View source for GIR1 branching ribozyme

The '''Lariat capping ribozyme''' (formerly called '''GIR1 branching ribozyme''') is a ~180 [[nucleotide|nt]] [[ribozyme]] with an apparent resemblance to a group I ribozyme.<ref>{{cite journal | vauthors = Johansen S, Einvik C, Nielsen H | title = DiGIR1 and NaGIR1: naturally occurring group I-like ribozymes with unique core organization and evolved biological role | journal = Biochimie | volume = 84 | issue = 9 | pages = 905–12 | date = September 2002 | pmid = 12458083 | doi = 10.1016/S0300-9084(02)01443-8 }}</ref>
It is found within a complex type of [[group I intron]]s also termed twin-ribozyme introns.<ref name="pmid8124711">{{cite journal | vauthors = Johansen S, Vogt VM | title = An intron in the nuclear ribosomal DNA of Didymium iridis codes for a group I ribozyme and a novel ribozyme that cooperate in self-splicing | journal = Cell | volume = 76 | issue = 4 | pages = 725–34 | date = February 1994 | pmid = 8124711 | doi = 10.1016/0092-8674(94)90511-8 | s2cid = 45868519 }}</ref>
Rather than [[RNA splicing|splicing]], it [[biocatalysis|catalyses]] a branching reaction in which the 2'[[hydroxyl|OH]] of an internal [[residue (chemistry)|residue]] is involved in a [[nucleophilic attack]] at a nearby [[phosphodiester bond]].<ref name="pmid16141078">{{cite journal | vauthors = Nielsen H, Westhof E, Johansen S | s2cid = 37002071 | title = An mRNA is capped by a 2', 5' lariat catalyzed by a group I-like ribozyme | journal = Science | volume = 309 | issue = 5740 | pages = 1584–7 | date = September 2005 | pmid = 16141078 | doi = 10.1126/science.1113645 | bibcode = 2005Sci...309.1584N }}</ref>
As a result, the RNA is cleaved at an internal processing site (IPS), leaving a 3'OH and a downstream product with a 3 [[Nucleotide|nt]] lariat at its [[5'|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,<ref name="pmid16141078" /><ref name="pmid12444968">{{cite journal | vauthors = Vader A, Johansen S, Nielsen H | title = The group I-like ribozyme DiGIR1 mediates alternative processing of pre-rRNA transcripts in Didymium iridis | journal = European Journal of Biochemistry | volume = 269 | issue = 23 | pages = 5804–12 | date = December 2002 | pmid = 12444968 | doi = 10.1046/j.1432-1033.2002.03283.x | doi-access = free }}</ref> thus conferring an [[evolution]]ary advantage to the HE.
== Biological context ==
[[Image:WikiDiGIR-rDNA.png|thumb|left|300px|Schematic view of ''Dydimium iridis'' extrachromosomal rDNA and its twin-ribozyme system.]]
The GIR1 ribozyme was originally discovered during the functional characterization of the [[intron]]s from the extrachromosomal [[Ribosomal DNA|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.<ref name="pmid8124711" />
== Structural organization ==
The twin-ribozyme introns represent some of the most complex organized group I introns known and consist of a [[homing endonuclease]] gene (HEG: I-''Dir''I 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.
== Catalytic activity ==
{{Infobox rfam
| Name = GIR1 Branching Ribozyme
| image = GIR1_SS.png
| width =
| caption = Conserved [[secondary structure]] of GIR1
| Symbol = GIR1
| AltSymbols =
| Rfam = RF01807
| miRBase =
| miRBase_family =
| RNA_type = Intron
| Tax_domain = ''[[Naegleria]]''
| GO =
| SO =
| CAS_number =
| EntrezGene =
| HGNCid =
| OMIM =
| PDB =
| RefSeq =
| Chromosome =
| Arm =
| Band =
| LocusSupplementaryData =
}}''In vitro'', DiGIR1 catalyses three different reactions. The first one consists in hydrolysis of the scissile 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 an ''in vitro'' artefact resulting from misfolding 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" />
These products are the only products observed by analysis of cellular RNA.<ref name="pmid12444968" /><ref>{{cite journal | vauthors = Vader A, Nielsen H, Johansen S | title = In vivo expression of the nucleolar group I intron-encoded I-dirI homing endonuclease involves the removal of a spliceosomal intron | journal = The EMBO Journal | volume = 18 | issue = 4 | pages = 1003–13 | date = February 1999 | pmid = 10022842 | pmc = 1171192 | doi = 10.1093/emboj/18.4.1003 }}</ref>
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 the Lariat capping (LC) Ribozyme ==
GIR1 models have been created using biochemical and mutational data.<ref name="EMBO">{{cite journal|vauthors=Beckert B, Nielsen H, Einvik C, Johansen SD, Westhof E, Masquida B|date=February 2008|title=Molecular modelling of the GIR1 branching ribozyme gives new insight into evolution of structurally related ribozymes|journal=The EMBO Journal|volume=27|issue=4|pages=667–78|doi=10.1038/emboj.2008.4|pmc=2219692|pmid=18219270}}</ref> The structure contains an extended substrate domain which contains a GoU pair. The pair differs from the typical [[Group I catalytic intron|group 1 ribozyme]] nucleophilic residue, the J8/7 region has been [[reduction (chemistry)|reduced.]]<ref name="EMBO" /> These findings provide the basis for an [[evolution|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]].<ref name="EMBO" />
== Crystal structure of the Lariat Capping Ribozyme ==
[[File:The lariat capping ribozyme crystal structure (pdb- 4p95).png|thumb]]
The crystal structure of the LC ribozyme was recently published.<ref>{{Cite journal|last1=Meyer|first1=M.|last2=Nielsen|first2=H.|last3=Olieric|first3=V.|last4=Roblin|first4=P.|last5=Johansen|first5=S. D.|last6=Westhof|first6=E.|last7=Masquida|first7=B.|date=2014-05-27|title=Speciation of a group I intron into a lariat capping ribozyme|journal=Proceedings of the National Academy of Sciences|volume=111|issue=21|pages=7659–7664|doi=10.1073/pnas.1322248111|issn=0027-8424|pmc=4040574|pmid=24821772|bibcode=2014PNAS..111.7659M|doi-access=free}}</ref> In brief, a circularly permutated (CP) ribozyme RNA was generated by in vitro transcription using T7 RNA polymerase.<ref>{{Citation|last1=Beckert|first1=Bertrand|title=Synthesis of RNA by in Vitro Transcription|volume=703|date=2011|work=RNA: Methods and Protocols|pages=29–41|editor-last=Nielsen|editor-first=Henrik|series=Methods in Molecular Biology|publisher=Humana Press|doi=10.1007/978-1-59745-248-9_3|pmid=21125481|isbn=978-1-59745-248-9|last2=Masquida|first2=Benoît|s2cid=26196836 }}</ref>
The 5' and 3' generated by circular permutation are located at the natural ribozyme cleavage site. To allow transcription of this construct, optimized  5' hammerhead and HdV (Hepatitis delay Virus) ribozymes were flanked to the LC CP construct.<ref>{{Citation|last1=Meyer|first1=Mélanie|title=Cis-Acting 5' Hammerhead Ribozyme Optimization for in Vitro Transcription of Highly Structured RNAs|volume=1086|date=2014|work=RNA Folding: Methods and Protocols|pages=21–40|editor-last=Waldsich|editor-first=Christina|series=Methods in Molecular Biology|publisher=Humana Press|doi=10.1007/978-1-62703-667-2_2|pmid=24136596|isbn=978-1-62703-667-2|last2=Masquida|first2=Benoît}}</ref>
The crystal structure of the LC ribozyme unravels how the regulatory domain formed by P2, P2.1 and P10 works. Two sets of tertiary interactions take place to constrain P2 and P2.1 allowing the formation of a 3-way junction, which acts as a receptor for nt A209. This snug fit interaction promotes formation of the catalytic site, provided that the lariat is pre-folded by the ribozyme core.
== References ==
{{reflist|30em}}
== Further reading ==
{{refbegin}}
* {{cite journal | vauthors = 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  }}
* {{cite journal | vauthors = Doherty EA, Doudna JA | title = Ribozyme structures and mechanisms | journal = Annual Review of Biophysics and Biomolecular Structure | volume = 30 | pages = 457–75 | year = 2001 | pmid = 11441810 | doi = 10.1146/annurev.biophys.30.1.457 }}
* {{cite journal | vauthors = Visser CM | title = Evolution of biocatalysis 1. Possible pre-genetic-code RNA catalysts which are their own replicase | journal = Origins of Life | volume = 14 | issue = 1–4 | pages = 291–300 | year = 1984 | pmid = 6205343 | doi = 10.1007/BF00933670 | bibcode = 1984OrLi...14..291V | s2cid = 31409366 }} RNA catalysis evolutionary insight
{{refend}}
== External links ==
* Labs working on GIR1 branching ribozyme characterisation:
** Henrik Nielsen lab [https://web.archive.org/web/20090806020436/http://icmm.ku.dk/Forskergrupper/rna/research_projects/]
** [[Eric Westhof]] lab [http://www-ibmc.u-strasbg.fr/arn/Westhof/index.html] {{Webarchive|url=https://web.archive.org/web/20090724115119/http://www-ibmc.u-strasbg.fr/arn/Westhof/index.html |date=2009-07-24 }}
** Steinar Johansen lab [https://archive.today/20130223001701/http://www2.uit.no/ikbViewer/page/ansatte/organisasjon/hjem?p_dimension_id=92436&p_menu=42374&p_lang=2]
*[https://web.archive.org/web/20081028204053/http://www.pulasthi.info/2007/08/not-all-enzymatic-reactions-are.html RNA catalysis]
* {{Rfam|id=RF01807|name=GIR1 branching ribozyme}}
{{DEFAULTSORT:Lariat Capping Ribozyme (former GIR1_branching_ribozyme)}}
[[Category:Ribozymes]]
[[Category:RNA splicing]]