Crumple: A Method for Complete Enumeration of All Possible Pseudoknot-Free RNA Secondary Structures

Bleckley, Samuel; Stone, Jonathan; Schroeder, Susan J.

doi:10.1371/journal.pone.0052414

Cited by 8 publications

(6 citation statements)

References 45 publications

(67 reference statements)

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“…We wanted to determine whether any RNA structures could be present that are encoded by degenerate sequences that could have escaped detection with Synplot2. We used the Crumple program (55) and generated all possible RNA structures in 30-nt sliding windows of sequences belonging to the naturally occurring PV1, -2, -3, and CAV20, all of which can be encapsidated into PV1, 2, 3 capsids to produce infectious viruses. We then compared the profile of conserved RNA structures to our synthetic viruses, Max and SD (Figs.…”

Section: Resultsmentioning

confidence: 99%

Limits of variation, specific infectivity, and genome packaging of massively recoded poliovirus genomes

Song¹,

Gorbatsevych²,

Liu³

et al. 2017

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

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Computer design and chemical synthesis generated viable variants of poliovirus type 1 (PV1), whose ORF (6,189 nucleotides) carried up to 1,297 "Max" mutations (excess of overrepresented synonymous codon pairs) or up to 2,104 "SD" mutations (randomly scrambled synonymous codons). "Min" variants (excess of underrepresented synonymous codon pairs) are nonviable except for P2 Min , a variant temperature-sensitive at 33 and 39.5 • C. Compared with WT PV1, P2 Min displayed a vastly reduced specific infectivity (si) (WT, 1 PFU/118 particles vs. P2 Min , 1 PFU/35,000 particles), a phenotype that will be discussed broadly. Si of haploid PV presents cellular infectivity of a single genotype. We performed a comprehensive analysis of sequence and structures of the PV genome to determine if evolutionary conserved cis-acting packaging signal(s) were preserved after recoding. We showed that conserved synonymous sites and/or local secondary structures that might play a role in determining packaging specificity do not survive codon pair recoding. This makes it unlikely that numerous "cryptic, poliovirus | genome recoding | packaging signal | specific infectivity T he capsid precursor P1 (881 amino acids) of type 1 poliovirus (PV), mapping to the N terminus of the polyprotein (PP) (Fig. 1A), can be encoded in 10 442 ways (1) due to the degenerate genetic code. The tiniest fraction of these possible sequences defines PV, the cause of poliomyelitis. PV occurs in three serotypes, of which the most neurovirulent type 1 Mahoney [PV1(M)], the main viral species analyzed in this study, was isolated in 1941 from pooled feces of three healthy children (2).Genome sequence (3, 4) and gene organization (3) of PV1(M) revealed highly complex structures in its 5'-terminal nontranslated region (5'-NTR), followed by a single ORF encoding the PP, followed by a complex 3'-heteropolymeric region and poly(A) tail (Fig. 1A) (5, 6). The PP (7) is an active molecule that cleaves itself into ∼29 polypeptides by two viral proteinases (2A pro and 3C pro /3CD pro ) and an enzyme-independent maturation cleavage (Fig. 1A) (5,6,8).Capsid domain P1 controls the identity of PV by determining virion structure (9), serotype identity (10), and interaction with the cellular receptor CD155 (10). Since PV replicates as quasispecies at an error rate of ∼10 −4 (11), the following questions arise: How conserved is its synonymous sequence given the astronomical number of alternative possibilities? What encoding could have coevolved that would be optimal to specify 881 capsid residues?If PV, a member of the genus Enterovirus of Picornaviridae, is an evolutionary descendant of C-cluster Coxsackie viruses (C-CAVs) (12), the evolution of PV nucleotide sequences was constrained as it adhered to the basic architecture of C-CAVs, its evolutionary parents (13). A second well-known restriction of sequence variability in ORFs is "codon bias" (14), the unequal use of synonymous codons. Encoding the PV1 P1 domain with an excess of "rarely used" (human) synonymous codons results in a ...

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Section: Resultsmentioning

confidence: 99%

Limits of variation, specific infectivity, and genome packaging of massively recoded poliovirus genomes

Song¹,

Gorbatsevych²,

Liu³

et al. 2017

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

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show abstract

“…45 Chemical probing and other experimental constraints can reduce the possible number of structures and improve the accuracy of free energy minimization predictions. 23 However, chemical probing constraints do not necessarily define a single structure, 45 and consideration of suboptimal structures or ensembles of structures provides additional insight for biological RNA structure and function. The abundance of computational tools to address the RNA folding problem highlights the problem that a single minimum free energy structure is often insufficient to describe or predict biologically relevant RNA secondary structures.…”

Section: ■ Philosophically Different Approaches Tomentioning

confidence: 99%

“…The Wuchty algorithm, the algorithm by Pipas and McMahon, and the Crumple algorithm calculate all possible non-pseduoknotted structures for a given RNA sequence. The Wuchty algorithm calculates all possible structures within a given free energy window, the size of which depends on the length of the sequence.…”

Section: Philosophically Different Approaches To Predicting Encapsida...mentioning

confidence: 99%

“…The Crumple algorithm can use thermodynamics as a filter to reduce the possible number of structures but does not require thermodynamic parameters. The advantage of the Crumple algorithm is the ability to modulate the importance of thermodynamic parameters in RNA structure predictions . Chemical probing and other experimental constraints can reduce the possible number of structures and improve the accuracy of free energy minimization predictions .…”

Section: Philosophically Different Approaches To Predicting Encapsida...mentioning

confidence: 99%

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Probing Viral Genomic Structure: Alternative Viewpoints and Alternative Structures for Satellite Tobacco Mosaic Virus RNA

Schroeder

2014

Biochemistry

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Viral RNA structure prediction is a valuable tool for development of drugs against viral disease. This work discusses different approaches to predicting encapsidated viral RNA and highlights satellite tobacco mosaic virus (STMV) RNA as a model system with excellent crystallography data. Fundamentally important issues for debate include thermodynamic versus kinetic control of virus assembly and the possible consequences of quasi-species in the primary structure on RNA secondary structure prediction of a single structure or an ensemble of structures. Multiple computational tools and chemical reagents are now available for improved viral RNA structure prediction. Two different predicted structures for encapsidated STMV RNA result from differences in three main areas: a different approach and philosophy to studying encapsidated viral RNA, an emphasis on different RNA motifs, and technical differences in computational methods and chemical reagents. The experiments with traditional chemical probing and SHAPE reagents are compared in terms of chemistry, results, and interpretation for STMV RNA as well as other RNA protein assemblies, such as the 5'UTR of HIV and the ribosome. This discussion of the challenges of viral RNA structure prediction will lead to new experiments and improved future predictions for viral RNA.

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“…The early Pipas-McMahon RNA structure prediction algorithm sought to completely enumerate and evaluate the free energy of all possible secondary structures, thereby constructing the entire energy landscape (20). More recent algorithms have made progress in making similar enumerations less computationally intensive (21), the most successful of which are the TT2NE algorithm and its stochastic version, McGenus (22,23). The complete landscape enumeration approach including all secondary structures has so far been limited to short (<30 nt) RNA molecules (24,25), and the field has instead almost entirely been dominated by dynamic programming approaches (26)(27)(28)(29)(30).…”

Section: Introductionmentioning

confidence: 99%

A Polymer Physics Framework for the Entropy of Arbitrary Pseudoknots

Kimchi

Cragnolini

Brenner

et al. 2019

Biophysical Journal

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The accurate prediction of RNA secondary structure from primary sequence has had enormous impact on research from the past 40 years. Although many algorithms are available to make these predictions, the inclusion of non-nested loops, termed pseudoknots, still poses challenges arising from two main factors: 1) no physical model exists to estimate the loop entropies of complex intramolecular pseudoknots, and 2) their NP-complete enumeration has impeded their study. Here, we address both challenges. First, we develop a polymer physics model that can address arbitrarily complex pseudoknots using only two parameters corresponding to concrete physical quantities-over an order of magnitude fewer than the sparsest state-of-the-art phenomenological methods. Second, by coupling this model to exhaustive enumeration of the set of possible structures, we compute the entire free energy landscape of secondary structures resulting from a primary RNA sequence. We demonstrate that for RNA structures of $80 nucleotides, with minimal heuristics, the complete enumeration of possible secondary structures can be accomplished quickly despite the NP-complete nature of the problem. We further show that despite our loop entropy model's parametric sparsity, it performs better than or on par with previously published methods in predicting both pseudoknotted and non-pseudoknotted structures on a benchmark data set of RNA structures of %80 nucleotides. We suggest ways in which the accuracy of the model can be further improved.

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Crumple: A Method for Complete Enumeration of All Possible Pseudoknot-Free RNA Secondary Structures

Cited by 8 publications

References 45 publications

Limits of variation, specific infectivity, and genome packaging of massively recoded poliovirus genomes

Limits of variation, specific infectivity, and genome packaging of massively recoded poliovirus genomes

Probing Viral Genomic Structure: Alternative Viewpoints and Alternative Structures for Satellite Tobacco Mosaic Virus RNA

A Polymer Physics Framework for the Entropy of Arbitrary Pseudoknots

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