Hepatitis delta virus ribozyme
Encyclopedia
The hepatitis delta virus (HDV) ribozyme is a non-coding RNA
that is necessary for viral replication and is thought to be the only catalytic RNA known to be required for viability of a human pathogen
. The ribozyme
acts to process the RNA transcripts to unit lengths in a self-cleavage reaction. The ribozyme is found to be active in vivo in the absence of any protein factors and is the fastest known naturally occurring self-cleaving RNA.
The crystal structure of this ribozyme has been solved using X-ray crystallography
and shows five helical segments connected by a double pseudoknot
.
In addition to the sense (genomic version), all HDV viruses also have an anti-genomic version of the HDV ribozyme. This version is not the exact complementary sequence but adopts the same structure as the sense (genomic) strand. The only "significant" differences between the two are a small bulge in P4 stem and a shorter J4/2 junction.
The hepatitis delta virus ribozyme is structurally and biochemically related to the Mammalian CPEB3 ribozyme
. Unrelated sequences with high similarity to the HDV ribozyme have evolved through convergent evolution
(e.g. in the R2 RNA element
).
Non-coding RNA
A non-coding RNA is a functional RNA molecule that is not translated into a protein. Less-frequently used synonyms are non-protein-coding RNA , non-messenger RNA and functional RNA . The term small RNA is often used for short bacterial ncRNAs...
that is necessary for viral replication and is thought to be the only catalytic RNA known to be required for viability of a human pathogen
Pathogen
A pathogen gignomai "I give birth to") or infectious agent — colloquially, a germ — is a microbe or microorganism such as a virus, bacterium, prion, or fungus that causes disease in its animal or plant host...
. The ribozyme
Ribozyme
A ribozyme is an RNA molecule with a well defined tertiary structure that enables it to catalyze a chemical reaction. Ribozyme means ribonucleic acid enzyme. It may also be called an RNA enzyme or catalytic RNA. Many natural ribozymes catalyze either the hydrolysis of one of their own...
acts to process the RNA transcripts to unit lengths in a self-cleavage reaction. The ribozyme is found to be active in vivo in the absence of any protein factors and is the fastest known naturally occurring self-cleaving RNA.
The crystal structure of this ribozyme has been solved using X-ray crystallography
X-ray crystallography
X-ray crystallography is a method of determining the arrangement of atoms within a crystal, in which a beam of X-rays strikes a crystal and causes the beam of light to spread into many specific directions. From the angles and intensities of these diffracted beams, a crystallographer can produce a...
and shows five helical segments connected by a double pseudoknot
Pseudoknot
A pseudoknot is a nucleic acid secondary structure containing at least two stem-loop structures in which half of one stem is intercalated between the two halves of another stem. The pseudoknot was first recognized in the turnip yellow mosaic virus in 1982...
.
In addition to the sense (genomic version), all HDV viruses also have an anti-genomic version of the HDV ribozyme. This version is not the exact complementary sequence but adopts the same structure as the sense (genomic) strand. The only "significant" differences between the two are a small bulge in P4 stem and a shorter J4/2 junction.
The hepatitis delta virus ribozyme is structurally and biochemically related to the Mammalian CPEB3 ribozyme
Mammalian CPEB3 ribozyme
The mammalian CPEB3 ribozyme is a self cleaving non-coding RNA located in the second intron of the CPEB3 gene which belongs to a family of genes regulating messenger RNA polyadenylation. This ribozyme is highly conserved and...
. Unrelated sequences with high similarity to the HDV ribozyme have evolved through convergent evolution
Convergent evolution
Convergent evolution describes the acquisition of the same biological trait in unrelated lineages.The wing is a classic example of convergent evolution in action. Although their last common ancestor did not have wings, both birds and bats do, and are capable of powered flight. The wings are...
(e.g. in the R2 RNA element
R2 RNA element
The R2 RNA element is a non-long terminal repeat retrotransposable element that inserts at a specific site in the 28S ribosomal RNA genes of most insect genomes...
).