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Multiple translational products from a five-nucleotide ribozyme.

ABSTRACT: An indispensable step in protein biosynthesis is the 2(')(3(')) aminoacylation of tRNA by aminoacyl-tRNA synthetases. Here we show that a similar activity exists in a tiny, 5-nt-long RNA enzyme with a 3-nt active center. The small ribozyme initially trans-phenylalanylates a partially complementary 4-nt RNA selectively at its terminal 2(')-ribose hydroxyl using PheAMP, the natural form for activated amino acid. The initial 2(') Phe-RNA product can be elaborated into multiple peptidyl-RNAs. Reactions do not require divalent cations, and have limited dependence on monovalent cations. Small size and minimal requirements for regiospecific translational activity strongly support the hypothesis that minuscule RNA enzymes participated in early forms of translation.

SUBMITTER: Turk RM

PROVIDER: S-EPMC2826339 | biostudies-literature | 2010 Mar

REPOSITORIES: biostudies-literature

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Multiple translational products from a five-nucleotide ribozyme.

Turk Rebecca M RM Chumachenko Nataliya V NV Yarus Michael M

Proceedings of the National Academy of Sciences of the United States of America 20100222 10

An indispensable step in protein biosynthesis is the 2(')(3(')) aminoacylation of tRNA by aminoacyl-tRNA synthetases. Here we show that a similar activity exists in a tiny, 5-nt-long RNA enzyme with a 3-nt active center. The small ribozyme initially trans-phenylalanylates a partially complementary 4-nt RNA selectively at its terminal 2(')-ribose hydroxyl using PheAMP, the natural form for activated amino acid. The initial 2(') Phe-RNA product can be elaborated into multiple peptidyl-RNAs. Reacti ...[more]

PMID: 20176971

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Project description:Despite the ubiquitous nature of misfolded intermediates in RNA folding, little is known about their physical properties or the folding transitions that allow them to continue folding productively. Folding of the Tetrahymena group I ribozyme includes sequential accumulation of two intermediates, termed I(trap) and misfolded (M). Here, we probe the structure and folding transition of I(trap) and compare them to those of M. Hydroxyl radical and dimethyl sulfate footprinting show that both I(trap) and M are extensively structured and crudely resemble the native RNA. However, regions of the core P3-P8 domain are more exposed to solvent in I(trap) than in M. I(trap) rearranges to continue folding nearly 1000-fold faster than M, and urea accelerates folding of I(trap) much less than M. Thus, the rate-limiting transition from I(trap) requires a smaller increase in exposed surface. Mutations that disrupt peripheral tertiary contacts give large and nearly uniform increases in re-folding of M, whereas the same mutations give at most modest increases in folding from I(trap). Intriguingly, mutations within the peripheral element P5abc give 5- to 10-fold accelerations in escape from I(trap), whereas ablation of P13, which lies on the opposite surface in the native structure, near the P3-P8 domain, has no effect. Thus, the unfolding required from I(trap) appears to be local, whereas the unfolding of M appears to be global. Further, the modest effects from several mutations suggest that there are multiple pathways for escape from I(trap) and that escape is aided by loosening nearby native structural constraints, presumably to facilitate local movements of nucleotides or segments that have not formed native contacts. Overall, these and prior results suggest a model in which the global architecture and peripheral interactions of the RNA are achieved relatively early in folding. Multiple folding and re-folding events occur on the predominant pathway to the native state, with increasing native core interactions and cooperativity as folding progresses.

Project description:ObjectivesMitigating carbon footprint of products used in resource-intensive areas such as surgical operating rooms will be important in achieving net zero carbon healthcare. The aim of this study was to evaluate the carbon footprint of products used within five common operations, and to identify the biggest contributors (hotspots).DesignA predominantly process-based carbon footprint analysis was conducted for products used in the five highest volume surgical operations performed in the National Health System in England.SettingThe carbon footprint inventory was based on direct observation of 6-10 operations/type, conducted across three sites within one NHS Foundation Trust in England.ParticipantsPatients undergoing primary elective carpal tunnel decompression, inguinal hernia repair, knee arthroplasty, laparoscopic cholecystectomy, tonsillectomy (March 2019 - January 2020).Main outcome measuresWe determined the carbon footprint of the products used in each of the five operations, alongside greatest contributors through analysis of individual products and of underpinning processes.ResultsThe mean average carbon footprint of products used for carpal tunnel decompression was 12.0 kg CO2e (carbon dioxide equivalents); 11.7 kg CO2e for inguinal hernia repair; 85.5 kg CO2e for knee arthroplasty; 20.3 kg CO2e for laparoscopic cholecystectomy; and 7.5 kg CO2e for tonsillectomy. Across the five operations, 23% of product types were responsible for ≥80% of the operation carbon footprint. Products with greatest carbon contribution for each operation type were the single-use hand drape (carpal tunnel decompression), single-use surgical gown (inguinal hernia repair), bone cement mix (knee arthroplasty), single-use clip applier (laparoscopic cholecystectomy) and single-use table drape (tonsillectomy). Mean average contribution from production of single-use items was 54%, decontamination of reusables 20%, waste disposal of single-use items 8%, production of packaging for single-use items 6% and linen laundering 6%.ConclusionsChange in practice and policy should be targeted towards those products making greatest contribution, and should include reducing single-use items and switching to reusables, alongside optimising processes for decontamination and waste disposal, modelled to reduce carbon footprint of these operations by 23%-42%.

Dataset Information

Multiple translational products from a five-nucleotide ribozyme.

Publications

Multiple translational products from a five-nucleotide ribozyme.

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