GIR1 branching ribozyme: Difference between revisions
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[[Image:GIR13DModel.png|thumb|right|300px|Overall model of ''Didymium'' GIR1 3D structure<ref>{{cite journal | last =Beckert | first = B. | coauthors = Masquida B. | year = 2008 | title = Molecular modelling of the GIR1 branching ribozyme gives new insight into evolution of structurally related ribozymes| journal = EMBO | volume = 27 | pages = |
[[Image:GIR13DModel.png|thumb|right|300px|Overall model of ''Didymium'' GIR1 3D structure<ref>{{cite journal | last =Beckert | first = B. | coauthors = Masquida B. | year = 2008 | title = Molecular modelling of the GIR1 branching ribozyme gives new insight into evolution of structurally related ribozymes| journal = EMBO | volume = 27 | pages = 667–78}}</ref>.]] |
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The '''GIR1 branching ribozyme''' is a 179 [[nucleotide|nt]] [[ribozyme]] with a structural resemblance to a group I ribozyme<ref>{{cite journal | last = Johansen | first = S. | coauthors = Nielsen H. | year = 2002 | title = DiGIR1 and NaGIR1: Naturally occurring group I-like ribozymes with unique core organization and evolved biological role| journal = Biochimie | volume = 84 | pages = |
The '''GIR1 branching ribozyme''' is a 179 [[nucleotide|nt]] [[ribozyme]] with a structural resemblance to a group I ribozyme<ref>{{cite journal | last = Johansen | first = S. | coauthors = Nielsen H. | year = 2002 | title = DiGIR1 and NaGIR1: Naturally occurring group I-like ribozymes with unique core organization and evolved biological role| journal = Biochimie | volume = 84 | pages = 905–12 | month=September | pmid=12458083 | url=http://linkinghub.elsevier.com/retrieve/pii/S0300908402014438}}</ref>. |
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It is found within a complex type of [[group I intron]]s also termed twin-ribozyme introns<ref name="pmid8124711">{{cite journal | last = Johansen | first = S. | coauthors = Vogt V.M. | year = 1994 | title = An intron in the nucelar ribosomal DNA of ''Didymium iridis'' encodes for a group I ribozyme and a novel ribozyme that cooperate in self-plicing | journal = Cell | volume = 76 | issue=4 | pages = |
It is found within a complex type of [[group I intron]]s also termed twin-ribozyme introns<ref name="pmid8124711">{{cite journal | last = Johansen | first = S. | coauthors = Vogt V.M. | year = 1994 | title = An intron in the nucelar ribosomal DNA of ''Didymium iridis'' encodes for a group I ribozyme and a novel ribozyme that cooperate in self-plicing | journal = Cell | volume = 76 | issue=4 | pages = 725–34 | month=February | pmid=8124711 | url=http://linkinghub.elsevier.com/retrieve/pii/0092-8674(94)90511-8}}</ref>. |
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Rather than [[RNA splicing|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]]<ref name="pmid16141078">{{cite journal | last = Nielsen | first = H. | coauthors = Johansen S. | year = 2005 | title = An mRNA is capped by a 2'5' lariat catalized by a group I-like ribozyme | journal = Science | volume = 309 | issue=5740 | pages = |
Rather than [[RNA splicing|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]]<ref name="pmid16141078">{{cite journal | last = Nielsen | first = H. | coauthors = Johansen S. | year = 2005 | title = An mRNA is capped by a 2'5' lariat catalized by a group I-like ribozyme | journal = Science | volume = 309 | issue=5740 | pages = 1584–7 |month=September | pmid=16141078 | doi=10.1126/science.1113645}}</ref>. |
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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 cap an intron-encoded [[mRNA]]. The resulting lariat cap seems to contribute by increasing the half-life of the HE mRNA<ref name="pmid16141078" /><ref name="pmid12444968">{{cite journal | last = Vader | first = A. | coauthors = Nielsen H. | year = 2002 | title = The group I-like ribozyme DiGIR1 mediates alternative processing of pre-rRNA transcripts in ''Didymium iridis''| journal = Biochem | volume = 269 |
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 cap an intron-encoded [[mRNA]]. The resulting lariat cap seems to contribute by increasing the half-life of the HE mRNA<ref name="pmid16141078" /><ref name="pmid12444968">{{cite journal | last = Vader | first = A. | coauthors = Nielsen H. | year = 2002 | title = The group I-like ribozyme DiGIR1 mediates alternative processing of pre-rRNA transcripts in ''Didymium iridis''| journal = Biochem | volume = 269 | issue=23 | pages = 5804–12 | month=December | pmid=12444968 | url=http://www3.interscience.wiley.com/resolve/openurl?genre=article&sid=nlm:pubmed&issn=0014-2956&date=2002&volume=269&issue=23&spage=5804}}</ref>, thus conferring an evolutionary advantage to the HE. |
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== Biological Context == |
== Biological Context == |
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''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 [[transesterification]] 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<ref name="pmid16141078" />. |
''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 [[transesterification]] 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<ref name="pmid16141078" />. |
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These products are the only products observed by analysis of cellular RNA |
These products are the only products observed by analysis of cellular RNA |
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<ref name="pmid12444968" /><ref>{{cite journal | last = Vader | first = A. | coauthors = Johansen S. | year = 1999 | title = In vivo expression of the nucleolar group I intron-encoded I-DirI homing endonuclease involves the removal of a spliceosomal intron| journal = EMBO J. | volume = 18 |
<ref name="pmid12444968" /><ref>{{cite journal | last = Vader | first = A. | coauthors = Johansen S. | year = 1999 | title = In vivo expression of the nucleolar group I intron-encoded I-DirI homing endonuclease involves the removal of a spliceosomal intron| journal = EMBO J. | volume = 18 | issue=4 | pages = 1003–13 | month=February | pmid=10022842 | pmc=1171192 | doi=10.1093/emboj/18.4.1003}}</ref>. |
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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. |
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. |
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== External links == |
== External links == |
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* |
*{{cite journal |author=Jäschke A |title=Book Review: Ribozymes and RNA Catalysis. Edited by David M. J. Lilley and Fritz Eckstein. |journal=Angewandte Chemie International Edition |volume=47 |issue=45 |pages=8558–9 |year=2008 |doi=10.1002/anie.200885598 |url=http://www3.interscience.wiley.com/journal/121471515/abstract?CRETRY=1&SRETRY=0}} |
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*{{cite journal |author=Doherty EA, Doudna JA |title=Ribozyme structures and mechanisms |journal=Annu Rev Biophys Biomol Struct |volume=30 |pages=457–75 |year=2001 |pmid=11441810 |doi=10.1146/annurev.biophys.30.1.457 |url=http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.biophys.30.1.457?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%3dncbi.nlm.nih.gov}} |
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*[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11441810&dopt=Abstract Ribozyme structures and mechanisms] |
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*{{cite journal |author=Visser CM |title=Evolution of Biocatalysis — Part One — Possible Pre-Genetic RNA Catalysts which are Their Own Replicas |journal=Origins of Life |volume=14 |issue=1-4 |pages=291–300 |year=1984 |doi=10.1007/BF00933670 }} RNA catalysis evolutionary insight |
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*[http://adsabs.harvard.edu/abs/1984OrLi...14..291V RNA catalysis evolutionary insight] |
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*[http://www.pulasthi.info/2007/08/not-all-enzymatic-reactions-are.html RNA catalysis] |
*[http://www.pulasthi.info/2007/08/not-all-enzymatic-reactions-are.html RNA catalysis] |
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Revision as of 10:47, 19 December 2009
The GIR1 branching ribozyme is a 179 nt ribozyme with a structural resemblance to a group I ribozyme[2]. It is found within a complex type of group I introns also termed twin-ribozyme introns[3]. 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[4]. 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 cap an intron-encoded mRNA. The resulting lariat cap seems to contribute by increasing the half-life of the HE mRNA[4][5], thus conferring an evolutionary advantage to the HE.
Biological Context
The GIR1 ribozyme was originally discovered during the functional characterization of the introns 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[3].
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 endonuclease 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 splicig 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 transesterification 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[4]. These products are the only products observed by analysis of cellular RNA [5][6]. 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 Structrure of GIR1
References
- ^ Beckert, B. (2008). "Molecular modelling of the GIR1 branching ribozyme gives new insight into evolution of structurally related ribozymes". EMBO. 27: 667–78.
{{cite journal}}: Unknown parameter|coauthors=ignored (|author=suggested) (help) - ^ Johansen, S. (2002). "DiGIR1 and NaGIR1: Naturally occurring group I-like ribozymes with unique core organization and evolved biological role". Biochimie. 84: 905–12. PMID 12458083.
{{cite journal}}: Unknown parameter|coauthors=ignored (|author=suggested) (help); Unknown parameter|month=ignored (help) - ^ a b Johansen, S. (1994). "An intron in the nucelar ribosomal DNA of Didymium iridis encodes for a group I ribozyme and a novel ribozyme that cooperate in self-plicing". Cell. 76 (4): 725–34. PMID 8124711.
{{cite journal}}: Unknown parameter|coauthors=ignored (|author=suggested) (help); Unknown parameter|month=ignored (help) - ^ a b c Nielsen, H. (2005). "An mRNA is capped by a 2'5' lariat catalized by a group I-like ribozyme". Science. 309 (5740): 1584–7. doi:10.1126/science.1113645. PMID 16141078.
{{cite journal}}: Unknown parameter|coauthors=ignored (|author=suggested) (help); Unknown parameter|month=ignored (help) - ^ a b Vader, A. (2002). "The group I-like ribozyme DiGIR1 mediates alternative processing of pre-rRNA transcripts in Didymium iridis". Biochem. 269 (23): 5804–12. PMID 12444968.
{{cite journal}}: Unknown parameter|coauthors=ignored (|author=suggested) (help); Unknown parameter|month=ignored (help) - ^ Vader, A. (1999). "In vivo expression of the nucleolar group I intron-encoded I-DirI homing endonuclease involves the removal of a spliceosomal intron". EMBO J. 18 (4): 1003–13. doi:10.1093/emboj/18.4.1003. PMC 1171192. PMID 10022842.
{{cite journal}}: Unknown parameter|coauthors=ignored (|author=suggested) (help); Unknown parameter|month=ignored (help)
External links
- Jäschke A (2008). "Book Review: Ribozymes and RNA Catalysis. Edited by David M. J. Lilley and Fritz Eckstein". Angewandte Chemie International Edition. 47 (45): 8558–9. doi:10.1002/anie.200885598.
- Doherty EA, Doudna JA (2001). "Ribozyme structures and mechanisms". Annu Rev Biophys Biomol Struct. 30: 457–75. doi:10.1146/annurev.biophys.30.1.457. PMID 11441810.
- Visser CM (1984). "Evolution of Biocatalysis — Part One — Possible Pre-Genetic RNA Catalysts which are Their Own Replicas". Origins of Life. 14 (1–4): 291–300. doi:10.1007/BF00933670. RNA catalysis evolutionary insight
- RNA catalysis