Real-time assembly of ribonucleoprotein complexes on nascent RNA transcripts

Duss, Olivier; Stepanyuk, Galina A.; Grot, Annette; O’Leary, Seán E.; Puglisi, Joseph D.; Williamson, James R.

doi:10.1038/s41467-018-07423-3

Cited by 51 publications

(67 citation statements)

References 62 publications

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“…Den Erfolg dieser Vorgehensweise hatten sie bereits mit dem Anfang der RNA-Synthese und der Bindung des ersten Proteins demonstriert. 3) Jetzt nutzte die Arbeitsgruppe diese Methode, um eine ganze Domänealso einen unabhängig strukturierten Bereich -der kleinen ribosomalen Untereinheit beim Entstehen zu beobachten. 4) In früheren Arbeiten hatten Forscher Schnappschüsse auf dem Weg der Assemblierung analysiert.…”

Section: So Entsteht Eine Proteinfabrikunclassified

So entsteht eine Proteinfabrik

Groß¹

2020

Nachr Chem

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Section: So Entsteht Eine Proteinfabrikunclassified

So entsteht eine Proteinfabrik

Groß¹

2020

Nachr Chem

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“…There are many gaps in our knowledge, but accumulating evidence (cf. [3][4][5][6][7][8]) suggests that the full story typically includes cotranscriptional explorations of secondary and tertiary structures, possibly accompanied by finely regulated transcription speeds, as well as a selection of proteins that may participate as stabilizers, catalysts, partners in a ribonculeoprotein complex, or chaperones to guide the process and detect errors. It is not surprising, then, that although many non-coding RNA molecules can be coxed into folding, properly, in artificial environments, the results rarely if ever match in vivo production in terms of speed or yield [3,4,9,10].…”

Section: Backgoundmentioning

confidence: 99%

Base-pair Ambiguity and the Kinetics of RNA Folding

Zhou

Loper

Geman

2018

Preprint

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Non-coding RNA molecules contribute to cellular function through diverse roles, including genome regulation, DNA and RNA repair, RNA splicing, catalysis, protein synthesis, and intracellular transportation [1,2]. The mechanisms of these actions can only be fully understood in terms of native secondary and tertiary structures. When provided with a sufficient number of homologous sequences, the gold standard for secondary structure prediction continues to be comparative analysis [3]. Alternatively, the prevailing computational approach to secondary structure is through the Gibbs (thermal) equilibrium, by Monte Carlo sampling or approximating the minimum free energy (MFE) configuration [4,5]. Aside from the necessary approximations, an enduring debate concerns the biological relevance of equilibrium configurations [6][7][8][9]. Here we adopt a kinetic perspective and argue that the existence of reliable folding on biologically relevant time scales suggests an intra-molecular statistical relationship between secondary and primary structures: as compared with other locations, nucleotide sequences in and around secondary-structure stems will have fewer Watson-Crick matches that are inconsistent with the native structure. An "ambiguity index", one for each pair of molecule and presumed secondary structure, measures the prevalence of false matches and hence the tendency to form metastable structures incompatible with native structures. The ambiguity index statistically separates an ensemble of RNA molecules that operate as single entities (Group I and II Introns) from an ensemble that operates as protein-RNA complexes (SRP and tmRNAs), and ensembles of secondary structures determined by comparative analysis from ones based on thermal equilibrium. We find lower average ambiguity in single-entity RNA's than protein-RNA complexes, and, among single-entity RNA's, lower ambiguity with comparative analyses than equilibrium analyses. Both comparisons are supported by exact and highly significant hypothesis tests. These experiments, motivated by a hypothesized mechanism of folding, and the first of their kind, are consistent with folding to metastable but not necessarily equilibrium structures. Author summaryRecent discoveries indicate that, in addition to being a messenger between DNA and protein, RNA molecules assume a wide range of biological functions. For biological macromolecules, structure is function. Experimental determination of RNA structures is still time-consuming, and computational approaches are of great importance. The prevailing computational approach tries to find the structure with the minimum energy, PLOS

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“…There are many gaps in our knowledge, but accumulating evidence (cf. [3–8]) suggests that the full story typically includes cotranscriptional explorations of secondary and tertiary structures, possibly accompanied by finely regulated transcription speeds, as well as a selection of proteins that may participate as stabilizers, catalysts, partners in a ribonculeoprotein complex, or chaperones to guide the process and detect errors. It is not surprising, then, that although many non-coding RNA molecules can be coxed into folding, properly, in artificial environments, the results rarely if ever match in vivo production in terms of speed or yield [3, 4, 9, 10].…”

Section: Introductionmentioning

confidence: 99%

Base-pair ambiguity and the kinetics of RNA folding

Zhou¹,

Loper

Geman

2019

BMC Bioinformatics

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BackgroundA pairings of nucleotide sequences. Given this forbidding free-energy landscape, mechanisms have evolved that contribute to a directed and efficient folding process, including catalytic proteins and error-detecting chaperones. Among structural RNA molecules we make a distinction between “bound” molecules, which are active as part of ribonucleoprotein (RNP) complexes, and “unbound,” with physiological functions performed without necessarily being bound in RNP complexes. We hypothesized that unbound molecules, lacking the partnering structure of a protein, would be more vulnerable than bound molecules to kinetic traps that compete with native stem structures. We defined an “ambiguity index”—a normalized function of the primary and secondary structure of an individual molecule that measures the number of kinetic traps available to nucleotide sequences that are paired in the native structure, presuming that unbound molecules would have lower indexes. The ambiguity index depends on the purported secondary structure, and was computed under both the comparative (“gold standard”) and an equilibrium-based prediction which approximates the minimum free energy (MFE) structure. Arguing that kinetically accessible metastable structures might be more biologically relevant than thermodynamic equilibrium structures, we also hypothesized that MFE-derived ambiguities would be less effective in separating bound and unbound molecules.ResultsWe have introduced an intuitive and easily computed function of primary and secondary structures that measures the availability of complementary sequences that could disrupt the formation of native stems on a given molecule—an ambiguity index. Using comparative secondary structures, the ambiguity index is systematically smaller among unbound than bound molecules, as expected. Furthermore, the effect is lost when the presumably more accurate comparative structure is replaced instead by the MFE structure.ConclusionsA statistical analysis of the relationship between the primary and secondary structures of non-coding RNA molecules suggests that stem-disrupting kinetic traps are substantially less prevalent in molecules not participating in RNP complexes. In that this distinction is apparent under the comparative but not the MFE secondary structure, the results highlight a possible deficiency in structure predictions when based upon assumptions of thermodynamic equilibrium.

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Real-time assembly of ribonucleoprotein complexes on nascent RNA transcripts

Cited by 51 publications

References 62 publications

So entsteht eine Proteinfabrik

So entsteht eine Proteinfabrik

Base-pair Ambiguity and the Kinetics of RNA Folding

Base-pair ambiguity and the kinetics of RNA folding

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