GIR1 branching ribozyme
Encyclopedia
The GIR1 branching ribozyme is a 179 nt
ribozyme
with a structural resemblance to a group I ribozyme.
It is found within a complex type of group I introns also termed twin-ribozyme introns.
Rather than splicing
, it catalyses
a branching reaction in which the 2'OH
of an internal residue
is involved in a nucleophilic attack at a nearby phosphodiester bond
.
As a result, the RNA is cleaved at an internal processing site (IPS), leaving a 3'OH and a downstream product with a tiny lariat at its 5' end. The lariat has the first and the third nucleotide joined by a 2',5' phosphodiester bond and is referred to as 'the lariat cap' because it caps an intron-encoded mRNA. The resulting lariat cap seems to contribute by increasing the half-life
of the HE mRNA, thus conferring an evolution
ary advantage to the HE.
The GIR1 ribozyme was originally discovered during the functional characterization of the intron
s from the extrachromosomal rDNA
of the Didymium iridis protist
. A combination of deletion and in vitro
self-splicing analyses revealed a twin-ribozyme intron organization: two distinct ribozyme domains within the intron.
gene (HEG: I-DirI homing endonuclease) embedded in two functionally distinct catalytic RNA domains. One of the catalytic RNAs is a conventional group I intron ribozyme (GIR2) responsible for the intron splicing and reverse splicing, as well as intron RNA circularization. The other catalytic RNA domain is the group I-like ribozyme (GIR1) directly involved in homing endonuclease mRNA maturation.
at the IPS site results in the cleavage of the RNA with a 3'OH and a downstream lariat cap made by joining of the first and the third nucleotide by a 2'-5' phosphodiester bond.
These products are the only products observed by analysis of cellular RNA.
This branching reaction is in equilibrium with a third one: a ligation reaction. It is a very efficient reaction and it tends to mask the branching reaction during the in vitro branching experiments with the full-length intron and length variants that include more than 166 nucleotides upstream of the IPS.
nucleophilic residue, the J8/7 region has been reduced. These findings provide the basis for an evolutionary mechanism
that accounts for the change from group I splicing ribozyme to the branching GIR1 architecture. This mechanism could potentially be applied to other large RNAs such as the ribonuclease P.
Nucleotide
Nucleotides are molecules that, when joined together, make up the structural units of RNA and DNA. In addition, nucleotides participate in cellular signaling , and are incorporated into important cofactors of enzymatic reactions...
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...
with a structural resemblance to a group I ribozyme.
It is found within a complex type of group I introns also termed twin-ribozyme introns.
Rather than splicing
RNA splicing
In molecular biology and genetics, splicing is a modification of an RNA after transcription, in which introns are removed and exons are joined. This is needed for the typical eukaryotic messenger RNA before it can be used to produce a correct protein through translation...
, it catalyses
Biocatalysis
Biocatalysis is the use of natural catalysts, such as protein enzymes, to perform chemical transformations on organic compounds. Both enzymes that have been more or less isolated and enzymes still residing inside living cells are employed for this task....
a branching reaction in which the 2'OH
Hydroxyl
A hydroxyl is a chemical group containing an oxygen atom covalently bonded with a hydrogen atom. In inorganic chemistry, the hydroxyl group is known as the hydroxide ion, and scientists and reference works generally use these different terms though they refer to the same chemical structure in...
of an internal residue
Residue (chemistry)
In chemistry, residue is the material remaining after a distillation or an evaporation, or to a portion of a larger molecule, such as a methyl group. It may also refer to the undesired byproducts of a reaction....
is involved in a nucleophilic attack at a nearby phosphodiester bond
Phosphodiester bond
A phosphodiester bond is a group of strong covalent bonds between a phosphate group and two 5-carbon ring carbohydrates over two ester bonds. Phosphodiester bonds are central to all known life, as they make up the backbone of each helical strand of DNA...
.
As a result, the RNA is cleaved at an internal processing site (IPS), leaving a 3'OH and a downstream product with a tiny lariat at its 5' end. The lariat has the first and the third nucleotide joined by a 2',5' phosphodiester bond and is referred to as 'the lariat cap' because it caps an intron-encoded mRNA. The resulting lariat cap seems to contribute by increasing the half-life
Half-life
Half-life, abbreviated t½, is the period of time it takes for the amount of a substance undergoing decay to decrease by half. The name was originally used to describe a characteristic of unstable atoms , but it may apply to any quantity which follows a set-rate decay.The original term, dating to...
of the HE mRNA, thus conferring an evolution
Evolution
Evolution is any change across successive generations in the heritable characteristics of biological populations. Evolutionary processes give rise to diversity at every level of biological organisation, including species, individual organisms and molecules such as DNA and proteins.Life on Earth...
ary advantage to the HE.
Biological context
Intron
An intron is any nucleotide sequence within a gene that is removed by RNA splicing to generate the final mature RNA product of a gene. The term intron refers to both the DNA sequence within a gene, and the corresponding sequence in RNA transcripts. Sequences that are joined together in the final...
s from the extrachromosomal rDNA
Ribosomal DNA
Ribosomal DNA codes for ribosomal RNA. The ribosome is an intracellular macromolecule that produces proteins or polypeptide chains. The ribosome itself consists of a composite of proteins and RNA. As shown in the figure, rDNA consists of a tandem repeat of a unit segment, an operon, composed of...
of the Didymium iridis protist
Protist
Protists are a diverse group of eukaryotic microorganisms. Historically, protists were treated as the kingdom Protista, which includes mostly unicellular organisms that do not fit into the other kingdoms, but this group is contested in modern taxonomy...
. A combination of deletion and in vitro
In vitro
In vitro refers to studies in experimental biology that are conducted using components of an organism that have been isolated from their usual biological context in order to permit a more detailed or more convenient analysis than can be done with whole organisms. Colloquially, these experiments...
self-splicing analyses revealed a twin-ribozyme intron organization: two distinct ribozyme domains within the intron.
Structural organization of the twin-ribozyme Introns
The twin-ribozyme introns represent some of the most complex organized group I introns known and consist of a homing endonucleaseHoming endonuclease
The homing endonucleases are a type of restriction enzymes typically encoded by introns or inteins. They act on the cellular DNA of the cells that synthesize them, in the opposite alleles of the genes that encode them.- Origin and mechanism :...
gene (HEG: I-DirI homing endonuclease) embedded in two functionally distinct catalytic RNA domains. One of the catalytic RNAs is a conventional group I intron ribozyme (GIR2) responsible for the intron splicing and reverse splicing, as well as intron RNA circularization. The other catalytic RNA domain is the group I-like ribozyme (GIR1) directly involved in homing endonuclease mRNA maturation.
GIR1 catalyzes three different reactions
In vitro, DiGIR1 catalyses three different reactions. The first one consists in hydrolysis of the scissil phosphate at the IPS site. This is the cleavage reaction observed with the full-length intron and several length variants with a relative low rate. The hydrolytic cleavage is irreversible and is considered as an in vitro artefact resulting from a miss-folding of the catalytic site to present the branch nucleotide (BP) correctly for the reaction. The second reaction,the natural one, is the branching reaction, in which a transesterificationTransesterification
In organic chemistry, transesterification is the process of exchanging the organic group R″ of an ester with the organic group R′ of an alcohol. These reactions are often catalyzed by the addition of an acid or base catalyst...
at the IPS site results in the cleavage of the RNA with a 3'OH and a downstream lariat cap made by joining of the first and the third nucleotide by a 2'-5' phosphodiester bond.
These products are the only products observed by analysis of cellular RNA.
This branching reaction is in equilibrium with a third one: a ligation reaction. It is a very efficient reaction and it tends to mask the branching reaction during the in vitro branching experiments with the full-length intron and length variants that include more than 166 nucleotides upstream of the IPS.
Modelling structure of GIR1
GIR1 models have been created using biochemical and mutational data. The structure contains an extended substrate domain which contains a GoU pair. The pair differs from the typical group 1 ribozymeGroup I catalytic intron
Group I introns are large self-splicing ribozymes. They catalyze their own excision from mRNA, tRNA and rRNA precursors in a wide range of organisms. The core secondary structure consists of nine paired regions...
nucleophilic residue, the J8/7 region has been reduced. These findings provide the basis for an evolutionary mechanism
Evolution
Evolution is any change across successive generations in the heritable characteristics of biological populations. Evolutionary processes give rise to diversity at every level of biological organisation, including species, individual organisms and molecules such as DNA and proteins.Life on Earth...
that accounts for the change from group I splicing ribozyme to the branching GIR1 architecture. This mechanism could potentially be applied to other large RNAs such as the ribonuclease P.
External links
- Labs working on GIR1 branching ribozyme characterisation:
- Henrik Nielsen lab http://icmm.ku.dk/Forskergrupper/rna/research_projects/
- Eric Westhof lab http://www-ibmc.u-strasbg.fr/arn/Westhof/index.html
- Steinar Johansen lab http://www2.uit.no/ikbViewer/page/ansatte/organisasjon/hjem?p_dimension_id=92436&p_menu=42374&p_lang=2
- RNA catalysis