Structural features of the binding site for ribosomal protein S8 in
            <i>Escherichia coli</i>
            16S rRNA defined using NMR spectroscopy

Kalurachchi, K.; Uma, K.; Zimmermann, Ra; Nikonowicz, Edward P.

doi:10.1073/pnas.94.6.2139

Cited by 38 publications

(18 citation statements)

References 26 publications

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“…This hairpin has obvious structural similarities to the demonstrated S8 binding site in 16S rRNA (Fig. 4B) (9,16,18,26). Comparison of the sequences of the spc operons showed that a hairpin similar to the S8 target hairpin of E. coli could form in V. cholerae (Fig.…”

Section: Fig 1 (A)mentioning

confidence: 99%

“…The contrast between the widespread organization of the major r-protein gene cluster and the much more limited distribution of the E. coli regulatory paradigms suggests that the regulatory mechanisms developed much later than the gene cluster itself. (4,9,15) and on E. coli spc mRNA (5) are indicated by filled boxes. The same region is also required for S8-mediated regulation of the spc operon in E. coli (2,26).…”

Section: Fig 1 (A)mentioning

confidence: 99%

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Regulation of Ribosomal Protein Synthesis in Vibrio cholerae

et al. 2004

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We have investigated the regulation of the S10 and spc ribosomal protein (r-protein) operons in Vibrio cholerae. Both operons are under autogenous control; they are mediated by r-proteins L4 and S8, respectively. Our results suggest that Escherichia coli-like strategies for regulating r-protein synthesis extend beyond the enteric members of the gamma subdivision of proteobacteria.In organisms as diverse as eubacteria, archaea, protist cyanelles, chloroplasts, and mitochondria, clusters of ribosomal protein (r-protein) genes are remarkably similar in organization (10,23,24). In spite of this striking degree of conservation, the mechanisms behind the expression of these genes are clearly diverse, since the positions of promoters and terminators are not well conserved. For example, in Escherichia coli, 28 r-protein genes in the S10-spc-alpha cluster are organized into three transcription units (12), but the corresponding genes in Bacillus subtilis are organized into a single transcription unit (8,11,21).In E. coli, most of the r-proteins are under autogenous control. That is, for a given r-protein operon, a specific rprotein has evolved to function not only as a component of the ribosome, but also as a regulatory protein responsible for coordinating expression of its operon with the availability of rRNA and other r-proteins (28). The 11-gene S10 operon of E. coli is regulated by r-protein L4, a component of the large ribosomal subunit, and encoded by the third gene of the operon. Unlike other autogenously controlled r-protein operons, which are regulated at the level of translation, the S10 operon is subject to both transcriptional and translational regulation (30). The two control mechanisms require partially overlapping but distinct determinants within the 172-base nontranslated region of the S10 mRNA (3,19).Previous studies have suggested that L4 proteins from species as divergent from E. coli as Bacillus stearothermophilus have maintained the determinants required for autogenous control of the S10 operon in E. coli (11,31). However, the autogenous control mechanism itself appears not to be so well conserved. For example, examination of potential secondary structures of RNA upstream of the S10 gene in other eubacterial species suggests that only a subset of species, confined to some members of the gamma branch of proteobacteria, have the structural determinants in the S10 leader that are necessary for L4-mediated autogenous control in E. coli (reference 1 and unpublished data). Moreover, when heterologous S10 leaders which can form those critical secondary structures are introduced into E. coli, they function as regulatory targets for L4, while those that do not have the potential to form the structures found in the E. coli S10 leader do not function as regulatory elements (1, 11).To directly address the mechanism for regulating r-protein synthesis within other eubacteria, we characterized the regulation of the S10 and spc operons in Vibrio cholerae, the most divergent of the gamma proteobacteria we suspected of...

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Section: Fig 1 (A)mentioning

confidence: 99%

Section: Fig 1 (A)mentioning

confidence: 99%

Regulation of Ribosomal Protein Synthesis in Vibrio cholerae

et al. 2004

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“…A solution structure has been obtained by NMR for an RNA oligonucleotide containing the S8-binding portion of helix 21 from E. coli 16S rRNA in the absence of S8 (Kalurachchi et al 1997). The family of structures reported has six members, which have an rmsd of 1.15 Å to the average, and within the S8-binding site, the average NMR structure superimposes on the crystal structure of mRNA1a with an rmsd of 1.5 Å (phosphorus atoms).…”

Section: Comparison Of Rna-binding Ligands Of Ribosomal Protein S8mentioning

confidence: 99%

“…In the ribosome, S8 binds to a site that includes sequences from helices 19,20,21,25, and 26a of 16S rRNA (Brodersen et al 2002), but biochemical experiments have shown that the interaction with helix 21 is energetically dominant (Mougel et al 1986). The secondary structures of the relevant region of helix 21 in the 16S rRNAs from T. thermophilus (Wimberly et al 2000) and E. coli (Kalurachchi et al 1997) are compared in Figure 1, A and 1B. The S8-binding sequence in the spc operon mRNA (Gregory et al 1988;Mattheakis and Nomura 1988) appears capable of adopting a similar secondary structure (Fig.…”

Section: Introductionmentioning

confidence: 99%

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

Merianos¹,

Wang²,

Moore³

2004

RNA

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In bacteria, translation of all the ribosomal protein cistrons in the spc operon mRNA is repressed by the binding of the product of one of them, S8, to an internal sequence at the 5 end of the L5 cistron. The way in which the first two genes of the spc operon are regulated, retroregulation, is mechanistically distinct from translational repression by S8 of the genes from L5 onward. A 2.8 Å resolution crystal structure has been obtained of Escherichia coli S8 bound to this site. Despite sequence differences, the structure of this complex is almost identical to that of the S8/helix 21 complex seen in the small ribosomal subunit, consistent with the hypothesis that autogenous regulation of ribosomal protein synthesis results from conformational similarities between mRNAs and rRNAs. S8 binding must repress the translation of its own mRNA by inhibiting the formation of a ribosomal initiation complex at the start of the L5 cistron.

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“…The similarity of cleavage patterns across virtually all the derivatized positions at helix 21 leads to the speculation that this helix can assume its tertiary structure in a minimal particle during biogenesis. The NMR structure of the binding site of S8 in the presence and absence of the protein also correlates this hypothesis (Kalurachchi et al 1997).…”

Section: Discussionmentioning

confidence: 58%

Interdependencies govern multidomain architecture in ribosomal small subunit assembly

Calidas

Culver²

2010

RNA

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The 30S subunit is composed of four structural domains, the body, platform, head, and penultimate/ultimate stems. The functional integrity of the 30S subunit is dependent upon appropriate assembly and precise orientation of all four domains. We examined 16S rRNA conformational changes during in vitro assembly using directed hydroxyl radical probing mediated by Fe(II)-derivatized ribosomal protein (r-protein) S8. R-protein S8 binds the central domain of 16S rRNA directly and independently and its iron derivatized substituents have been shown to mediate cleavage in three domains of 16S rRNA, thus making it an ideal probe to monitor multidomain orientation during assembly. Cleavages in minimal ribonucleoprotein (RNP) particles formed with Fe(II)-S8 and 16S rRNA alone were compared with that in the context of the fully assembled subunit. The minimal binding site of S8 at helix 21 exists in a structure similar to that observed in the mature subunit, in the absence of other r-proteins. However, the binding site of S8 at the junction of helices 25-26a, which is transcribed after helix 21, is cleaved with differing intensities in the presence and absence of other r-proteins. Also, assembly of the body helps establish an architecture approximating, but perhaps not identical, to the 30S subunit at helix 12 and the 59 terminus. Moreover, the assembly or orientation of the neck is dependent upon assembly of both the head and the body. Thus, a complex interrelationship is observed between assembly events of independent domains and the incorporation of primary binding proteins during 30S subunit formation.

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Structural features of the binding site for ribosomal protein S8 in Escherichia coli 16S rRNA defined using NMR spectroscopy

Cited by 38 publications

References 26 publications

Regulation of Ribosomal Protein Synthesis in Vibrio cholerae

Regulation of Ribosomal Protein Synthesis in Vibrio cholerae

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

Interdependencies govern multidomain architecture in ribosomal small subunit assembly

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