Spliceosome

Abstract

The removal of noncoding regions or introns and the splicing together of the protein‐coding regions or exons from precursor messenger ribonucleic acid (pre‐mRNA) transcripts is fundamental to metzoan cell development, as well as its maintenance. The nuclear process of pre‐mRNA splicing is a complex phenomenon catalysed by the ‘spliceosome’. The spliceosome consists of greater than a hundred protein and RNA molecules. Integral to the spliceosome are five RNA–protein complexes, the U1, U2, U4, U5 and U6 small nuclear ribonucleoproteins (snRNPs). The numerous proteins and the U snRNPs that make up the spliceosome come on and off during the spliceosome's reaction cycle. This article places an emphasis on our current understanding of the dynamics, composition and structure of the spliceosome.

Key Concepts:

  • Specific sequences defining the boundaries between a protein‐coding gene's noncoding regions or introns and its protein‐coding regions or exons are recognised by components of the pre‐mRNA splicing ‘machinery’ – the spliceosome.

  • The spliceosome is composed of a large number of RNA and protein molecules. The protein subunits have diverse domain structures, whereas the RNA subunits form hydrogen bonding or base‐pairing interactions with critical sequences in a pre‐mRNA as well as with each other.

  • The spliceosome reaction cycle involves an ordered assembly onto a pre‐mRNA transcript to ultimately catalyse two trans‐esterification reactions that result in the removal or excision of an intron and the splicing together of two exons.

  • Integral to the function of the spliceosome are five U snRNPs, each of which has a single RNA and 3–12 protein constituents including a homologous set of proteins (Sm or LSm) that forms a structural unit critical to the biogensis and integrity of each U snRNP.

  • The U1, U2, U4 and U5 snRNPs all have a common core structure that consists of seven Sm proteins which assemble around a short U‐rich single‐stranded RNA sequence (the Sm site) present in the U1, U2, U4 and U5 snRNAs to form a heptameric ring with the single‐stranded RNA Sm site leafing through the central hole.

  • Metazoan U1 snRNP functions to initiate the assembly of the spliceosome onto a pre‐mRNA transcript; its single RNA subunit (U1 snRNA) forms a cruciform‐like structure onto which the Sm proteins assemble to form the Sm core, while its three additional U‐specific proteins (U1‐A, U1‐70K, and U1‐C) participate in particle specific functions – including recognition of a pre‐mRNA transcripts 5' splice site sequence.

Keywords: pre‐mRNA splicing; spliceosome; pre‐mRNA transcript; U snRNP; introns

Figure 1.

Intron sequence conservation. H. sapiens and S. cerevisiae as well as other eukaryotic pre‐mRNA transcripts of protein‐coding genes contain short consensus sequences at the junction of the 5′ exon and intron (the 5′ splice site, 5′ SS), around the BP region containing the highly conserved adenosine (BP), and at the junction of the intron and 3′ exon (the 3′ splice site, 3′ SS). Indicated is the locale of a pyrimidine‐rich tract (Py‐tract), a region present in metazoan transcripts. The size of the letter corresponds to the degree of conservation of that nucleotide at the position indicated.

Figure 2.

Secondary structures of the five human spliceosomal U snRNAs. U snRNAs range in size from 106 to 187 nucleotides and are modified post‐transcriptionally (nucleotides 2′‐O‐methylated or pseudouridylated (ψ) are shown in red). The seven Sm proteins recognise and form a heptameric ring around the Sm site nucleotides (shaded in cyan) of U1, U2, U4 and U5 snRNAs, whereas seven LSm proteins similarly assemble into a heptameric ring but recognise the LSm site nucleotides (shaded in pink) that are specific to the 3′ single‐stranded end of U6 snRNA. Each of the U snRNAs plays a significant role(s) during the splicing cycle by direct interactions with a pre‐mRNA transcripts 5′ splice site (5′ SS), exons and BP. U snRNA sequences that contact the pre‐mRNA transcript are shaded in yellow. Sequence highlighted in brown, green and purple are sites of base pairing between U2–U6 snRNAs.

Figure 3.

Spliceosome reaction cycle. (a) Spliceosomal assembly onto a pre‐mRNA transcript. Proceeding clockwise, the U1 snRNP recognises a 5′ splice site (5′ SS) and non‐U snRNP proteins SF1 and the heterodimer U2AF the BP and 3′ splice site (3′ SS), respectively (E complex). U2 snRNP binds to the BP, displacing SF1 (A complex). The U4/U6‐U5 tri‐snRNP is then incorporated (B complex). U1, U4 and U2AF dissociate and a catalytically active spliceosome is formed (B* complex). The first catalytic reaction takes place to yield a free 5′ exon and intron lariat joined with the 3′ exon (C complex). A second reaction yields an mRNA transcript and intron lariat. (b) Schematic of the two trans‐esterification reactions catalysed by the spliceosome. In the first step, the 2′ hydroxyl (2′‐OH) of the bulged BP adenosine acts as a nucleophile and attacks the phosphodiester bond of the conserved guanosine at the 5′ SS. The transfer of an organophosphate of the 5′ SS guanosine to the BP adenosine creates a lariat‐like structure within the intron and a nucleophile out of the 3′ hydroxyl (3′‐OH) of the now free 5′ exon. In the second reaction, the 3′‐OH of the 5′ exon attacks an organophosphate at the 3′ SS. These two reactions yield an mRNA transcript consisting of the conjoined 5′ and 3′ exons and the excised intron. Invariant nucleotides and exons are coloured as in Figure .

Figure 4.

Structure of the Sm proteins. (a) Primary sequence alignment of H. sapiens Sm proteins (protein sequences used for alignment: SmD1, NP_008869.1; SmD2, NP_808210.2; SmD3, NP_004166.1; SmB, NP_937859.1; SmE, NP_003085.1; SmF, NP_003086.1 and SmG, NP_003087.1). Residues coloured in the Sm1 and Sm2 sequence motifs are hydrophobic (grey), positively charged (blue), negatively charged (red), polar (cyan) and glycine (green). (b) Two views differing by 90 ° of the Sm fold: an N‐terminal α‐helix (red) preceeding a five highly bent β‐strands (blue and yellow) that assume an antiparallel β‐barrel‐like structure. Strands coloured blue comprise those that form the Sm 2 motif, those coloured yellow comprise those of the Sm1 motif. (c) SmD3‐SmB heterodimer displayed, highlighting the pairwise interaction between Sm proteins where the β4 strand of one interacts with the β5 strand of an adjacent Sm protein (Protein Databank identification code 1B34) (Kambach et al., ). (d) Structure of the heptameric Sm ring. The β4 and β5 strands of one Sm protein interact with the β5 and β4 strands, respectively, of a neighbouring Sm protein to assemble the heptameric ring around a single‐stranded Sm site (shown in grey). The Sm site RNA assumes a right‐handed spiral with the bases splayed outward.

Figure 5.

Structure of human U1 snRNP. (a) Secondary structure of U1 snRNA and general location of its 10 protein subunits (U1‐A, green; U1‐C, orange; U1–70K, red; seven Sm proteins, cyan). (b) Structure of human U1 snRNP (Protein Databank identification code 3CW1) (Pomeranz Krummel et al., ). Coloured as in (a). Pre‐mRNA transcript strand is coloured magenta. (c) Sequence alignment of the N‐terminal 90 amino acids of U1–70K (Protein sequences used for alignment: H. sapiens, NP_003080.2; Mus musculus, NP_033250.3; Xenopus laevis, NP_001081603.1 and Drosophila melanogaster, NP_001260173.1). (d) Path of U1–70K (red) in the crystal structure of U1 snRNP. Two perspectives of the path of U1–70K highlighting its C‐terminal RBD or RRM, an α helix that extends the length of stem 2, and then its traversing the Sm ring by crossing near the junctions of four of the seven Sm proteins.

close

References

Auweter SD, Oberstrass FC and Allain F (2006) Sequence‐specific binding of single‐stranded RNA: is there a code for recognition? Nucleic Acids Research 34: 4943–4959.

Burge C, Tuschl T and Sharp PA (1999) Splicing of precursors to mRNAs by the spliceosomes. In: Gesteland R, Cech T and Atkins J (eds) RNA World II, p. 525–560. New York: Cold Spring Harbor Laboratory Press.

Cordin O, Hahn D and Beggs JD (2012) Structure, function and regulation of spliceosomal RNA helicases. Current Opinion in Cell Biology 24: 431–438.

Dyson HJ and Wright PE (2005) Intrinsically unstructured proteins and their functions. Nature Reviews Molecular Cell Biology 6: 197–208.

Friesen WJ, Paushkin S, Wyce A et al. (2001) The methylosome, a 20S complex containing JBP1 and pICln, produces dimethylarginine-modified Sm proteins. Molecular and Cellular Biology 21: 8289–8300.

Gozani O, Potashkin J and Reed R (1998) A potential role for U2AF‐SAP 155 interactions in recruiting U2 snRNP to the branch site. Molecular and Cellular Biology 18: 4752–4760.

Horowitz DS, Kobayashi R and Krainer AR (1997) A new cyclophilin and the human homologues of yeast Prp3 and Prp4 form a complex associated with U4/U6 snRNPs. RNA 3: 1374–1387.

Irimia M and Blencowe BJ (2012) Alternative splicing: decoding an expansive regulatory layer. Current Opinion in Cell Biology 24: 323–332.

Kambach C, Walke S, Young R et al. (1999) Crystal structures of two Sm protein complexes and their implications for the assembly of the spliceosomal snRNPs. Cell 96: 375–387.

Korneta I and Bujnicki JM (2012) Intrinsic disorder in the human spliceosomal proteome. PLoS Computational Biology 8: e1002641.

Leung AK, Nagai K and Li J (2011) Structure of the spliceosomal U4 snRNP core domain and its implication for snRNP biogenesis. Nature 473: 536–539.

Oubridge C, Ito N, Evans PR, Teo CH and Nagai K (1994) Crystal structure at 1.92 Å resolution of the RNA‐binding domain of the U1A spliceosomal protein complexed with an RNA hairpin. Nature 372: 432–438.

Pomeranz Krummel DA, Oubridge C, Leung AK, Li J and Nagai K (2009) Crystal structure of human spliceosomal U1 snRNP at 5.5 Å resolution. Nature 458: 475–480.

Price SR, Evans PR and Nagai K (1998) Crystal structure of the spliceosomal U2B′′‐U2A′ protein complex bound to a fragment of U2 small nuclear RNA. Nature 394: 645–650.

Rymond BC and Rosbash M (1992) Yeast pre‐mRNA splicing. In: Broach JR, Pringle J and Jones EW (eds) The Molecular and Cellular Biology of the Yeast Saccharomyces, vol. 2, 143 p. New York: Cold Spring Harbor Laboratory Press.

Santos KF, Jovin SM, Weber G et al. (2012) Structural basis for functional cooperation between tandem helicase cassettes in Brr2‐mediated remodeling of the spliceosome. Proceedings of the National Academy of Sciences of the USA 109: 17418–17423.

Schellenberg MJ, Wu T, Ritchie DB et al. (2013) A conformational switch in PRP8 mediates metal ion coordination that promotes pre‐mRNA exon ligation. Nature Structural and Molecular Biology 20: 728–734.

Seraphin B (1995) Sm and Sm‐like proteins belong to a large family: identification of proteins of the U6 as well as the U1, U2, U4 and U5 snRNPs. EMBO Journal 14: 2089–2098.

Singh RK and Cooper TA (2012) Pre‐mRNA splicing in disease and therapeutics. Trends in Molecular Medicine 18: 472–482.

Sontheimer EJ and Steitz JA (1993) The U5 and U6 small nuclear RNAs as active site components of the spliceosome. Science 262: 1989–1996.

Tazi J, Kornstadt U, Rossi F et al. (1993) Thiophosphorylation of U1‐70K protein inhibits pre‐mRNA splicing. Nature 363: 283–286.

Wu S, Romfo CM, Nilsen TW and Green MR (1999) Functional recognition of the 3′ splice site AG by the splicing factor U2AF35. Nature 402: 832–835.

Further Reading

Berget SM, Moore C and Sharp PA (1977) Spliced segments at the 5′ terminus of adenovirus 2 late mRNA. Proceedings of the National Academy of Sciences of the USA 74: 3171–3175.

Burd CG and Dreyfuss G (1994) Conserved structures and diversity of functions of RNA‐binding proteins. Science 265: 615–621.

Chow LT, Gelinas RE, Broker TR and Roberts RJ (1977) An amazing sequence arrangement at the 5′ ends of adenovirus 2 messenger RNA. Cell 12: 1–8.

van der Feltz C, Anthony K, Brilot A and Krummel P (2012) Architecture of the spliceosome. Biochemistry 51: 3321–3333.

Mermoud JE, Cohen PT and Lamond AI (1994) Regulation of mammalian spliceosome assembly by a protein phosphorylation mechanism. EMBO Journal 13: 5679–5688.

Mount SM (2000) Genomic sequence, splicing, and gene annotation. American Journal of Human Genetics 67: 788–792.

Reed R (2000) Mechanisms of fidelity in pre‐mRNA splicing. Current Opinion in Cell Biology 12: 340–345.

Sharp PA (1994) Split genes and RNA splicing (Nobel Lecture). Cell 77: 805–815.

Sleeman JE and Lamond AI (1999) Nuclear organization of pre‐mRNA splicing factors. Current Opinion in Cell Biology 11: 372–377.

Contact Editor close
Submit a note to the editor about this article by filling in the form below.

* Required Field

How to Cite close
Anthony, Kelsey C, and Pomeranz Krummel, Daniel(Nov 2013) Spliceosome. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0005323.pub2]