High-Affinity RNA Ligands to Escherichia coli Ribosomes and Ribosomal Protein S1: Comparison of Natural and Unnatural Binding Sites

Ringquist, Steven; Jones, Thomas R.; Snyder, Eric E.; Gibson, Terri; Boni, Irina V.; Gold, Larry

doi:10.1021/bi00011a019

Cited by 116 publications

(77 citation statements)

References 61 publications

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“…These gene products may play a role in rescuing stalled ribosomes, which is a requirement for cellular survival at low temperatures. Cold shock conditions also induced the expression of a protein with an S1 RNA binding domain, which is thought to mediate single-stranded RNA and RNA-pseudoknot binding (45) and may contribute to RNA stability at low temperatures. As shown in Fig.…”

Section: Discussionmentioning

confidence: 99%

Characterization of the Staphylococcus aureus Heat Shock, Cold Shock, Stringent, and SOS Responses and Their Effects on Log-Phase mRNA Turnover

et al. 2006

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Despite its being a leading cause of nosocomal and community-acquired infections, surprisingly little is known about Staphylococcus aureus stress responses. In the current study, Affymetrix S. aureus GeneChips were used to define transcriptome changes in response to cold shock, heat shock, stringent, and SOS responseinducing conditions. Additionally, the RNA turnover properties of each response were measured. Each stress response induced distinct biological processes, subsets of virulence factors, and antibiotic determinants. The results were validated by real-time PCR and stress-mediated changes in antimicrobial agent susceptibility. Collectively, many S. aureus stress-responsive functions are conserved across bacteria, whereas others are unique to the organism. Sets of small stable RNA molecules with no open reading frames were also components of each response. Induction of the stringent, cold shock, and heat shock responses dramatically stabilized most mRNA species. Correlations between mRNA turnover properties and transcript titers suggest that S. aureus stress response-dependent alterations in transcript abundances can, in part, be attributed to alterations in RNA stability. This phenomenon was not observed within SOS-responsive cells.

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Section: Discussionmentioning

confidence: 99%

Characterization of the Staphylococcus aureus Heat Shock, Cold Shock, Stringent, and SOS Responses and Their Effects on Log-Phase mRNA Turnover

et al. 2006

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“…When S1 was depleted from in vitro-translation extracts, SsrA RNA did not associate with ribosomes (10). S1 is conserved in most bacteria and has been implicated in the selection of translation-start sites, especially for mRNAs lacking Shine-Dalgarno ribosome binding sites upstream of the ATG initiation codon (16,18). It seems likely, therefore, that binding of one or more S1 proteins plays some role in helping the SsrA⅐SmpB complex bind ribosomes and reinitiate transcription correctly on the peptide-reading frame.…”

Section: Discussionmentioning

confidence: 99%

Protein factors associated with the SsrA⋅SmpB tagging and ribosome rescue complex

Karzai

Sauer

2001

Proc. Natl. Acad. Sci. U.S.A.

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SsrA RNA acts as a tRNA and mRNA to modify proteins whose synthesis on ribosomes has stalled. Such proteins are marked for degradation by addition of peptide tags to their C termini in a reaction mediated by SsrA RNA and SmpB, a specific SsrA-RNA binding protein. Evidence is presented here for the existence of a larger ribonucleoprotein complex that contains ribosomal protein S1, phosphoribosyl pyrophosphate synthase, RNase R, and YfbG in addition to SsrA RNA and SmpB. Biochemical, genetic, and phylogenetic results suggest potential roles for some of these factors in various stages of the ribosome rescue and tagging process and͞or the presence of functional interactions between one or more of these proteins and SsrA.tmRNA ͉ 10Sa RNA ͉ trans translation ͉ protein-RNA recognition ͉ VacB

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“…Additional structural perturbations of tmRNA, when S1 binds, might await further structural mapping to be delineated, including other probes such as Iron-EDTA (riboses) or ethyl nitroso urea (phosphates). Ribosomal protein S1 affects the conformation of most, if not all, pseudoknots of tmRNA; using selection/amplification methods (SELEX), pseudoknotcontaining high affinity RNA ligands were generated against purified S1 protein [16]. Moreover, the loops of the selected pseudoknots were highly conserved, implicating them in binding.…”

Section: Discussionmentioning

confidence: 99%

Ribosomal protein S1 induces a conformational change of tmRNA; more than one protein S1 per molecule of tmRNA

Bordeau¹,

Felden²

2002

Biochimie

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To cite this version:Valérie Bordeau, Brice Felden. Ribosomal protein S1 induces a conformational change of tmRNA; more than one protein S1 per molecule of tmRNA.. Biochimie, Elsevier, 2002, 84 (8) Abstract tmRNA (10Sa RNA, ssrA) acts to rescue stalled bacterial ribosomes while encoding a peptide tag added trans-translationally to the nascent peptide, targeting it for proteolysis. Ribosomal protein S1 is required for tmRNA binding to isolated and poly U-programmed ribosomes. Mobility assays on native gels indicate that the binding curves of both recombinant and purified proteins S1 from E. coli is biphasic with apparent binding constants of ∼90 and ∼300 nM, respectively, suggesting that more than one protein interacts with tmRNA. Structural probing of native tmRNA in the presence and absence of the purified protein suggest that when S1 binds, tmRNA undergoes a significant conformational change. In the presence of the protein, nucleotides from tmRNA with enhanced (H2, H3, PK1, PK2, PK4, in and around the first triplet to be translated), or decreased (H5 and PK2), reactivity towards a probe specific for RNA single-strands are scattered throughout the molecule, with the exception of the tRNA-like domain that may be dispensable for the interaction. Converging experimental evidence suggests that ribosomal protein S1 binds to pseudoknot PK2. Previous structural studies of tmRNA in solution have revealed several discrepancies between the probing data and the phylogeny, and most of these are reconciled when analyzing tmRNA structure in complex with the protein(s). Ribosomal protein(s) S1 is proposed to set tmRNA in the mRNA mode, relieving strains that may develop when translating a looped mRNA.

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High-Affinity RNA Ligands to Escherichia coli Ribosomes and Ribosomal Protein S1: Comparison of Natural and Unnatural Binding Sites

Cited by 116 publications

References 61 publications

Characterization of the Staphylococcus aureus Heat Shock, Cold Shock, Stringent, and SOS Responses and Their Effects on Log-Phase mRNA Turnover

Characterization of the Staphylococcus aureus Heat Shock, Cold Shock, Stringent, and SOS Responses and Their Effects on Log-Phase mRNA Turnover

Protein factors associated with the SsrA⋅SmpB tagging and ribosome rescue complex

Ribosomal protein S1 induces a conformational change of tmRNA; more than one protein S1 per molecule of tmRNA

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