Prp8

Key takeaways

Prp8 belongs to biology; place it in that map before memorising details.
Learn the definition first, then one example that makes the definition concrete.
Connect Prp8 to a quantity you can measure, compute or draw — that is where exam questions come from.
Reproduce the core statement of Prp8 from memory before moving on to harder problems.

Reference excerpt

Prp8 refers to both the Prp8 protein and Prp8 gene. Prp8's name originates from its involvement in pre-mRNA processing. The Prp8 protein is a large, highly conserved, and unique protein that resides in the catalytic core of the spliceosome and has been found to have a central role in molecular rearrangements that occur there. Prp8 protein is a major central component of the catalytic core in the spliceosome, and the spliceosome is responsible for splicing of precursor mRNA that contains introns and exons. Unexpressed introns are removed by the spliceosome complex in order to create a more concise mRNA transcript. Splicing is just one of many different post-transcriptional modifications that mRNA must undergo before translation. Prp8 has also been hypothesized to be a cofactor in RNA catalysis.

History The systematic name for the PRP8 protein is YHR165C. Prp8 protein is coded by a single gene in humans with 42 exons. The size of Prp8 ranges between 230 and 280 kDa depending on the organism. The sequence coding for the Prp8 protein is highly conserved between eukaryotic organisms, with a 61% identity match between humans and yeast in amino acid sequence. The Prp8 gene is located on chromosome VIII in yeast and chromosome 17 in humans.

Role in splicing

Pre-mRNA splicing involves two trans-esterification reactions and attacks by hydroxyl groups within the spliceosome. In these reactions, spliceosomal intron removal is catalyzed by the spliceosome using the same mechanism as Group II introns. There are five key small nuclear RNA-protein complexes (snRNP) involved in this process. All of the snRNPs together contribute about 50 proteins to the core spliceosome. The Prp8 gene encodes for a protein that is a central part of the U5 snRNP and the U5-U4/U6 tri-snRNP. The U5-U4/U6 tri-snRNP is involved with Complex B, the pre-catalytic spliceosome, where the U5 snRNP binds to exons at the 5’ end of the mRNA before shifting to introns. The U5 snRNP is involved with Complex C, the catalytic spliceosome, where the U5 snRNP binds to an exon at the 3’ splice site and the lariat loop forms. The U5 snRNP is also involved with Complex C*, the post-catalytic spliceosome, where it remains bound to the lariat before the spliced RNA is released and the snRNPs are recycled. Common research methods for studying the structure and functions of Prp8 are co-immunoprecipitation and Western blot analysis. The structure of Prp8 includes a RNA recognition motif, a MPN / JAB ubiquitin-binding domain near the C-terminus, and a nuclear localization signal (NLS) that tags the protein to be moved to the cell nucleus. The crystal structure of Prp8 protein (residues 885–2413) reveals tightly associated domains that resemble an intron reverse transcriptase and a type II restriction endonuclease. This implies that Prp8 might play roles similar to both the creation of cDNA and in cutting the DNA during splicing.

Prp8 is also more involved with maintaining proper conformation of the bound RNA cofactors and substrates of the splicing reaction. Prp8, along with two other U5 snRNP proteins, helps to activate the spliceosome and form its catalytic active center. It has been proposed that GTP hydrolysis results in a rearrangement of Prp8 that releases the U1 and U4 snRNPs and is responsible for this activation of the catalytic core of the spliceosome. Prp8 performs a scaffold-like function in the spliceosome and holds onto many of the interacting substrates and subunits. It has been cross-linked at both the 3’ and 5’ splice sites in mRNA. Due to these structural elements, it has been assumed that Prp8 may have evolved from inactivated retroelements of reverse transcriptases, with the snRNPs replacing the catalytic domains of self-splicing ancestors.

Mutation and disease

Deficiencies Prp8 mutation has been linked to the human disease Retinitis Pigmentosa causing vision loss, especially progressing into adulthood. This autosomal dominant affliction results with degeneration of the photoreceptors of the retina of the eye. This disorder is caused by mutations in the C-terminus. Retinitis Pigmentosa results from nine missense mutations in the last exon of the mature mRNA result with changes in seven highly conserved amino acids. Studies in yeast indicate that mutation of the C-terminus affects interactions with Brr2p, a helicase responsible for necessary function for the unwinding of the U1 snRNA/5’SS and U4/U6 RNA helices.

Phenotype mutations of Prp8 across species Caenorhabditis elegans Prp8 has been linked to reproduction and development. RNAi, or RNA Interference, was used to knockout Prp8. This resulted in a high level of sterility, a clear body, and protruding vulva, all phenotypical expressions linked to reproduction and development. Mouse Prp8 mutation has resulted in Retinitis Pigmentosa (see above). Yeast Prp8 mutation results in a U5 snRNP maturation defect. The U5 snRNAP component of the splicesosome is necessary to bind to the 5' and 3' exons during pre-mRNA splicing. Mutations with this subunit correlate to reduced or inaccurate editing of RNA. In severe cases, mutations in Prp8 can lead to cell death.

Illustrations

Worked examples

Example 1 — a first encounter with Prp8

Start with the simplest possible case. Write down what Prp8 claims or describes in one sentence, then invent the smallest concrete situation in which that sentence is true. In biology, 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 Prp8 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 Prp8 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 Prp8

In research: Prp8 appears in biology 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 Prp8 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: Prp8 is common in secondary-school and first-year university syllabi. It links to neighbouring topics Fungal proteins, RNA splicing, Saccharomyces cerevisiae genes, so understanding it makes those chapters shorter.
In everyday life: Look for Prp8 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.

How to study Prp8 in 20 minutes

Read the reference excerpt below once, without taking notes.
Close the page and write down what Prp8 means in your own words.
Compare your version with the excerpt and mark what you missed.
Work through the three examples above with pen and paper.
Explain Prp8 out loud to somebody else — or to Teacher Smith in the lgStudy chat.

Frequently asked questions

What is Prp8 in simple terms?

Prp8 refers to both the Prp8 protein and Prp8 gene. Prp8's name originates from its involvement in pre-mRNA processing.

Why does Prp8 matter?

Because it connects several biology 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 Prp8?

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 Prp8.