A widespread self-cleaving ribozyme class is revealed by bioinformatics

Roth, Adam; Weinberg, Zasha; Chen, Andy G.Y.; Kim, Peter B; Ames, Tyler D.; Breaker, Ronald R.

doi:10.1038/nchembio.1386

Cited by 229 publications

(485 citation statements)

References 56 publications

Supporting

Mentioning

441

Contrasting

Order By: Relevance

“…1) [10]. From the analysis of the genoma, twister RNAs have been suggested to be similar to hammerhead in size and structural complexity, and their self-cleavage rate constants are also similar.…”

mentioning

confidence: 95%

Molecular mechanism of the site-specific self-cleavage of the RNA phosphodiester backbone by a twister ribozyme

et al. 2017

View full text Add to dashboard Cite

isotope effects on the nucleophile and leaving oxygen atoms, in very good agreement with experiments, also support this description. Nevertheless, the free energy profiles in the enzyme and in solution are almost coincident which, despite that the rate-limiting activation free energy is in very good agreement with experimental data of counterpart reactions in solution, rule out this substrate-assisted catalysis mechanism for the twister ribozyme from O. sativa. Catalysis must come from the role of alternative acid-base species not available in aqueous solution, but the rate-limiting transition state must be associated with the P-O5′ bond cleavage.

show abstract

mentioning

confidence: 95%

Molecular mechanism of the site-specific self-cleavage of the RNA phosphodiester backbone by a twister ribozyme

et al. 2017

View full text Add to dashboard Cite

show abstract

“…In this work, we extended our sequencing‐based ribozyme assay to exhaustively assay all of the single and double mutants of a 48‐nucleotide section of the 54‐nucleotide Oryza sativa Osa‐1‐4 ribozyme sequence belonging to the twister ribozyme class recently discovered by the Breaker group 5. Crystal structures of Osa‐1‐46 and other variants7 adapting a characteristic double‐pseudoknot structure have been described recently (Figure 1 A) and their catalytic mechanisms have been scrutinized 8.…”

mentioning

confidence: 99%

“…Crystal structures of Osa‐1‐46 and other variants7 adapting a characteristic double‐pseudoknot structure have been described recently (Figure 1 A) and their catalytic mechanisms have been scrutinized 8. Ten positions are reported to be more than 97 % conserved among the twister ribozyme variants 5. By exhaustive mutagenesis, we sought to elucidate which bases in the ribozyme are essential for ribozyme activity, as well as to understand the global tolerance of the ribozyme to mutations.…”

mentioning

confidence: 99%

“…The arrowhead indicates the cleavage site. The bases shown in red are more than 97 % conserved among twister ribozymes 5. B) llustration of the library preparation procedure.…”

mentioning

confidence: 99%

“…Nucleotides in L2 are not only phylogenetically less conserved among the twister ribozymes, but some subclasses of the twister ribozymes accommodate additional P3 and P5 helices within this region 5. Therefore, it is reasonable that most mutants in L2 exhibit a relatively high RA.…”

mentioning

confidence: 99%

See 2 more Smart Citations

High‐Throughput Mutational Analysis of a Twister Ribozyme

Kobori

Yokobayashi

2016

Angew Chem Int Ed

View full text Add to dashboard Cite

Recent discoveries of new classes of self‐cleaving ribozymes in diverse organisms have triggered renewed interest in the chemistry and biology of ribozymes. Functional analysis and engineering of ribozymes often involve performing biochemical assays on multiple ribozyme mutants. However, because each ribozyme mutant must be individually prepared and assayed, the number and variety of mutants that can be studied are severely limited. All of the single and double mutants of a twister ribozyme (a total of 10 296 mutants) were generated and assayed for their self‐cleaving activity by exploiting deep sequencing to count the numbers of cleaved and uncleaved sequences for every mutant. Interestingly, we found that the ribozyme is highly robust against mutations such that 71 % and 30 % of all single and double mutants, respectively, retain detectable activity under the assay conditions. It was also observed that the structural elements that comprise the ribozyme exhibit distinct sensitivity to mutations.

show abstract

Catalytic RNA

Kent¹,

Burke²,

Lupták³

2021

Encyclopedia of Life Sciences

View full text Add to dashboard Cite

RNA molecules have diverse roles in biological systems. While some code for proteins or act to translate codons to amino acids, others fold into specific shapes that endow them with the ability to catalyse specific chemical transformations. These catalytic RNAs, ribozymes, are responsible for protein synthesis, tRNA processing, self‐splicing of certain introns, self‐scission during rolling circle replication of some single‐stranded RNA viruses and cofactor‐dependent gene regulation in bacteria. Other ribozymes have been evolved in vitro to perform a wide variety of transformations. Two of these, tRNA aminoacylase and RNA polymerase ribozymes, are featured here because molecules with such capabilities are thought to have existed on early Earth, before proteins took over as the dominant biological catalysts. Most of the ribozymes have been shown to perform multiturnover catalysis and thus act as true enzymes, either in their natural, biological form or as engineered constructs. Key Concepts RNA molecules can fold into specific conformations and accelerate chemical transformations, thus acting as catalytic biomacromolecules, ribozymes. Ribozymes can accelerate chemical reactions by many orders of magnitude. Many ribozymes are capable of multiturnover catalysis, acting as enzymes. Protein synthesis templated by mRNA is catalysed by ribosomal RNA. Most ribozymes are phosphoryl transferases. In vitro selected ribozymes have been shown to catalyse a wide variety of reactions. The existence of ribozymes supports the RNA World hypothesis.

show abstract

A widespread self-cleaving ribozyme class is revealed by bioinformatics

Cited by 229 publications

References 56 publications

Molecular mechanism of the site-specific self-cleavage of the RNA phosphodiester backbone by a twister ribozyme

Molecular mechanism of the site-specific self-cleavage of the RNA phosphodiester backbone by a twister ribozyme

High‐Throughput Mutational Analysis of a Twister Ribozyme

Catalytic RNA

Contact Info

Product

Resources

About