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  • Review Article
  • Published:

Mechanistic insights into precursor messenger RNA splicing by the spliceosome

Nature Reviews Molecular Cell Biology volume 18, pages 655–670 (2017)Cite this article

Subjects

Key Points

  • Analysis of the recent atomic-resolution cryo-electron microscopy structures of the spliceosome reveals that during splicing all spliceosomal complexes share a rigid core of 20 RNAs and proteins.

  • The active site of the spliceosome is positioned in the catalytic cavity of pre-mRNA-splicing factor 8 (Prp8), is stabilized by surrounding proteins and remains static throughout the two steps of transesterification.

  • The catalytic metals in the active site are coordinated by U6 small nuclear RNA and the catalytic triplex.

  • The interconversion of the various spliceosomal complexes is driven by eight conserved, RNA-dependent ATPase/helicases.

  • The spliceosome is a protein-directed metalloribozyme.

Abstract

Precursor messenger RNA (pre-mRNA) splicing is an essential step in the flow of information from DNA to protein in all eukaryotes. Research over the past four decades has molecularly delineated the splicing pathway, including characterization of the detailed splicing reaction, definition of the spliceosome and identification of its components, and biochemical analysis of the various splicing complexes and their regulation. Structural information is central to mechanistic understanding of pre-mRNA splicing by the spliceosome. X-ray crystallography of the spliceosomal components and subcomplexes is complemented by electron microscopy of the intact spliceosome. In this Review, I discuss recent atomic-resolution structures of the intact spliceosome at different stages of the splicing cycle. These structures have provided considerable mechanistic insight into pre-mRNA splicing and have corroborated and explained a large body of genetic and biochemical data. Together, the structural data have proved that the spliceosome is a protein-directed metalloribozyme.

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Figure 1: The pre-mRNA splicing reactions and the splicing cycle.
Figure 2: Atomic structures of the spliceosome.
Figure 3: Organization of the splicing active site and the catalytic metal ions.
Figure 4: Prp8 and its catalytic motifs.
Figure 5: Recognition of the intron sequences.
Figure 6: A shared rigid core of the various spliceosomal complexes.
Figure 7: Step I and II splicing factors facilitate transesterifications by participating in the formation of the active site.

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Acknowledgements

The author apologizes to those colleagues whose important work is not cited in this review owing to space limitation or inadvertent omission. The author thanks R. Wan, R. Bai, J. Hang, X. Zhang, X. Zhan and C. Yan for preparation of the figures and suggestions on text and references. This work was supported by funds from the Beijing Advanced Innovation Center for Structural Biology at Tsinghua University, Beijing, China.

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  1. Institute of Biology, Westlake Institute for Advanced Study, Shilongshan Road No. 18, Xihu District, Hangzhou 310064, Zhejiang Province, China.

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  1. Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, 100084, Beijing, China

    Yigong Shi

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Supplementary information

Supplementary information S1 (table)

Cryo-EM studies of the spliceosome (PDF 117 kb)

Supplementary information S2 (figure)

Recognition of the exon sequences. (PDF 8180 kb)

Supplementary information S3 (figure)

Distinct classes of spliceosomal proteins. (PDF 252 kb)

Supplementary information S4 (figure)

Comparison of the catalytic centers between the spliceosome and the self-splicing group IIB intron. (PDF 3340 kb)

PowerPoint slides

Glossary

Intron lariat

A lasso-like intron structure formed by the first transesterification of the splicing cycle.

Branch point sequence

(BPS). Also known as a branch site. A conserved intron sequence, which contains an invariant adenosine nucleotide that serves as the nucleophile for the branching reaction.

SN2-type transesterification

Transesterification in which one ester bond is broken and another ester bond is formed synchronously; named for substitution nucleophilic and bi-molecular transesterification.

Group II self-splicing introns

A large class of self-splicing catalytic RNAs found in bacteria, fungi and plants.

MS2-tagged

RNA prepared for affinity purification using a technique based on the interactions of the MS2 bacteriophage coat protein with a stem–loop RNA structure from the phage genome.

Lariat junction

The three-way junction in which a 2′ to 5′ linkage is formed between the ribose 2′-OH of an adenosine nucleotide in the intron branch site and the phosphate of a guanine nucleotide at the 5′ end of the intron 5′ splice site.

HEAT repeats

Repetitive motifs frequently found in signalling proteins; each HEAT repeat comprises a pair of anti-parallel α-helices, linked by a short loop.

HAT repeats

Repetitive motifs implicated in RNA processing; each HAT repeat comprises two α-helices.

WD40 domain

Also known as β-propeller or WD repeats. A type of circular solenoid protein domain that consists of 5–8 short structural motifs of approximately 40 amino acids each, often terminating in a tryptophan–aspartic acid (WD) dipeptide.

Sm ring

Also known as heptameric Sm complex. A doughnut-shaped structure formed by seven distinct Sm proteins, with single-stranded RNA bound within the hollow centre.

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Shi, Y. Mechanistic insights into precursor messenger RNA splicing by the spliceosome. Nat Rev Mol Cell Biol 18, 655–670 (2017). https://doi.org/10.1038/nrm.2017.86

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