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Group I catalytic intron

Group I catalytic intron is a science topic covered in the lgStudy science library. This page brings together a partial reference excerpt, illustrations, worked examples, real-world applications and a short study plan, so you can understand Group I catalytic intron rather than just read about it. In short: 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.

Group I catalytic intron — main illustration
Group I catalytic intron — illustration

Key takeaways

  • Group I catalytic intron belongs to science; place it in that map before memorising details.
  • Learn the definition first, then one example that makes the definition concrete.
  • Connect Group I catalytic intron to a quantity you can measure, compute or draw — that is where exam questions come from.
  • Reproduce the core statement of Group I catalytic intron from memory before moving on to harder problems.

Reference excerpt

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 two domains – the P4-P6 domain (the "scaffolding" domain, which is formed from the stacking of P5, P4, P6 and P6a helices) and the P3-P9 domain (the "catalytic" domain, which is formed from the P8, P3, P7 and P9 helices). The secondary structure mark-up for this family represents only this conserved core. Certain subclasses of Group I introns also contain peripheral structural domains that provide additional structural support to the intron. Group I introns often have long open reading frames inserted in loop regions.

Catalysis Splicing of group I introns is processed by two sequential transesterification reactions. First an exogenous guanosine or guanosine nucleotide (exoG) docks onto the active G-binding site located in P7, and then its 3'-OH is aligned to attack the phosphodiester bond at the "upstream" (closer to the 5' end) splice site located in P1, resulting in a free 3'-OH group at the upstream exon and the exoG being attached to the 5' end of the intron. Then the terminal G (omega G) of the intron swaps out the exoG and occupies the G-binding site, preparing the second ester-transfer reaction: the 3'-OH group of the upstream exon in P1 is aligned to attack the downstream splice site in P10, leading to the ligation of the adjacent upstream and downstream exons and release of the catalytic intron.

The two-metal-ion mechanism seen in protein polymerases and phosphatases was proposed to be used by group I and group II introns to process the phosphoryl transfer reactions, which was unambiguously proved by a high-resolution structure of the Azoarcus group I intron in 2006.

Intron folding Since the early 1990s, scientists started to study how the group I intron achieves its native structure in vitro, and some mechanisms of RNA folding 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 bacteria, lower eukaryotes and higher plants. However, their occurrence in bacteria 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 bacterial genomes, as well as in mitochondrial and chloroplast 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 chloroplasts and mitochondria. Group I introns are also found inserted into genes of a wide variety of bacteriophages of Gram-positive bacteria. However, their distribution in the phage of Gram-negative bacteria is mainly limited to the T4, T-even and T7-like bacteriophages. 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.

See also Intron Group I Intron Sequence and Structure Database Splice site Nuclear introns Group II intron Group III intron Twintron LtrA Cyclic di-GMP-II riboswitch, where there is an example of a riboswitch acting together with a group I intron to regulate the expression of a gene

References

Further reading Chauhan, S; Caliskan G; Briber RM; Perez-Salas U; Rangan P; Thirumalai D; Woodson SA (2005). "RNA tertiary interactions mediate native collapse of a bacterial group I ribozyme". J Mol Biol. 353 (5): 1199–1209. doi:10.1016/j.jmb.2005.09.015. PMID 16214167. Haugen, P; Simon DM; Bhattacharya D (2005). "The natural history of group I introns". Trends in Genetics. 21 (2): 111–119. doi:10.1016/j.tig.2004.12.007. PMID 15661357. Rangan, P; Masquida, B; Westhof E; Woodson SA (2003). "Assembly of core helices and rapid tertiary folding of a small bacterial group I ribozyme". Proc Natl Acad Sci USA. 100 (4): 1574–1579. Bibcode:2003PNAS..100.1574R. doi:10.1073/pnas.0337743100. PMC 149874. PMID 12574513. Schroeder, R; Barta A; Semrad K (2004). "Strategies for RNA folding and assembly". Nat Rev Mol Cell Biol. 5 (11): 908–919. doi:10.1038/nrm1497. PMID 15520810. S2CID 22030359. Thirumalai, D; Lee N; Woodson SA; Klimov D (2001). "Early events in RNA folding". Annu Rev Phys Chem. 52: 751–762. Bibcode:2001ARPC...52..751T. doi:10.1146/annurev.physchem.52.1.751. PMID 11326079. Treiber, DK; Williamson JR (1999). "Exposing the kinetic traps in RNA folding". Curr Opin Struct Biol. 9 (3): 339–345. doi:10.1016/S0959-440X(99)80045-1. PMID 10361090. Xiao, M; Leibowitz MJ; Zhang Y (2003). "Concerted folding of a Candida ribozyme into the catalytically active structure posterior to a rapid RNA compaction". Nucleic Acids Res. 31 (14): 3901–3908. doi:10.1093/nar/gkg455. PMC 165970. PMID 12853605.

… excerpt ends here. Continue reading the full article.

Illustrations

Group I catalytic intron illustration
Group I catalytic intron illustration
Group I catalytic intron: A 3D representation of the Group I catalytic intron. This view shows the active site in the crystal structure of the Tetrahymena ribozyme.[9]
A 3D representation of the Group I catalytic intron. This view shows the active site in the crystal structure of the Tetrahymena ribozyme.[9]
Group I catalytic intron: A 3D representation of the Group I catalytic intron. This is the crystal structure of a phage Twort group I ribozyme-product complex.[10]
A 3D representation of the Group I catalytic intron. This is the crystal structure of a phage Twort group I ribozyme-product complex.[10]
Group I catalytic intron: A 3D representation of the Group I catalytic intron. This is the structure of the Tetrahymena ribozyme with a base triple sandwich and metal ion at the active site.[11]
A 3D representation of the Group I catalytic intron. This is the structure of the Tetrahymena ribozyme with a base triple sandwich and metal ion at the active site.[11]

Worked examples

Example 1 — a first encounter with Group I catalytic intron

Start with the simplest possible case. Write down what Group I catalytic intron claims or describes in one sentence, then invent the smallest concrete situation in which that sentence is true. In science, the smallest case is usually a single object, a single equation or a single measurement. Check that every symbol or term in your sentence has a meaning in that case.

Example 2 — changing one variable

Take the situation from Example 1 and change exactly one quantity: double it, halve it, or set it to zero. Predict what should happen to Group I catalytic intron before you calculate. Comparing your prediction with the result is the fastest way to find out whether you understand the idea or only the words.

Example 3 — an exam-style question

Typical questions about Group I catalytic intron ask you to (a) state it precisely, (b) apply it to given data, and (c) explain a limitation. Practise writing all three answers in under five minutes; the third part is what separates a full-mark answer from an average one.

Applications of Group I catalytic intron

In research
Group I catalytic intron appears in science research whenever the underlying quantities have to be modelled precisely. Papers usually cite it as a starting assumption and then explore where it breaks down.
In technology and industry
Engineering practice reuses Group I catalytic intron in design rules, simulations and safety margins. Knowing the idea lets you read a specification sheet and understand why the numbers look the way they do.
In the classroom
Group I catalytic intron is common in secondary-school and first-year university syllabi. It links to neighbouring topics RNA splicing, Ribozymes, so understanding it makes those chapters shorter.
In everyday life
Look for Group I catalytic intron outside the textbook — in sport, cooking, traffic, electronics or the sky above you. An example you found yourself is remembered far longer than one you were given.
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How to study Group I catalytic intron in 20 minutes

  1. Read the reference excerpt below once, without taking notes.
  2. Close the page and write down what Group I catalytic intron means in your own words.
  3. Compare your version with the excerpt and mark what you missed.
  4. Work through the three examples above with pen and paper.
  5. Explain Group I catalytic intron out loud to somebody else — or to Teacher Smith in the lgStudy chat.

Frequently asked questions

What is Group I catalytic intron in simple terms?

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.

Why does Group I catalytic intron matter?

Because it connects several science ideas at once: it gives you a definition you can apply, a quantity you can calculate, and a way to check whether a result is plausible.

How should I study Group I catalytic intron?

Read the excerpt, restate it from memory, then work through the examples and applications listed on this page. The five-step study plan above takes about twenty minutes.

What does this page cover?

It gives you a compact reference excerpt plus original lgStudy explanations, examples, applications and study material on Group I catalytic intron.

Tags

  • RNA splicing
  • Ribozymes

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