View source for Group II intron

{{Short description|Class of self-catalyzing ribozymes}}
{{Infobox rfam|Symbol=Intron_gpII|Name=Group II catalytic intron, D5|Rfam=RF00029|PDB=6cih|image=IntronGroupII.jpg|caption=full secondary structure of group II intron|extra=Entry contains Splicing domain V (D5) and some consensus 3' to it.}}
{{Infobox rfam|Symbol=group-II-D1D4|Name=Group II catalytic intron, D1-D4|Rfam_clan=CL00102|PDB=4fb0|extra=Entry contains D1-D4, parts 5' to D5.}}
'''Group II introns''' are a large class of self-catalytic [[ribozyme]]s and mobile genetic elements found within the [[gene]]s of all three [[Domain (biology)|domains of life]]. Ribozyme activity (e.g., self-[[RNA splicing|splicing]]) can occur under high-salt conditions ''[[in vitro]]''.  However, assistance from [[protein]]s is required for ''[[in vivo]]'' splicing.<ref name=Lambowitz2011>{{cite journal | vauthors = Lambowitz AM, Zimmerly S | title = Group II introns: mobile ribozymes that invade DNA | journal = Cold Spring Harbor Perspectives in Biology | volume = 3 | issue = 8 | pages = a003616 | date = August 2011 | pmid = 20463000 | pmc = 3140690 | doi = 10.1101/cshperspect.a003616 }}</ref> In contrast to [[Group I catalytic intron|group I introns]], intron excision occurs in the absence of [[Guanosine triphosphate|GTP]] and involves the formation of a [[Lariat (disambiguation)|lariat]], with an A-residue branchpoint strongly resembling that found in lariats formed during splicing of nuclear pre-mRNA. It is hypothesized that pre-mRNA splicing (see [[spliceosome]]) may have evolved from group II introns, due to the similar catalytic mechanism as well as the structural similarity of the Group II Domain V substructure to the U6/U2 extended [[Small nuclear RNA|snRNA]].<ref name=Seetharaman2006>{{cite journal | vauthors = Seetharaman M, Eldho NV, Padgett RA, Dayie KT | title = Structure of a self-splicing group II intron catalytic effector domain 5: parallels with spliceosomal U6 RNA | journal = RNA | volume = 12 | issue = 2 | pages = 235–47 | date = February 2006 | pmid = 16428604 | pmc = 1370903 | doi = 10.1261/rna.2237806 }}</ref><ref name=Valadkhan2010>{{cite journal | vauthors = Valadkhan S |author-link1=Saba Valadkhan| title = Role of the snRNAs in spliceosomal active site | journal = RNA Biology | volume = 7 | issue = 3 | pages = 345–53 | date = May–Jun 2010 | pmid = 20458185 | doi = 10.4161/rna.7.3.12089 | doi-access = free }}</ref> Finally, their ability to site-specifically insert into DNA sites has been exploited as a tool for [[biotechnology]].<ref name=Karberg2001>{{cite journal | vauthors = Karberg M, Guo H, Zhong J, Coon R, Perutka J, Lambowitz AM | title = Group II introns as controllable gene targeting vectors for genetic manipulation of bacteria | journal = Nat Biotechnol | volume = 19 | issue = 12 | pages = 1162–7 | date = December 2001 | pmid = 11731786 | doi = 10.1038/nbt1201-1162| s2cid = 18669663 }} </ref> For example, group II introns can be modified to make site-specific genome insertions and deliver cargo DNA such as reporter genes or ''lox'' sites <ref name=Cerisy2019>{{cite journal | vauthors = Cerisy T, Rostain W, Chhun A, Boutard M, Salanoubat M, Tolonen AC | title = A Targetron-Recombinase System for Large-Scale Genome Engineering of Clostridia | journal = mSphere | volume = 4 | issue = 6 | pages = e00710-19 | date = December 2019 | pmid = 31826971 | doi = 10.1128/mSphere.00710-19| pmc = 6908422 }} </ref>

==Structure and catalysis==

[[File:Domain-V-secondary-structure.svg|thumb|left|The Domain V substructure that is shared between Group II introns and [[U6 spliceosomal RNA]].]]

The secondary structure of group II introns is characterized by six typical stem-loop structures, also called domains I to VI (DI to DVI, or D1 to D6). The domains radiate from a central core that brings the 5' and 3' splice junctions into close proximity. The proximal helix structures of the six domains are connected by a few [[nucleotide]]s in the central region (linker or joiner sequences). Due to its enormous size, the domain I was divided further into subdomains a, b, c, and d.  Sequence differences of group II introns that led to a further division into subgroups IIA, IIB and IIC were identified, along with varying distance of the bulged [[adenosine]] in domain VI (the prospective branch point forming the lariat) from the 3' splice site, and the inclusion or omission of structural elements such as a coordination loop in domain I, which is present in IIB and IIC introns but not IIA.<ref name=Lambowitz2011/> Group II introns also form very complicated [[RNA Tertiary Structure]].

Group II introns possess only a very few conserved nucleotides, and the nucleotides important for the catalytic function are spread over the complete intron structure. The few strictly conserved primary sequences are the consensus at the 5' and 3' splicing site (...↓GUGYG&... and ...AY↓..., with the Y representing a [[pyrimidine]]), some of the nucleotides of the central core (joiner sequences), a relatively high number of nucleotides of DV and some short-sequence stretches of DI. The unpaired adenosine in DVI (marked by an asterisk in the figure and located 7 or 8 nt away from the 3' splicing site) is also conserved and plays a central role in the splicing process. The 2' hydroxyl of the bulged [[adenosine]] attacks the 5' splice site, followed by [[nucleophilic attack]] on the 3' splice site by the 3' OH of the upstream [[exon]]. This results in a branched intron lariat connected by a 2' phosphodiester linkage at the DVI adenosine.

Protein machinery is required for splicing ''[[in vivo]]'', and long-range intron-intron and intron-exon interactions are important for splice site positioning, as well as a number of tertiary contacts between motifs, including kissing-loop and tetraloop-receptor interactions. In 2005, A. De Lencastre et al. found that during splicing of Group II introns, all reactants are preorganized before the initiation of splicing. The branch site, both exons, the catalytically essential regions of DV and J2/3, and ε−ε' are in close proximity before the first step of splicing occurs. In addition to the bulge and AGC triad regions of DV, the J2/3 linker region, the ε−ε' nucleotides and the coordination loop in DI are crucial for the architecture and function of the active-site.<ref name= deLancastre2005>{{cite journal | vauthors = de Lencastre A, Hamill S, Pyle AM | title = A single active-site region for a group II intron | journal = Nature Structural & Molecular Biology | volume = 12 | issue = 7 | pages = 626–7 | date = July 2005 | pmid = 15980867 | doi = 10.1038/nsmb957 | s2cid = 27639877 }}</ref>

The first crystal structure of a group II intron was resolved in 2008 for the ''Oceanobacillus iheyensis'' group IIC catalytic intron, and was joined by the ''Pylaiella littoralis'' (P.li.LSUI2) group IIB intron in 2014. Attempts have been made to model the tertiary structure of other group II introns, such as the ai5γ group IIB intron, using a combination of programs for homology mapping onto known structures and ''de novo'' modeling of previously unresolved regions.<ref name=Somarowthu2014>{{cite journal | vauthors = Somarowthu S, Legiewicz M, Keating KS, Pyle AM | title = Visualizing the ai5γ group IIB intron | journal = Nucleic Acids Research | volume = 42 | issue = 3 | pages = 1947–58 | date = February 2014 | pmid = 24203709 | pmc = 3919574 | doi = 10.1093/nar/gkt1051 }}</ref> Group IIC are characterized by a catalytic triad made up by CGC, while Group IIA and Group IIB are made up by AGC catalytic triad, which is more similar to the catalytic triad of the spliceosome. It is believed that the Group IIC are also smaller, more reactive and more ancient. The first step of splicing in Group IIC intron is done by water and it form a linear structure instead of lariat.<ref>{{cite journal | vauthors = Keating KS, Toor N, Perlman PS, Pyle AM | title = A structural analysis of the group II intron active site and implications for the spliceosome | journal = RNA | volume = 16 | issue = 1 | pages = 1–9 | date = January 2010 | pmid = 19948765 | pmc = 2802019 | doi = 10.1261/rna.1791310 }}</ref>

==Distribution and phylogeny==
{{Pfam box|Name=Domain X|Pfam_clan=CL0359|Pfam=PF01348|Symbol=Domain_X|InterPro=IPR024937}}
{{Pfam box|Pfam=PF08388|Pfam_clan=CL0359|Symbol=GIIM|InterPro=IPR013597|Name=Group II intron, maturase-specific}}
'''Group II introns''' are found in [[rRNA]], [[tRNA]], and [[mRNA]] of [[organelle]]s (chloroplasts and mitochondria) in [[fungi]], [[plants]], and [[protists]], and also in mRNA in [[bacteria]]. The first intron to be identified as distinct from group I was the ai5γ group IIB intron, which was isolated in 1986 from a pre-mRNA transcript of the ''oxi 3'' mitochondrial gene of ''Saccharomyces cerevisiae''.<ref name=Peebles1986>{{cite journal | vauthors = Peebles CL, Perlman PS, Mecklenburg KL, Petrillo ML, Tabor JH, Jarrell KA, Cheng HL | title = A self-splicing RNA excises an intron lariat | journal = Cell | volume = 44 | issue = 2 | pages = 213–23 | date = January 1986 | pmid = 3510741 | doi = 10.1016/0092-8674(86)90755-5 | s2cid = 42307152 }}</ref>

A subset of group II [[intron]]s encode essential splicing proteins, known as intron-encoded proteins or IEPs, in intronic [[Open reading frame|ORF]]s.  The length of these introns can, as a result, be up to 3 kb. Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing with two transesterification steps, with both also using magnesium ions to stabilize the leaving group in each step, which has led some to theorize a phylogenetic link between group II introns and the nuclear spliceosome. Further evidence for this link includes structural similarity between the U2/U6 junction of spliceosomal RNA and domain V of group II introns, which contains the catalytic AGC triad and much of the heart of the active site, as well as parity between conserved 5' and 3' end sequences.<ref name=Gordon2000>{{cite journal | vauthors = Gordon PM, Sontheimer EJ, Piccirilli JA | title = Metal ion catalysis during the exon-ligation step of nuclear pre-mRNA splicing: extending the parallels between the spliceosome and group II introns | journal = RNA | volume = 6 | issue = 2 | pages = 199–205 | date = February 2000 | pmid = 10688359 | pmc = 1369906 | doi = 10.1017/S1355838200992069 | url = http://rnajournal.cshlp.org/content/6/2/199.long }}</ref>

Many of these IEPs, including [[LtrA]], share a reverse transcriptase domain and a "Domain X".<ref name=pmid16763758/> [[Maturase K]] (MatK) is a protein somewhat similar to those intron-encoded proteins, found in plant chloroplasts. It is required for ''in vivo'' splicing of Group II introns, and can be found in chloroplastic introns or in the nuclear genome. Its RT domain is broken.<ref name=pmid16763758>{{cite journal | vauthors = Ahlert D, Piepenburg K, Kudla J, Bock R | title = Evolutionary origin of a plant mitochondrial group II intron from a reverse transcriptase/maturase-encoding ancestor | journal = Journal of Plant Research | volume = 119 | issue = 4 | pages = 363–71 | date = July 2006 | pmid = 16763758 | doi = 10.1007/s10265-006-0284-0 | bibcode = 2006JPlR..119..363A | s2cid = 8277547 }}</ref>

=== Protein domain ===
Group II IEPs share a related conserved domain, known as either "Domain X" in organelles or "GIIM" in bacteria, that is not found in other retroelements.<ref>{{cite journal | vauthors = Mohr G, Perlman PS, Lambowitz AM | title = Evolutionary relationships among group II intron-encoded proteins and identification of a conserved domain that may be related to maturase function | journal = Nucleic Acids Research | volume = 21 | issue = 22 | pages = 4991–7 | date = November 1993 | pmid = 8255751 | pmc = 310608 | doi = 10.1093/nar/21.22.4991 }}</ref><ref name=SmG2>{{cite journal | vauthors = Centrón D, Roy PH | title = Presence of a group II intron in a multiresistant Serratia marcescens strain that harbors three integrons and a novel gene fusion | journal = Antimicrobial Agents and Chemotherapy | volume = 46 | issue = 5 | pages = 1402–9 | date = May 2002 | pmid = 11959575 | pmc = 127176 | doi = 10.1128/AAC.46.5.1402-1409.2002 }}</ref> Domain X is essential for splicing in yeast mitochondria.<ref>{{cite journal | vauthors = Moran JV, Mecklenburg KL, Sass P, Belcher SM, Mahnke D, Lewin A, Perlman P | title = Splicing defective mutants of the COXI gene of yeast mitochondrial DNA: initial definition of the maturase domain of the group II intron aI2 | journal = Nucleic Acids Research | volume = 22 | issue = 11 | pages = 2057–64 | date = June 1994 | pmid = 8029012 | pmc = 308121 | doi = 10.1093/nar/22.11.2057 }}</ref> This domain may be responsible for recognizing and binding to intron RNA<ref name=SmG2/> or DNA.<ref>{{cite journal | vauthors = Guo H, Zimmerly S, Perlman PS, Lambowitz AM | title = Group II intron endonucleases use both RNA and protein subunits for recognition of specific sequences in double-stranded DNA | journal = The EMBO Journal | volume = 16 | issue = 22 | pages = 6835–48 | date = November 1997 | pmid = 9362497 | pmc = 1170287 | doi = 10.1093/emboj/16.22.6835 }}</ref>

== See also ==
*[[Database for bacterial group II introns]]
*[[Intron]]
*[[Splice site]]
*[[Splicing (genetics)#Spliceosomal|Nuclear introns]]
*[[Group I catalytic intron|Group I intron]]
*[[Group III intron]]
*[[Twintron]]
*''[[LtrA]]''

== References ==
{{reflist}}

== Further reading ==
{{refbegin}}
* {{cite journal | vauthors = Bonen L, Vogel J | title = The ins and outs of group II introns | journal = Trends in Genetics | volume = 17 | issue = 6 | pages = 322–31 | date = June 2001 | pmid = 11377794 | doi = 10.1016/S0168-9525(01)02324-1 }}
* {{cite journal | vauthors = Chu VT, Adamidi C, Liu Q, Perlman PS, Pyle AM | title = Control of branch-site choice by a group II intron | journal = The EMBO Journal | volume = 20 | issue = 23 | pages = 6866–76 | date = December 2001 | pmid = 11726522 | pmc = 125754 | doi = 10.1093/emboj/20.23.6866 }}
* {{cite journal | vauthors = Lehmann K, Schmidt U | title = Group II introns: structure and catalytic versatility of large natural ribozymes | journal = Critical Reviews in Biochemistry and Molecular Biology | volume = 38 | issue = 3 | pages = 249–303 | year = 2003 | pmid = 12870716 | doi = 10.1080/713609236 | s2cid = 20944113 }}
* {{cite journal | vauthors = Michel F, Umesono K, Ozeki H | title = Comparative and functional anatomy of group II catalytic introns--a review | journal = Gene | volume = 82 | issue = 1 | pages = 5–30 | date = October 1989 | pmid = 2684776 | doi = 10.1016/0378-1119(89)90026-7 }}
{{refend}}

== External links ==

{{Self-replicating organic structures}}

[[Category:RNA]]
[[Category:Ribozymes]]
[[Category:RNA splicing]]