A novel cGUUAg tetraloop structure with a conserved yYNMGg-type backbone conformation from cloverleaf 1 of bovine enterovirus 1 RNA

Ihle, Yvonne; Ohlenschläger, Oliver; Häfner, Sabine; Duchardt, Elke; Zacharias, Martin; Seitz, Simone; Zell, Roland; Ramachandran, Ramadurai; Görlach, Matthias

doi:10.1093/nar/gki501

Cited by 22 publications

(21 citation statements)

References 49 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…(i) Domain I. The cloverleaf structure of domain I is well supported by comparative sequence analysis, and the 3Ј stem-loop, known as stem-loop d, has been analyzed by nuclear magnetic resonance (NMR) (12,23,47). Our probing results provide solid experimental support for the cloverleaf structure.…”

Section: Resultsmentioning

confidence: 65%

Structure of the 5′ Nontranslated Region of the Coxsackievirus B3 Genome:Chemical Modification and Comparative Sequence Analysis

Bailey

Tapprich

2007

J Virol

View full text Add to dashboard Cite

Coxsackievirus B3 (CVB3) is a picornavirus which causes myocarditis and pancreatitis and may play a role in type I diabetes. The viral genome is a single 7,400-nucleotide polyadenylated RNA encoding 11 proteins in a single open reading frame. The 5 end of the viral genome contains a highly structured nontranslated region (5NTR) which folds to form an internal ribosome entry site (IRES) as well as structures responsible for genome replication, both of which are critical for virulence. A structural model of the CVB3 5NTR, generated primarily by comparative sequence analysis and energy minimization, shows seven domains (I to VII). While this model provides a preliminary basis for structural analysis, the model lacks comprehensive experimental validation. Here we provide experimental evidence from chemical modification analysis to determine the structure of the CVB3 5NTR. Chemical probing results show that the theoretical model for the CVB3 5NTR is largely, but not completely, supported experimentally. In combination with our chemical probing data, we have used the RNASTRUCTURE algorithm and sequence comparison of 105 enterovirus sequences to provide evidence for novel secondary and tertiary interactions. A comprehensive examination of secondary structure is discussed, along with new evidence for tertiary interactions. These include a loop E motif in domain III and a long-range pairing interaction that links domain II to domain V. The results of our work provide mechanistic insight into key functional elements in the cloverleaf and IRES, thereby establishing a base of structural information from which to interpret experiments with CVB3 and other picornaviruses.Coxsackievirus B3 (CVB3) is a member of the Enterovirus genus of the family Picornaviridae. As with all picornaviruses, the CVB3 genome is a single-stranded positive-sense RNA that is organized into four sections: a highly structured 5Ј nontranslated region (5ЈNTR), a single open reading frame encoding a polyprotein, a 3ЈNTR, and a poly(A) tail (48). For CVB3 the 7,400-nucleotide genome is composed of a 5ЈNTR of approximately 742 bases, a coding region that specifies a 2,185-amino-acid polyprotein, a 98-nucleotide (nt) 3ЈNTR, and a poly(A) tail (30,36). Upon entering a permissive host cell, the enterovirus genome first serves as a template for translation, producing the viral polyprotein, and then becomes a template for replication of the minus strand. Both of these functions, as well as the regulatory switch between them, require critical structural elements in the 5ЈNTR RNA (18,19,45,52). Alteration of structural elements in the 5ЈNTR severely compromises viral multiplication and also abrogates virulence (6).The enterovirus cap-independent translation mechanism has been studied extensively, particularly in poliovirus, and serves as a model for all enteroviruses, including CVB3. In this translation mechanism, the 5ЈNTR contains a cis-acting internal ribosome entry site (IRES) (26,50,60) that recruits ribosomes directly to a downstream AUG codon, thereby circu...

show abstract

Section: Resultsmentioning

confidence: 65%

Structure of the 5′ Nontranslated Region of the Coxsackievirus B3 Genome:Chemical Modification and Comparative Sequence Analysis

Bailey

Tapprich

2007

J Virol

View full text Add to dashboard Cite

show abstract

“…In particular, the stacking pattern with the second and third bases on the opposite sides of the backbone, and presence of a trans sugar edge/Watson-Crick base pair with a syn nucleotide provide for easily recognizable features indicating the structural equivalence. In a recent study, Gorlach and coworkers (Ihle et al 2005) solved the structure of the bovine enterovirus 1 (BEV1) apical D-loop with a uGUUAg sequence, the sole naturally occurring enterovirus cloverleaf structure with a deviating GNYA sequence. However, no G-A(syn) base pair but rather a displaced pseudo-base pair without direct hydrogen bonds was found for the BEV1 GUUA loop (Ihle et al 2005).…”

Section: Discussionmentioning

confidence: 99%

“…In a recent study, Gorlach and coworkers (Ihle et al 2005) solved the structure of the bovine enterovirus 1 (BEV1) apical D-loop with a uGUUAg sequence, the sole naturally occurring enterovirus cloverleaf structure with a deviating GNYA sequence. However, no G-A(syn) base pair but rather a displaced pseudo-base pair without direct hydrogen bonds was found for the BEV1 GUUA loop (Ihle et al 2005). Although we do not have a direct explanation for this difference, it might be a subtle sequence dependency of the second nucleotide (the second cytidine in the GCUA structure descends lower into the minor groove than the second uridine in the GUUA structure).…”

Section: Discussionmentioning

confidence: 99%

A GCUA tetranucleotide loop found in the poliovirus oriL by in vivo SELEX (un)expectedly forms a YNMG-like structure: Extending the YNMG family with GYYA

Melchers

Zoll²,

Tessari³

et al. 2006

RNA

View full text Add to dashboard Cite

The cloverleaf structure in the 59-untranslated region of enterovirus RNA that regulates viral RNA replication contains an evolutionarily conserved YNMG tetraloop closed by a Y-G base pair. This loop is believed to interact specifically with the viral protease 3C. To further characterize the specificity of this interaction, the tetraloop and two flanking base pairs of the poliovirus RNA were randomized, and viable viral clones were obtained using in vivo SELEX. Among many different mutants with the canonical YNMG sequences to be described elsewhere, a large-plaque-forming clone contained a deviating uGCUAg sequence. The NMR structure of a small hairpin capped with uGCUAg that we present here shows that the GCUA tetraloop adopts a novel fold, which is highly similar to that of the YNMG tetraloop with common stacking properties and hydrogen-bond interactions including an unusual syn conformation of the adenosine. Thermodynamic studies show moderate stabilities of hairpins with canonical YNMG and the novel GCUA loops, which, together with the similarity of spatial structures, illustrates that the tetraloop structure itself is crucial for the RNA-protein interaction required for the viral replication. A re-evaluation of the ribosomal secondary structure database reveals a hairpin containing a GCUA loop, which covaries with YNMG and is involved in a tertiary interaction, and in the 50S ribosomal subunit from Haloarcula marismortui the structurally comparable apex of stem-loop 35a is a recognition site for protein L2. These observations show a more general occurrence and importance of the so-far unrecognized GYYA hairpin loops.

show abstract

“…3C) has been reported, where the tetranucleotide sequence adopts a U-turn (Table 1). Yet, NMR experiments illustrated that a cGUUAg loop (Ihle et al 2005) and a uGCUAg loop (Melchers et al 2006) can adopt a Z-turn rather than the anticipated Uturn (PDB codes: 1Z30 and 2EVY).…”

Section: Gnra and Gnya Dimorphismmentioning

confidence: 99%

Revisiting GNRA and UNCG folds: U-turns versus Z-turns in RNA hairpin loops

D’Ascenzo¹,

Leonarski²,

Vicens³

et al. 2016

RNA

View full text Add to dashboard Cite

When thinking about RNA three-dimensional structures, coming across GNRA and UNCG tetraloops is perceived as a boon since their folds have been extensively described. Nevertheless, analyzing loop conformations within RNA and RNP structures led us to uncover several instances of GNRA and UNCG loops that do not fold as expected. We noticed that when a GNRA does not assume its "natural" fold, it adopts the one we typically associate with a UNCG sequence. The same folding interconversion may occur for loops with UNCG sequences, for instance within tRNA anticodon loops. Hence, we show that some structured tetranucleotide sequences starting with G or U can adopt either of these folds. The underlying structural basis that defines these two fold types is the mutually exclusive stacking of a backbone oxygen on either the first (in GNRA) or the last nucleobase (in UNCG), generating an oxygen-π contact. We thereby propose to refrain from using sequences to distinguish between loop conformations. Instead, we suggest using descriptors such as U-turn (for "GNRA-type" folds) and a newly described Z-turn (for "UNCG-type" folds). Because tetraloops adopt for the largest part only two (inter)convertible turns, we are better able to interpret from a structural perspective loop interchangeability occurring in ribosomes and viral RNA. In this respect, we propose a general view on the inclination for a given sequence to adopt (or not) a specific fold. We also suggest how long-noncoding RNAs may adopt discrete but transient structures, which are therefore hard to predict.

show abstract

A novel cGUUAg tetraloop structure with a conserved yYNMGg-type backbone conformation from cloverleaf 1 of bovine enterovirus 1 RNA

Cited by 22 publications

References 49 publications

Structure of the 5′ Nontranslated Region of the Coxsackievirus B3 Genome:Chemical Modification and Comparative Sequence Analysis

Structure of the 5′ Nontranslated Region of the Coxsackievirus B3 Genome:Chemical Modification and Comparative Sequence Analysis

A GCUA tetranucleotide loop found in the poliovirus oriL by in vivo SELEX (un)expectedly forms a YNMG-like structure: Extending the YNMG family with GYYA

Revisiting GNRA and UNCG folds: U-turns versus Z-turns in RNA hairpin loops

Contact Info

Product

Resources

About