Folding of group II introns: a model system for large, multidomain RNAs?

Pyle, Anna Marie; Fedorova, Olga; Waldsich, Christina

doi:10.1016/j.tibs.2007.01.005

Cited by 96 publications

(94 citation statements)

References 63 publications

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“…6B). In support of this model, the formation of a compact intermediate that possesses native tertiary interactions (i.e., correctly oriented helices) is a key step during folding of large RNAs such as ribozymes (Bokinsky et al 2003;Buchmueller and Weeks 2003;Pyle et al 2007;Behrouzi et al 2012). The role of L3 very early in 60S subunit assembly is consistent with this compaction.…”

Section: Discussionmentioning

confidence: 70%

A hierarchical model for assembly of eukaryotic 60S ribosomal subunit domains

et al. 2014

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Despite having high-resolution structures for eukaryotic large ribosomal subunits, it remained unclear how these ribonucleoprotein complexes are constructed in living cells. Nevertheless, knowing where ribosomal proteins interact with ribosomal RNA (rRNA) provides a strategic platform to investigate the connection between spatial and temporal aspects of 60S subunit biogenesis. We previously found that the function of individual yeast large subunit ribosomal proteins (RPLs) in precursor rRNA (pre-rRNA) processing correlates with their location in the structure of mature 60S subunits. This observation suggested that there is an order by which 60S subunits are formed. To test this model, we used proteomic approaches to assay changes in the levels of ribosomal proteins and assembly factors in preribosomes when RPLs functioning in early, middle, and late steps of pre-60S assembly are depleted. Our results demonstrate that structural domains of eukaryotic 60S ribosomal subunits are formed in a hierarchical fashion. Assembly begins at the convex solvent side, followed by the polypeptide exit tunnel, the intersubunit side, and finally the central protuberance. This model provides an initial paradigm for the sequential assembly of eukaryotic 60S subunits. Our results reveal striking differences and similarities between assembly of bacterial and eukaryotic large ribosomal subunits, providing insights into how these RNA-protein particles evolved.

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Section: Discussionmentioning

confidence: 70%

A hierarchical model for assembly of eukaryotic 60S ribosomal subunit domains

et al. 2014

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“…A persistent and incompletely explained observation is that many RNAs fold very slowly, on timescales requiring minutes or longer. RNAs that fold slowly span all sizes including small riboswitch and catalytic RNAs, medium-sized catalytic introns, and the large RNAs in ribosomes (2)(3)(4)(5)(6).…”

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confidence: 99%

C2′-endo nucleotides as molecular timers suggested by the folding of an RNA domain

Mortimer

Weeks

2009

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

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A striking and widespread observation is that higher-order folding for many RNAs is very slow, often requiring minutes. In some cases, slow folding reflects the need to disrupt stable, but incorrect, interactions. However, a molecular explanation for slow folding in most RNAs is unknown. The specificity domain of the Bacillus subtilis RNase P ribozyme undergoes a rate-limiting folding step on the minute time-scale. This RNA also contains a C2 -endo nucleotide at A130 that exhibits extremely slow local conformational dynamics. This nucleotide is evolutionarily conserved and essential for tRNA recognition by RNase P. Here we show that deleting this single nucleotide accelerates folding by an order of magnitude even though this mutation does not change the global fold of the RNA. These results demonstrate that formation of a single stacking interaction at a C2 -endo nucleotide comprises the rate-determining step for folding an entire 154 nucleotide RNA. C2 -endo nucleotides exhibit slow local dynamics in structures spanning isolated helices to complex tertiary interactions. Because the motif is both simple and ubiquitous, C2 -endo nucleotides may function as molecular timers in many RNA folding and ligand recognition reactions.RNA folding ͉ RNA SHAPE chemistry T o function properly inside the cell, RNA molecules undergo complex folding transitions to form specific, biologically active, three-dimensional structures (1). These essential structures involve both local base pairing and also complex higherorder tertiary interactions. A persistent and incompletely explained observation is that many RNAs fold very slowly, on timescales requiring minutes or longer. RNAs that fold slowly span all sizes including small riboswitch and catalytic RNAs, medium-sized catalytic introns, and the large RNAs in ribosomes (2-6).Slow folding has important consequences both because correct folding ultimately governs the rate at which an RNA can perform its biological function and because bottlenecks in assembly potentially require cellular mechanisms to overcome slow folding. In some cases, slow folding results from formation of stable, non-native, and kinetically trapped states (7,8). Such misfolding is remedied, in part, by cellular chaperone activities (9-11). In many cases, the molecular basis for slow folding is unknown.The intricate three-dimensional structures formed by RNA molecules ultimately reflect the underlying contributions of individual nucleotides. Most nucleotides in an RNA molecule exist in the C3Ј-endo conformation. Although less frequent, the C2Ј-endo conformation is highly overrepresented in catalytic active sites and in critical tertiary structures (12, 13). At the static structure level, the C2Ј-endo conformation induces greater helical twist in an A-form helix (14, 15) and spans a much longer 5Ј-to-3Ј distance (12,16). At the level of local motion, some C2Ј-endo nucleotides exhibit extraordinarily slow conformational dynamics with half-lives on the 10-100-s timescale (17).Here we show that the slow conformational ...

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“…Hitherto several folding paradigms have been discovered. [1][2][3][4][5][6][7][8][9][10] In principle, RNA encounters two major folding problems: 11 (i) RNA molecules are prone to misfold, thereby becoming trapped in inactive, often long-lived conformations, the escape from which becomes ratelimiting during the folding process; (ii) the native, functional RNA conformation might not be thermodynamically favored over other intermediate structures, thus requiring the assistance of a specific RNA-binding protein (or high salt) for stabilization of the tertiary structure.…”

Section: Introductionmentioning

confidence: 99%

“…[1][2][3][4][5][6][7][8][9][10] As the cellular environment differs significantly from the in vitro refolding scenario, the question of how well in vitro and in vivo folding pathways correlate remains to be addressed. In the past decade there has been considerable effort to investigate RNA folding in vivo, providing the first profound insights into the forces governing intracellular RNA structure formation.…”

Section: Introductionmentioning

confidence: 99%