Related Experiment Video
Updated: May 7, 2026
12:02
Molecular Evolution of the Tre Recombinase
Published on: May 29, 2008
Evolution of the R2 retrotransposon ribozyme and its self-cleavage site
Danna G Eickbush1, William D Burke, Thomas H Eickbush
1Department of Biology, University of Rochester, Rochester, New York, United States of America.
Plos One
|September 26, 2013
Summary
R2 retrotransposons use a ribozyme to self-cleave from host rRNA. Cleavage site variations influence retrotransposon insertion, impacting gene evolution.
Area of Science:
- Molecular Biology
- Genetics
- Evolutionary Biology
Background:
- R2 retrotransposons insert into 28S rRNA genes in animals.
- R2 RNA previously showed self-cleavage via a hepatitis D virus (HDV)-like ribozyme in Drosophila.
Purpose of the Study:
- Investigate R2 RNA self-cleavage activity across diverse R2 lineages.
- Determine the correlation between cleavage site location and R2 5' junction types.
Main Methods:
- In vitro RNA self-cleavage assays.
- Analysis of R2 5' junctions from various species.
Main Results:
- R2 RNAs from diverse species fold into active HDV-like ribozymes.
- Cleavage occurred upstream of the R2/28S rRNA junction in many lineages.
- Cleavage site location correlated with R2 5' junction uniformity or variability.
Conclusions:
- Upstream cleavage promotes uniform priming of second-strand DNA synthesis.
- Variable cleavage sites may arise from microhomology priming.
- R2 ribozyme evolution shows changes in cleavage sites and active site convergence.
Related Concept Videos
02:47Ribozymes
The term ribozyme is used for RNA that can act as an enzyme. Ribozymes are mainly found in selected viruses, bacteria, plant organelles, and lower eukaryotes. Ribozymes were first discovered in 1982 when Tom Cech’s laboratory observed Group I introns acting as enzymes. This was shortly followed by the discovery of another ribozyme, Ribonulcease P, by Sid Altman’s laboratory. Both Cech and Altman received the Nobel Prize in chemistry in 1989 for their work on ribozymes.
Ribozymes can be...
Ribozymes can be...
02:47Ribozymes
The term ribozyme is used for RNA that can act as an enzyme. Ribozymes are mainly found in selected viruses, bacteria, plant organelles, and lower eukaryotes. Ribozymes were first discovered in 1982 when Tom Cech’s laboratory observed Group I introns acting as enzymes. This was shortly followed by the discovery of another ribozyme, Ribonulcease P, by Sid Altman’s laboratory. Both Cech and Altman received the Nobel Prize in chemistry in 1989 for their work on ribozymes.
Ribozymes can be...
Ribozymes can be...
03:08LTR Retrotransposons
LTR retrotransposons are class I transposable elements with long terminal repeats flanking an internal coding region. These elements are less abundant in mammals compared to other class I transposable elements. About 8 percent of human genomic DNA comprises LTR retrotransposons. Some of the common examples of LTR retrotransposons are Ty elements in yeast and Copia elements in Drosophila.
The internal coding region of LTR retrotransposons and their mechanism of transposition closely resembles a...
The internal coding region of LTR retrotransposons and their mechanism of transposition closely resembles a...
03:18Non-LTR Retrotransposons
As the name suggests, non-LTR retrotransposons lack the long terminal repeats characteristic of the LTR retrotransposons. Additionally, both LTR and non-LTR retrotransposons use distinct mechanisms of mobilization. Non-LTR retrotransposons are further divided into two classes - Long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs), both of which occur abundantly in most mammals, including humans. Some of the active non-LTR retrotransposons in humans are L1...
02:53Conservative Site-specific Recombination and Phase Variation
Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
The recognition sites for Cre recombinase called LoxP...
The recognition sites for Cre recombinase called LoxP...
00:43Bacterial RNA Polymerase
Unlike eukaryotes, bacteria use a single RNA Polymerase (RNAP) to transcribe all genes. The different subunits of bacterial RNAPhave distinct functions. The multisubunit structure of the bacterial RNAP helps the enzyme to maintain catalytic function, facilitate assembly, interact with DNA and RNA, and self-regulate its activity.
In most genes, the transcription site is a single base present upstream of the coding sequence. Though RNAP is a catalytically efficient enzyme, it does not recognize...
In most genes, the transcription site is a single base present upstream of the coding sequence. Though RNAP is a catalytically efficient enzyme, it does not recognize...