is a valuable addition to the canon of ribosomal protein mRNA interactions. This work shows how experimental verification translates computational results into concrete knowledge of biological systems.

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Section: Discussionmentioning

confidence: 80%

Section: Introductionmentioning

confidence: 99%

Bacterial RNA motif in the 5′ UTR of rpsF interacts with an S6:S18 complex

Deiorio-Haggar

Soo

et al. 2013

RNA

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“…Numerous studies have shown that the similarity between these two types of binding sites is detectable at the structural level (Serganov et al 2003;Merianos et al 2004;Nevskaya et al 2005), and sometimes they also share common sequence patterns (Olins and Nomura 1981;Iben and Draper 2008). The regulatory sites can be conserved in closely related bacteria (Robert and Brakier-Gingras 2001;Aseev et al 2008), between different bacterial phyla (Fu et al 2013), or even between domains of life (Kraft et al 1999), but in many cases they appear to have originated independently in the individual taxonomic groups (Allen et al 1999;Springer and Portier 2003).…”

Section: Introductionmentioning

confidence: 99%

S6:S18 ribosomal protein complex interacts with a structural motif present in its own mRNA

Matelska

Purta

Panek

et al. 2013

RNA

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Prokaryotic ribosomal protein genes are typically grouped within highly conserved operons. In many cases, one or more of the encoded proteins not only bind to a specific site in the ribosomal RNA, but also to a motif localized within their own mRNA, and thereby regulate expression of the operon. In this study, we computationally predicted an RNA motif present in many bacterial phyla within the 5 ′ untranslated region of operons encoding ribosomal proteins S6 and S18. We demonstrated that the S6:S18 complex binds to this motif, which we hereafter refer to as the S6:S18 complex-binding motif (S6S18CBM). This motif is a conserved CCG sequence presented in a bulge flanked by a stem and a hairpin structure. A similar structure containing a CCG trinucleotide forms the S6:S18 complex binding site in 16S ribosomal RNA. We have constructed a 3D structural model of a S6:S18 complex with S6S18CBM, which suggests that the CCG trinucleotide in a specific structural context may be specifically recognized by the S18 protein. This prediction was supported by site-directed mutagenesis of both RNA and protein components. These results provide a molecular basis for understanding protein-RNA recognition and suggest that the S6S18CBM is involved in an auto-regulatory mechanism.

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“…The third C-DTJ, 1S03-37, is present in the mRNA of operon spc complexed with the ribosomal protein S8 ( Fig. 11D; Merianos et al 2004), while the fourth one, 1XJR-40, is found in the stem-loop II motif (abbreviated as s2m) of the RNA element in the genome of the SARS virus ( Fig. 11E; Robertson et al 2005).…”

Section: C-dtjsmentioning

confidence: 99%

“…Motif 1S03-37 is present in the mRNA of the spc operon of E. coli (Merianos et al 2004). Motif 1XJR-40 exists in the RNA element of the stem-loop II motif (s2m) of the genome of the SARS virus (Robertson et al 2005).…”

Section: C-dtjsmentioning

confidence: 99%

Twist-joints and double twist-joints in RNA structure

Boutorine

Steinberg

2012

RNA

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Analysis of available RNA crystal structures has allowed us to identify a new family of RNA arrangements that we call double twist-joints, or DTJs. Each DTJ is composed of a double helix that contains two bulges incorporated into different strands and separated from each other by 2 or 3 bp. At each bulge, the double helix is over-twisted, while the unpaired nucleotides of both bulges form a complex network of stacking and hydrogen-bonding with nucleotides of helical regions. In total, we identified 14 DTJ cases, which can be combined in three groups based on common structural characteristics. One DTJ is found in a functional center of the ribosome, another DTJ mediates binding of the pre-tRNA to the RNase P, and two more DTJs form the sensing domains in the glycine riboswitch.

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The structure of a ribosomal protein S8/spc operon mRNA complex

Cited by 58 publications

References 37 publications

Bacterial RNA motif in the 5′ UTR of rpsF interacts with an S6:S18 complex

Bacterial RNA motif in the 5′ UTR of rpsF interacts with an S6:S18 complex

S6:S18 ribosomal protein complex interacts with a structural motif present in its own mRNA

Twist-joints and double twist-joints in RNA structure

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