Group I intronsAn intron is a DNA region within a gene that is not translated into protein. These non-coding sections are transcribed to precursor mRNA and some other RNAs , and subsequently removed by a process called splicing during the processing to mature RNA. After intron splicing An intron is a DNA region...
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 structureIn biochemistry and structural biology, secondary structure is the general three-dimensional form of local segments of biopolymers such as proteins and nucleic acids...
consists of nine paired regions (P1-P9). These fold to essentially two domains - the P4-P6 domain (formed from the stacking of P5, P4, P6 and P6a helices) and the P3-P9 domain (formed from the P8, P3, P7 and P9 helices).
Group I intronsAn intron is a DNA region within a gene that is not translated into protein. These non-coding sections are transcribed to precursor mRNA and some other RNAs , and subsequently removed by a process called splicing during the processing to mature RNA. After intron splicing An intron is a DNA region...
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 structureIn biochemistry and structural biology, secondary structure is the general three-dimensional form of local segments of biopolymers such as proteins and nucleic acids...
consists of nine paired regions (P1-P9). These fold to essentially two domains - the P4-P6 domain (formed from the stacking of P5, P4, P6 and P6a helices) and the P3-P9 domain (formed from the P8, P3, P7 and P9 helices). The secondary structure mark-up for this family represents only this conserved core. Group I introns often have long
open reading framesIn molecular genetics, an open reading frame is a portion of an organism's genome which contains a sequence of bases that could potentially encode a protein. The start-points and end-points of a given ORF are not equivalent to the ends of the messenger RNA , but the ends of the ORF are usually...
inserted in
loop regionsStem-loop intramolecular base pairing is a pattern that can occur in single-stranded DNA or, more commonly, in RNA. The structure is also known as a hairpin or hairpin loop. It occurs when two regions of the same molecule, usually palindromic Stem-loop intramolecular base pairing is a pattern that...
.
Catalysis
SplicingIn molecular biology, 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...
of
group I introns is processed by two sequential ester-transfer reactions. The
exogenousExogenous refers to an action or object coming from outside a system. It is the opposite of endogenous, something generated from within the system....
guanosineGuanosine is a nucleoside comprising guanine attached to a ribose ring via a β-N
9-glycosidic bond.Guanosine can be phosphorylated to become GMP , cGMP , GDP and GTP .When guanine is attached to a deoxyribose ring, it is known as a...
or guanosine
nucleotideNucleotides are molecules that, when joined together, make up the structural units of RNA and DNA. In addition, nucleotides play central roles in metabolism...
(
exoG) first docks onto the active G-binding site located in P7, and its 3'-OH is aligned to attack the
phosphodiester bondA phosphodiester bond is a group of strong covalent bonds between a phosphate group and two other molecules over two ester bonds. Phosphodiester bonds are central to all life on Earth, as they make up the backbone of the strands of DNA...
at the 5' splice site located in P1, resulting in a free 3'-OH group at the upstream
exonAn exon is a nucleic acid sequence that is represented in the mature form of an RNA molecule after either portions of a precursor RNA have been removed by cis-splicing or by two or more precursor RNA molecules have been ligated by trans-splicing. The mature RNA molecule can be a messenger RNA or...
and the exoG being attached to the 5' end of the intron. Then the terminal G (omega G) of the intron swaps the exoG and occupies the G-binding site to organize the second ester-transfer reaction, the 3'-OH group of the upstream exon in P1 is aligned to attacks the 3' splice site in P10, leading to the
ligationLigation may refer to:Ligation is the process of joining two pieces of DNA to a single piece through the use of ligase .* The act of making a ligature . In medicine, a ligature is a device, similar to a tourniquet, usually of thread or string, tied around a limb, blood vessel or similar to restrict...
of the adjacent upstream and downstream exons and free of the catalytic intron.
Two-metal-ion mechanism seen in protein polymerases and phosphatases was proposed to be used by group I and
group II intronGroup II intron is a class of self-catalytic ribozymes and retroelements found in rRNA, tRNA, mRNA of organelles in fungi, plants, protists, and bacteria. Self-splicing occurs in vitro , but protein machinery is probably required in vivo...
s to process the phosphoryl transfer reactions, which was unambiguously proven by a recently resolved high-resolution structure of the Azoarcus group I intron.
Intron Folding
Since early 1990s, scientists started to study how the group I intron achieves its native structure in vitro, and some mechanisms of RNA
foldingIn chemistry folding is the process by which a molecule assumes its shape or conformation. The process can also be described as intramolecular self-assembly where the molecule is directed to form a specific shape through noncovalent interactions, such as hydrogen bonding, metal coordination,...
have been appreciated thus far. It is agreed that the tertiary structure is folded after the formation of the secondary structure. During folding, RNA molecules are rapidly populated into different folding intermediates, the intermediates containing native interactions are further folded into the native structure through a fast folding pathway, while those containing non-native interactions are trapped in metastable or stable non-native conformations, and the process of conversion to the native structure occurs very slowly. It is evident that group I introns differing in the set of peripheral elements display different potentials in entering the fast folding pathway. Meanwhile, cooperative assembly of the tertiary structure is important for the folding of the native structure. Nevertheless, folding of group I introns in vitro encounters both thermodynamic and kinetic challenges. A few RNA binding proteins and chaperones have been shown to promote the folding of group I introns in vitro and in bacteria by stabilizing the native intermediates, and by destabilizing the non-native structures, respectively.
Distribution, Phylogeny and Mobility
Group I introns are distributed in
bacteriaThe bacteria are a large group of unicellular microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals...
, lower eukaryotes and higher
plants. However, their occurrence in
bacteriaThe bacteria are a large group of unicellular microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals...
seems to be more sporadic than in lower
eukaryotes, and they have become prevalent in higher plants. The genes that group I
introns interrupt differ significantly: They interrupt rRNA, mRNA and tRNA
genes in
bacteriaThe bacteria are a large group of unicellular microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals...
l genomes, as well as in mitochondrial and
chloroplastChloroplasts are organelles found in plant cells and other eukaryotic organisms that conduct photosynthesis. Chloroplasts capture light energy to conserve free energy in the form of ATP and reduce NADP to NADPH through a complex set of processes called photosynthesis.The word chloroplast is...
genomes of lower eukaryotes, but only invade rRNA genes in the nuclear genome of
lower eukaryotes. In higher plants, these introns seem to be restricted to a few
tRNA and mRNA genes of the
chloroplastChloroplasts are organelles found in plant cells and other eukaryotic organisms that conduct photosynthesis. Chloroplasts capture light energy to conserve free energy in the form of ATP and reduce NADP to NADPH through a complex set of processes called photosynthesis.The word chloroplast is...
s and mitochondria. Both intron-early
and intron-late theories have found evidences in explaining the origin of group I introns.
Some group I introns encode homing
endonuclease (HEG), which catalyzes intron mobility. It is proposed that HEGs move the
intron from one location to another, from one organism to another and thus account for the
wide spreading of the selfish group I introns. No biological role has been
identified for group I introns thus far except for splicing of themselves from the precursor
to prevent the death of the host that they live by. A small number of group I introns are
also found to encode a class of proteins called maturases that facilitate the intron
splicing.
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