Review
The evolution of spliceosomal introns

https://doi.org/10.1016/S0959-437X(02)00360-XGet rights and content

Abstract

Although the widespread proliferation of introns in eukaryotic protein-coding genes remains one of the most poorly understood aspects of genomic architecture, major advances have emerged recently from large-scale genome sequencing projects and functional analyses of mRNA-processing events. Evidence supports the idea that spliceosomal introns were not only present in the stem eukaryote but diverged into at least two distinct classes very early in eukaryotic evolution. Some rough estimates of intron turnover rates are provided, and a testable hypothesis for the origin of new introns is proposed. In light of recent findings on the molecular natural history of splicing, various aspects of the phylogenetic and physical distributions of introns can now be interpreted in a theoretical framework that jointly considers the population-genetic roles of mutation, random genetic drift, and natural selection.

Introduction

One of the greatest enigmas of eukaryotic genome evolution is the widespread existence of introns. Most genes in multicellular eukaryotes contain at least one intron, and many contain a dozen or more. In some lineages, mammals in particular, the size of individual introns substantially exceeds that of their surrounding exons. Intragenic noncoding DNA poses three significant problems for the organism: they must be accurately spliced out of precursor mRNAs (pre-mRNAs) if proper proteins are to be produced; the magnitude of the genome-wide investment in nucleotides contained within introns must impose a metabolic cost at the DNA and RNA levels; and the burden of critical intron recognition sites increases the mutation rate to null alleles. How, then, did the eukaryotic genome arrive at the point at which ‘genes in pieces’ has become the norm?

Our review focuses on the predominant class of eukaryotic introns: the spliceosomal introns of nuclear-encoded protein genes. Such introns are transcribed along with their surrounding exons, and their removal from pre-mRNAs is performed within the nucleus by the spliceosomal complex. Involving five small nuclear RNAs (snRNAs) and ∼100 proteins, the spliceosome carries out a cohesive series of partially overlapping interactions that culminate in intron excision and exon joining.

Until recently, studies regarding the evolution of eukaryotic introns were largely focused on a single issue, their potential involvement in the ancient origin of genes by exon shuffling 1., 2., 3., 4., 5., 6.. However, although many details regarding the origin of introns remain to be resolved, their approximate time of origin is no longer in doubt. None of the 100 or so sequenced prokaryotic genomes harbors the signature of current or past introns in protein-coding genes, whereas every basal eukaryotic lineage that has been examined contains at least some spliceosomal introns and/or orthologues of spliceosomal components found in higher eukaryotes 7., 8., 9•., 10•.. Some protist genes contain as many introns as their orthologues in multicellular species, and there is considerable evidence for intron loss and gain in independent lineages [9•], consistent with the view that the distribution of introns reflects ongoing birth/death processes [11•].

Some have argued that this phylogenetic pattern might be an illusion, with selection for streamlined genomes having led to the loss of introns from all lineages of prokaryotes after the primordial set of genes had been produced by exon shuffling 1., 3.. However, simple population-genetic principles suggest that the enormous population sizes of prokaryotes — probably well beyond 1010 in most cases — combined with the weak selective disadvantage of intron-containing alleles would have presented a significant barrier to the proliferation of introns [11•]. The physical positions of introns have also been cited as indirect evidence for their involvement in the creation of early genes 12., 13., 14., but the observed patterns are also consistent with the differential selective elimination of introns in sites that are most prone to conversion to null alleles [11•].

Thus, the most reasonable explanation of the data are that spliceosomal introns were never present in prokaryotes but rose to prominence soon after the origin of the stem eukaryote. This issue having been largely resolved, attention is now shifting to the adaptive significance and differential proliferation of today's introns. Achieving a general understanding of these issues will require a deeper appreciation of the basic natural history of splicing and transcript processing and of the dynamics and stability of introns from a population-genetics perspective.

Section snippets

A group II intron ancestry?

The leading hypothesis for the origin of spliceosome-dependent introns is that they and the spliceosome itself were derived from one or more self-splicing group II introns 15., 16., 17., 18.. Such introns have been found in the chromosomes and plasmids of numerous eubacteria [19••] as well as in one member of the archaea (S Zimmerly, personal communication). (Technically speaking, however, some of the eubacterial group II elements are not introns at all, in that they lie between rather than

Twin spliceosomes?

Intrigue with respect to the origin of the spliceosome increased with the discovery that before the origin of multicellularity, eukaryotes evolved not just one, but two, spliceosomal complexes 39., 40.. The major spliceosome deals with the classic set of introns that usually start with GT and end with AG, whereas the minor spliceosome processes another set, many of which start with AT and end with AC. Members of the latter class of introns have come to be known as U12-dependent introns, in

The evolutionary demography of introns

A burst of intron proliferation may have followed the invention of the spliceosome, which would have mitigated the negative consequences of recognizable intergenic inserts. However, it is also clear that all species are subject to ongoing stochastic gains and losses of spliceosomal introns 48., 49., 50•., 51•.. Although we can provide only two quantitative estimates for the rate of intron turnover, these are remarkably consistent. In a comparison of the genomes of the congeneric nematodes C.

Genomic assimilation and accommodation

Once introns had spread throughout the eukaryotic genome, the new norm of genes-in-pieces apparently provided a novel physical structure for adaptive exploitation in the grand tradition of descent with modification. In today's eukaryotes, almost all of the major events in the production of mature mRNAs are highly coupled with exon definition and/or intron splicing [73••]. For example, interactions between various splicing factors and elongation factors promote transcription elongation 74., 75••.

Nonsense-mediated decay and intron proliferation

One of the most significant services provided by introns is their indirect role in the cell's surveillance for inappropriate transcripts, in particular those harboring premature termination codons (PTCs). PTC-containing mRNAs arise from the direct transcription of inherited mutant alleles as well as from errors in transcription or splicing of otherwise functional alleles. Although such transcripts are expected to lead to potentially deleterious truncated proteins, eukaryotes protect themselves

Conclusions

Much of the early intrigue with the evolution of introns was focused on their potential role in the origin of the primordial set of protein-coding genes and on their present adaptive significance (or lack thereof). Advances in phylogenetic analysis — made possible by high-throughput genomic sequencing — now suggest that at as many as two refined spliceosomes, and the introns serviced by them, were well established in the stem eukaryote. On the other hand, the near 100 fully sequenced

Acknowledgements

We are very grateful to N Kane, L Maquat, S Mount, L Rieseberg, A Stoltzfus, and S Zimmerly for helpful comments during the preparation of this manuscript. The work was supported by National Institutes of Health support to M Lynch and by an NSF IGERT fellowship in Evolution, Development, and Genomics to A Richardson.

References and recommended reading

Papers of particular interest, published within the annual period of review, have been highlighted as:

  • • of special interest

  • •• of outstanding interest

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