Structure–function analysis of the ribozymes of chrysanthemum chlorotic mottle viroid: a loop–loop interaction motif conserved in most natural hammerheads

Dufour, David; Peña, Marcos de la; Gago, Selma; Flores, Ricardo; Gallego, José

doi:10.1093/nar/gkn918

Cited by 52 publications

(60 citation statements)

References 36 publications

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“…More precisely, tertiary interactions between HHR helixes (de la Peña et al 2003;Khvorova et al 2003) show significant conservation in stem size and loop composition (Supplemental Fig. S1; Chi et al 2008;Dufour et al 2009;de la Peña et al 2009). Thus, natural HHR motifs were split into two major helical motifs (seeds), each one composed of either the SC site/Helix I/ U box (I-type seeds) or the U box/Helix II/P box (II-type seeds).…”

Section: Bioinformatic Search Of Hhrsmentioning

confidence: 99%

Ubiquitous presence of the hammerhead ribozyme motif along the tree of life

Peña¹,

García-Robles²

2010

RNA

Self Cite

107

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Examples of small self-cleaving RNAs embedded in noncoding regions already have been found to be involved in the control of gene expression, although their origin remains uncertain. In this work, we show the widespread occurrence of the hammerhead ribozyme (HHR) motif among genomes from the Bacteria, Chromalveolata, Plantae, and Metazoa kingdoms. Intergenic HHRs were detected in three different bacterial genomes, whereas metagenomic data from Galapagos Islands showed the occurrence of similar ribozymes that could be regarded as direct relics from the RNA world. Among eukaryotes, HHRs were detected in the genomes of three water molds as well as 20 plant species, ranging from unicellular algae to vascular plants. These HHRs were very similar to those previously described in small RNA plant pathogens and, in some cases, appeared as close tandem repetitions. A parallel situation of tandemly repeated HHR motifs was also detected in the genomes of lower metazoans from cnidarians to invertebrates, with special emphasis among hematophagous and parasitic organisms. Altogether, these findings unveil the HHR as a widespread motif in DNA genomes, which would be involved in new forms of retrotransposable elements.

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Section: Bioinformatic Search Of Hhrsmentioning

confidence: 99%

Ubiquitous presence of the hammerhead ribozyme motif along the tree of life

Peña¹,

García-Robles²

2010

RNA

Self Cite

107

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“…4A; Dufour et al 2009). Despite these differences, a conserved tertiary interaction motif embedded within the loop-loop complexes has been detected in at least four different hammerheads ( Fig.…”

Section: Hammerhead Ribozymesmentioning

confidence: 98%

“…Despite these differences, a conserved tertiary interaction motif embedded within the loop-loop complexes has been detected in at least four different hammerheads ( Fig. 4; Dufour et al 2009). The 59 U of L2 and the 39 A of L3 form a reverse Hoogsteen pair across the major groove in the X-ray structures of the Schistosoma mansoni (Martick and Scott 2006) and tobacco ring spot virus satellite RNA (Chi et al 2008) (sTRSV) hammerheads, a base pair also supported by site-directed mutagenesis experiments in the hammerheads of the (+) and (À) polarity RNAs Total number of hydrogen bonds contained in the interaction.…”

Section: Hammerhead Ribozymesmentioning

confidence: 99%

“…of chrysanthemum chlorotic mottle viroid (CChMVd) (Dufour et al 2009). In addition, the penultimate U of L2 in the sTRSV hammerhead forms a Watson-Crick pair with the 39 A of L3, so that a base triple is formed by these two nucleotides and the L2 59 U (Chi et al 2008); this basetriple interaction is also consistent with the mutagenesis analyses of CchMVd(+) and CchMVd(À) hammerheads (Dufour et al 2009).…”

Section: Hammerhead Ribozymesmentioning

confidence: 99%

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Three-way RNA junctions with remote tertiary contacts: A recurrent and highly versatile fold

Peña¹,

Dufour²,

Gallego³

2009

RNA

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Three-way junction RNAs adopt a recurrent Y shape when two of the helices form a coaxial stack and the third helix establishes one or more tertiary contacts several base pairs away from the junction. In this review, the structure, distribution, and functional relevance of these motifs are examined. Structurally, the folds exhibit conserved junction topologies, and the distal tertiary interactions play a crucial role in determining the final shape of the structures. The junctions and remote tertiary contacts behave as flexible hinge motifs that respond to changes in the other region, providing these folds with switching mechanisms that have been shown to be functionally useful in a variety of contexts. In addition, the juxtaposition of RNA domains at the junction and at the distal tertiary complexes enables the RNA helices to adopt unusual conformations that are frequently used by proteins, RNA molecules, and antibiotics as platforms for specific binding. As a consequence of these properties, Y-shaped junctions are widely distributed in all kingdoms of life, having been observed in small naked RNAs such as riboswitches and ribozymes or embedded in complex ribonucleoprotein systems like ribosomal RNAs, RNase P, or the signal recognition particle. In all cases, the folds were found to play an essential role for the functioning or assembly of the RNA or ribonucleoprotein systems that contain them.

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“…Several studies have indicated a great variation of tertiary interacting sequences in individual HHRz motifs (Przybilski and Hammann 2007a;Shepotinovskaya and Uhlenbeck 2008), although recurrent signatures were also observed (Dufour et al 2009). The variability of tertiary interacting motifs became even further apparent in several recent database searches for novel HHRz motifs carried out in this and other laboratories Rojas et al 2000;Gräf et al 2005;Przybilski et al 2005;Martick et al 2008;De la Peña and Garcia-Robles 2010;Jimenez et al 2011;Perreault et al 2011;Seehafer et al 2011).…”

Section: Introductionmentioning

confidence: 99%

G17-modified hammerhead ribozymes are active in vitro and in vivo

Kalweit

Hammann

2013

RNA

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Natural hammerhead ribozymes (HHRz) feature tertiary interactions between hairpin loops or bulges in two of three helices that surround the catalytic core of conserved nucleotides. Their conservation was originally established on minimal versions lacking the tertiary interactions. While those sequence requirements in general also apply to natural versions, we show here differences for the HHRz cleavage site N17. A guanosine at this position strongly impairs cleavage activity in minimal versions, whereas we observe for the G17 variants of four tertiary stabilized HHRz significant cleavage and ligation activity in vitro. Kinetic analyses of these variants revealed a reduced rate and extent of cleavage, compared with wild-type sequences, while variants with distorted tertiary interactions cleaved at a reduced rate, but to the same extent. Contrary to this, G17 variants exhibit similar in vitro ligation activity as compared with the respective wild-type motif. To also address the catalytic performance of these motifs in vivo, we have inserted HHRz cassettes in the lacZ gene and tested this β-galactosidase reporter in Dictyostelium discoideum. In colorimetric assays, we observe differences in the enzymatic activity of β-galactosidase, which correlate well with the activity of the different HHRz variants in vitro and which can be unambiguously attributed to ribozyme cleavage by primer extension analysis.

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Structure–function analysis of the ribozymes of chrysanthemum chlorotic mottle viroid: a loop–loop interaction motif conserved in most natural hammerheads

Cited by 52 publications

References 36 publications

Ubiquitous presence of the hammerhead ribozyme motif along the tree of life

Ubiquitous presence of the hammerhead ribozyme motif along the tree of life

Three-way RNA junctions with remote tertiary contacts: A recurrent and highly versatile fold

G17-modified hammerhead ribozymes are active in vitro and in vivo

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