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Splicing double: insights from the second spliceosome

Key Points

  • The genomes of most multicellular organisms contain a new class of introns that have non-canonical consensus sequences. These minor-class introns occur extremely rarely and are not restricted to the genes of a particular functional class.

  • Minor-class introns are spliced by a distinct, low-abundance splicing machinery that includes four small nuclear ribonucleoprotein particles (snRNPs; U11, U12, U4atac and U6atac) that are functionally analogous to the well-characterized major-class U1, U2, U4 and U6 snRNPs. The U5 snRNP is common to both spliceosomes.

  • The two spliceosomes have remarkable mechanistic similarities that enhance our understanding of the inner workings of the spliceosome. Although the sequences of the major- and minor-class small nuclear RNAs are significantly diverged, they have highly analogous secondary structures, snRNP–snRNP interactions and snRNP–pre-messenger RNA interactions. Some of the most conserved features of the two spliceosomes are thought to be involved in catalysis of the splicing reaction.

  • Although minor-class introns are rare within the genome of any given species, they are found in most metazoan taxa that have been examined, including vertebrates, insects and cnidarians (jellyfish), and plants. Phylogenetic analysis of U12-type introns shows that they can be conserved at homologous positions in homologous genes of species that diverged up to a billion years ago. Perhaps most surprising is the observation of minor-class introns at non-homologous positions in paralogous genes.

  • Spliceosomal factors that are bound to adjacent major-class introns are thought to form bridging interactions across exons, defining the exons as recognition units and preventing the unintended skipping of exons or introns. Evidence suggests that similar exon-spanning interactions also occur between spliceosomes that are assembled on adjacent minor- and major-class introns. Also, the incompatibility of minor- and major-class donor and acceptor splice sites has given rise to unique patterns of alternative splicing.

  • Phylogenetic analysis of minor-class introns has led to the conclusion that they must have occurred much more frequently earlier in evolutionary history, and were either lost or converted to major-class introns over time. It has been proposed that the few minor-class introns that have resisted conversion or loss could have functional roles that are indispensable to the cells that have them.

Abstract

Almost 20 years after the discovery of introns and RNA splicing, a second spliceosome was uncovered. Although this new spliceosome is structurally and functionally analogous to the well-characterized major-class splicing apparatus, it mediates the excision of a minor class of evolutionarily conserved introns that have non-canonical consensus sequences. This unanticipated diversity in the splicing machinery is refining both the mechanistic understanding and evolutionary models of RNA splicing.

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Figure 1: Pre-mRNA splicing occurs by two sequential trans-esterification reactions.
Figure 2: Pathways of assembly and catalysis of the major-class and minor-class spliceosomes.
Figure 3: Consensus sequences of major-class and minor-class introns.
Figure 4: Sequences and predicted secondary structures of the human spliceosomal snRNAs.
Figure 5: The phylogenetic distribution of minor-class introns.
Figure 6: Comparison of U2–U6 and U12–U6atac interactions at the catalytic core of the two spliceosomes.

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Acknowledgements

We thank C. B. Burge, R. A. Padgett, R. Luhrmann, M. Frilander, A. Krainer and R. Durbin for sharing unpublished information. We appreciate the critical reading of the manuscript by R. A. Padgett, K. Tycowski, L. Szewczak, T. Hirose and R. Lytle.

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Correspondence to Joan A. Steitz.

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DATABASES

FlyBase

prospero

LocusLink

Huntingtin

p14

SF3b

U2AF

Swiss-Prot

Prp8

Glossary

INTRON

An intervening non-coding sequence that interrupts two exons and that must be excised from pre-messenger RNA transcripts before translation.

EXON

The segment of a pre-messenger RNA transcript that contains protein-coding sequence and/or the 5′ or 3′ untranslated sequences, which must be spliced together with other exons to produce a mature messenger RNA.

SPLICEOSOME

A large complex that consists of five splicing small nuclear ribonucleoprotein particles as well as numerous protein factors. It mediates the excision of introns from pre-messenger RNA transcripts and ligates exon ends to produce mature mRNAs.

SMALL NUCLEAR RIBONUCLEOPROTEIN PARTICLE

(snRNP). A particle that is found in the cell nucleus and consists of a tight complex between a short RNA molecule (<300 nucleotides) and one or more proteins. SnRNPs are involved in pre-mRNA processing and transfer RNA biogenesis.

LARIAT

An RNA, the 5′ end of which is joined by a phosphodiester linkage to the 2′ hydroxyl of an internal nucleotide, thereby creating a lasso-shaped molecule.

METAZOAN

Refers to all animal species that contain multiple cells differentiated into tissues and organs.

INTRON BRANCH SITE

The adenosine residue near the 3′ end of an intron the 2′ hydroxyl group of which becomes linked to the 5′ end of the intron during the first step of splicing.

INTRON-DEFINITION MODEL

A model that proposes the initial pairwise interaction of spliceosomal components across introns, defining intron units that subsequently interact to promote spliceosome assembly and catalysis.

EXON-DEFINITION MODEL

A model in which exon units, rather than intron units, are initially defined by pairing of spliceosomal components across exons.

PSEUDOURIDYLATION

The conversion of a uridine residue within an RNA chain into a pseudouridine residue, which requires the scission and reattachment of the base to the sugar.

SM PROTEIN

A protein that belongs to a group of seven core proteins that are common to the splicing small nuclear ribonucleoprotein particles (except for U6 and U6atac, which have Sm-like proteins). Several are recognized by anti-Sm antibodies that are produced by patients with the autoimmune disease systemic lupus erythematosus.

GROUP II INTRONS

A rare class of autocatalytic introns, the excision of which is assisted by, but does not require, trans-acting protein factors.

RIBOZYME

An enzyme that consists of RNA.

SR FAMILY OF PROTEINS

A group of essential protein splicing factors with one or more RNA-recognition motif and a region containing arginine/serine (S/R) dipeptide repeats, which facilitate spliceosome assembly onto a pre-messenger RNA.

PARALOGOUS GENES

Genes for which sequence similarity is the result of gene duplication within the same species and that encode proteins that carry out similar, but not identical functions.

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Patel, A., Steitz, J. Splicing double: insights from the second spliceosome. Nat Rev Mol Cell Biol 4, 960–970 (2003). https://doi.org/10.1038/nrm1259

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