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Group II introns are a large class of self-catalytic
ribozyme Ribozymes (ribonucleic acid enzymes) are RNA molecules that have the ability to catalyze specific biochemical reactions, including RNA splicing in gene expression, similar to the action of protein enzymes. The 1982 discovery of ribozymes demonst ...
s and mobile genetic elements found within the
gene In biology, the word gene (from , ; "...Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a ba ...
s of all three
domains of life In Biology, biological Taxonomy (biology), taxonomy, a domain ( or ) (Latin: ''regio''), also dominion, superkingdom, realm, or empire, is the highest taxonomic rank of all organisms taken together. It was introduced in the three-domain system of ...
. Ribozyme activity (e.g., self- splicing) can occur under high-salt conditions ''
in vitro ''In vitro'' (meaning in glass, or ''in the glass'') studies are performed with microorganisms, cells, or biological molecules outside their normal biological context. Colloquially called "test-tube experiments", these studies in biology an ...
''. However, assistance from
protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respo ...
s is required for ''
in vivo Studies that are ''in vivo'' (Latin for "within the living"; often not italicized in English) are those in which the effects of various biological entities are tested on whole, living organisms or cells, usually animals, including humans, and ...
'' splicing. In contrast to group I introns, intron excision occurs in the absence of GTP and involves the formation of a
lariat A lasso ( or ), also called lariat, riata, or reata (all from Castilian, la reata 're-tied rope'), is a loop of rope designed as a restraint to be thrown around a target and tightened when pulled. It is a well-known tool of the Spanish an ...
, 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 A spliceosome is a large ribonucleoprotein (RNP) complex found primarily within the nucleus of eukaryotic cells. The spliceosome is assembled from small nuclear RNAs (snRNA) and numerous proteins. Small nuclear RNA (snRNA) molecules bind to specifi ...
) 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
snRNA Small nuclear RNA (snRNA) is a class of small RNA molecules that are found within the splicing speckles and Cajal bodies of the cell nucleus in eukaryotic cells. The length of an average snRNA is approximately 150 nucleotides. They are transcribed ...
. Finally, their ability to site-specifically insert into DNA sites has been exploited as a tool for
biotechnology Biotechnology is the integration of natural sciences and engineering sciences in order to achieve the application of organisms, cells, parts thereof and molecular analogues for products and services. The term ''biotechnology'' was first used b ...
. 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


Structure and catalysis

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 Nucleotides are organic molecules consisting of a nucleoside and a phosphate. They serve as monomeric units of the nucleic acid polymers – deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both of which are essential biomolecules wi ...
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 Adenosine ( symbol A) is an organic compound that occurs widely in nature in the form of diverse derivatives. The molecule consists of an adenine attached to a ribose via a β-N9-glycosidic bond. Adenosine is one of the four nucleoside building ...
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. Group II introns also form very complicated
RNA Tertiary Structure Nucleic acid tertiary structure is the Biomolecular structure#Tertiary structure, three-dimensional shape of a nucleic acid polymer. RNA and DNA molecules are capable of diverse functions ranging from molecular recognition to catalysis. Such fun ...
. 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 Pyrimidine (; ) is an aromatic, heterocyclic, organic compound similar to pyridine (). One of the three diazines (six-membered heterocyclics with two nitrogen atoms in the ring), it has nitrogen atoms at positions 1 and 3 in the ring. The other ...
), 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 Adenosine ( symbol A) is an organic compound that occurs widely in nature in the form of diverse derivatives. The molecule consists of an adenine attached to a ribose via a β-N9-glycosidic bond. Adenosine is one of the four nucleoside building ...
attacks the 5' splice site, followed by
nucleophilic attack In chemistry, a nucleophile is a chemical species that forms bonds by donating an electron pair. All molecules and ions with a free pair of electrons or at least one pi bond can act as nucleophiles. Because nucleophiles donate electrons, they are ...
on the 3' splice site by the 3' OH of the upstream
exon An exon is any part of a gene that will form a part of the final mature RNA produced by that gene after introns have been removed by RNA splicing. The term ''exon'' refers to both the DNA sequence within a gene and to the corresponding sequen ...
. 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 Studies that are ''in vivo'' (Latin for "within the living"; often not italicized in English) are those in which the effects of various biological entities are tested on whole, living organisms or cells, usually animals, including humans, and ...
'', 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. 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. 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.


Distribution and phylogeny

Group II introns are found in
rRNA Ribosomal ribonucleic acid (rRNA) is a type of non-coding RNA which is the primary component of ribosomes, essential to all cells. rRNA is a ribozyme which carries out protein synthesis in ribosomes. Ribosomal RNA is transcribed from ribosoma ...
,
tRNA Transfer RNA (abbreviated tRNA and formerly referred to as sRNA, for soluble RNA) is an adaptor molecule composed of RNA, typically 76 to 90 nucleotides in length (in eukaryotes), that serves as the physical link between the mRNA and the amino ac ...
, and
mRNA In molecular biology, messenger ribonucleic acid (mRNA) is a single-stranded molecule of RNA that corresponds to the genetic sequence of a gene, and is read by a ribosome in the process of Protein biosynthesis, synthesizing a protein. mRNA is ...
of
organelle In cell biology, an organelle is a specialized subunit, usually within a cell, that has a specific function. The name ''organelle'' comes from the idea that these structures are parts of cells, as organs are to the body, hence ''organelle,'' the ...
s (chloroplasts and mitochondria) in
fungi A fungus ( : fungi or funguses) is any member of the group of eukaryotic organisms that includes microorganisms such as yeasts and molds, as well as the more familiar mushrooms. These organisms are classified as a kingdom, separately from ...
,
plants Plants are predominantly Photosynthesis, photosynthetic eukaryotes of the Kingdom (biology), kingdom Plantae. Historically, the plant kingdom encompassed all living things that were not animals, and included algae and fungi; however, all curr ...
, and
protists A protist () is any eukaryotic organism (that is, an organism whose cells contain a cell nucleus) that is not an animal, plant, or fungus. While it is likely that protists share a common ancestor (the last eukaryotic common ancestor), the excl ...
, and also in mRNA in
bacteria Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were among ...
. 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''. A subset of group II
intron An intron is any nucleotide sequence within a gene that is not expressed or operative in the final RNA product. The word ''intron'' is derived from the term ''intragenic region'', i.e. a region inside a gene."The notion of the cistron .e., gene. ...
s encode essential splicing proteins, known as intron-encoded proteins or IEPs, in intronic
ORF ORF or Orf may refer to: * Norfolk International Airport, IATA airport code ORF * Observer Research Foundation, an Indian research institute * One Race Films, a film production company founded by Vin Diesel * Open reading frame, a portion of the ...
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. Many of these IEPs, including LtrA, share a reverse transcriptase domain and a "Domain X".
Maturase K Maturase K (matK) is a plant plastidial gene. The protein it encodes is an organelle intron maturase, a protein that splices Group II introns. It is essential for ''in vivo'' splicing of Group II introns. Amongst other maturases, this prote ...
(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.


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. Domain X is essential for splicing in yeast mitochrondria. This domain may be responsible for recognizing and binding to intron RNA or DNA.


See also

*
Database for bacterial group II introns The Database for Bacterial Group II Introns is a repository of full-length, non-redundant group II introns present in bacterial DNA sequence. The database is first established in 2002 with roughly 40 introns. In less than 10 years, the database has ...
*
Intron An intron is any nucleotide sequence within a gene that is not expressed or operative in the final RNA product. The word ''intron'' is derived from the term ''intragenic region'', i.e. a region inside a gene."The notion of the cistron .e., gene. ...
*
Splice site RNA splicing is a process in molecular biology where a newly-made precursor messenger RNA (pre-mRNA) transcript is transformed into a mature messenger RNA (mRNA). It works by removing all the introns (non-coding regions of RNA) and ''splicing'' ba ...
* Nuclear introns *
Group I 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 (P1-P9). These fold to essentially ...
*
Group III intron Group III intron is a class of introns found in mRNA genes of chloroplasts in euglenid protists. They have a conventional group II-type dVI with a bulged adenosine, a streamlined dI, no dII-dV, and a relaxed splice site consensus. Splicing is done ...
*
Twintron In molecular biology, a twintron is an intron-within-intron excised by sequential splicing reactions. A twintron is presumably formed by the insertion of a mobile intron into an existing intron. Discovery Twintrons were discovered by Donald W. ...
*'' LtrA''


References


Further reading

* * * *


External links

{{Self-replicating organic structures RNA Ribozymes RNA splicing