A widespread self-cleaving ribozyme class is revealed by bioinformatics.

Nat Chem Biol

1] Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA. [2] Howard Hughes Medical Institute, Yale University, New Haven, Connecticut, USA. [3] Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA.

Published: January 2014

Ribozymes are noncoding RNAs that promote chemical transformations with rate enhancements approaching those of protein enzymes. Although ribozymes are likely to have been abundant during the RNA world era, only ten classes are known to exist among contemporary organisms. We report the discovery and analysis of an additional self-cleaving ribozyme class, called twister, which is present in many species of bacteria and eukarya. Nearly 2,700 twister ribozymes were identified that conform to a secondary structure consensus that is small yet complex, with three stems conjoined by internal and terminal loops. Two pseudoknots provide tertiary structure contacts that are critical for catalytic activity. The twister ribozyme motif provides another example of a natural RNA catalyst and calls attention to the potentially varied biological roles of this and other classes of widely distributed self-cleaving RNAs.

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3867598PMC
http://dx.doi.org/10.1038/nchembio.1386DOI Listing

Publication Analysis

Top Keywords

self-cleaving ribozyme
8
ribozyme class
8
widespread self-cleaving
4
class revealed
4
revealed bioinformatics
4
bioinformatics ribozymes
4
ribozymes noncoding
4
noncoding rnas
4
rnas promote
4
promote chemical
4

Similar Publications

CHiTA: A scarless high-throughput pipeline for characterization of ribozymes.

Methods

December 2024

Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA; Center for RNA and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA; Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA. Electronic address:

Small self-cleaving ribozymes are catalytic RNAs that cleave their phosphodiester backbone rapidly and site-specifically, without the assistance of proteins. Their catalytic properties make them ideal targets for applications in RNA pharmaceuticals and bioengineering. Consequently, computational pipelines that predict or design thousands of self-cleaving ribozyme candidates have been developed.

View Article and Find Full Text PDF
Article Synopsis
  • The study highlights the rarity and under-exploration of self-cleaving ribozymes in the human genome, focusing on LINE-1 and OR4K15.
  • Researchers found that these ribozymes consist of two short essential segments totaling only 35 and 31 nucleotides, making them the simplest known self-cleaving ribozymes.
  • The ribozymes exhibit unique structural characteristics, resembling lantern shapes, with significant differences in mutational impact compared to related ribozyme classes, suggesting they represent a primitive ribozyme structure.
View Article and Find Full Text PDF

Viroid-like colonists of human microbiomes.

Cell

November 2024

Stanford University, Department of Genetics, Stanford, CA, USA; Stanford University, Department of Pathology, Stanford, CA, USA. Electronic address:

Here, we describe "obelisks," a class of heritable RNA elements sharing several properties: (1) apparently circular RNA ∼1 kb genome assemblies, (2) predicted rod-like genome-wide secondary structures, and (3) open reading frames encoding a novel "Oblin" protein superfamily. A subset of obelisks includes a variant hammerhead self-cleaving ribozyme. Obelisks form their own phylogenetic group without detectable similarity to known biological agents.

View Article and Find Full Text PDF

Evaluating Performance of Different RNA Secondary Structure Prediction Programs Using Self-cleaving Ribozymes.

Genomics Proteomics Bioinformatics

September 2024

State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, China.

Accurate identification of the correct, biologically relevant RNA structures is critical to understanding various aspects of RNA biology since proper folding represents the key to the functionality of all types of RNA molecules and plays pivotal roles in many essential biological processes. Thus, a plethora of approaches have been developed to predict, identify, or solve RNA structures based on various computational, molecular, genetic, chemical, or physicochemical strategies. Purely computational approaches hold distinct advantages over all other strategies in terms of the ease of implementation, time, speed, cost, and throughput, but they strongly underperform in terms of accuracy that significantly limits their broader application.

View Article and Find Full Text PDF

As discovery of cellular diversity in the brain accelerates, so does the need for tools that target cells based on multiple features. Here we developed Conditional Viral Expression by Ribozyme Guided Degradation (ConVERGD), an adeno-associated virus-based, single-construct, intersectional targeting strategy that combines a self-cleaving ribozyme with traditional FLEx switches to deliver molecular cargo to specific neuronal subtypes. ConVERGD offers benefits over existing intersectional expression platforms, such as expanded intersectional targeting with up to five recombinase-based features, accommodation of larger and more complex payloads and a vector that is easy to modify for rapid toolkit expansion.

View Article and Find Full Text PDF

Want AI Summaries of new PubMed Abstracts delivered to your In-box?

Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!