More Intron-Shaped Bunny Prints

We have seen that that last common ancestor of all eukaryotes had a genome that contained as many, if not more, introns as complex, metazoan life forms. So how did these ancient organisms process all these introns? Did they have a simple mechanism for doing so or did they rely on something like a modern-day spliceosome?

Recently, a study was published that addressed just this issue [1]. It began by listing three possible hypotheses:

Investigating the distribution of splicing mechanisms and spliceosome components among eukaryotic lineages can reveal how splicing and the spliceosome evolved within eukaryotes. In this study, we investigate three hypotheses of spliceosome evolution.

The first is that the spliceosome appeared in eukaryotes shortly after the eukaryotic ancestor, possibly by invasion by self-splicing introns. It is possible under this hypothesis that some eukaryotic lineages do not contain introns or spliceosomal components.

The second hypothesis is that the eukaryotic ancestor had a basic spliceosome that increased in complexity in multicellular eukaryotes. This complexity increase through time would be similar to intron length which appears to have increased in multicellular eukaryotes. Under this scenario, we could expect to find some, but not many, highly conserved splicing proteins present throughout extant eukaryotes.

These first two hypotheses are not mutually exclusive in that an invading self-splicing intron could lead to a spliceosome that increased in complexity over time.

The third hypothesis is that the eukaryotic ancestor contained a spliceosome that is similar in complexity to the spliceosome present in today’s eukaryotes, with the expectation that we could find many spliceosomal proteins throughout eukaryotic lineages.

So which hypothesis is best supported by the evidence?

After an extensive, comparative analysis of the spliceosomal components across various lineages, the authors conclude:

This study sets out to ascertain whether or not (Hypothesis 1) the spliceosome existed in the eukaryotic ancestor and, if so, whether it was a simplified version of today’s spliceosomes (Hypothesis 2) or just as complex (Hypothesis 3). Table 4 shows that splicing-specific proteins from the full range of the spliceosomal cycle are conserved throughout eukaryotes. Thus, a major conclusion of this work is that the splicing process in the eukaryotic ancestor would be similar in overall complexity to that seen today in living eukaryotes, that is, not simplified but complex and thus supporting the third hypothesis stated in the Introduction.


Splicing can now be seen as a fundamental aspect of all modern eukaryotic life and appears to have evolved before the last ancestor of living eukaryotes. Contrary to the idea that splicing may have been a much simpler mechanism in this ancient organism, it now appears that this was not the case and that splicing and the spliceosome had already evolved in a sophisticated cellular process, already linked to other cellular processes such as transcription, capping, mRNA export, and polyadenylation. At this point we can say nothing about the origin of the spliceosome or its nature in the first eukaryote. There must have been a significant period of time between this first eukaryote and the organism we have called the eukaryotic ancestor.

So the eukaryotic ancestor had a spliceosome that was about as complex as that which is needed to remove introns from metazoan genomes. And this raises a very interesting thought. We have seen that introns have been costly to the unicellular way of life, as dozens of different lineages among the five major groups of eukaryotes have shed introns independently. Yet how did this ancestral eukaryotic genome cope with all these introns? By evolving a splicing process and spliceosome “similar in overall complexity to that seen today in living eukaryotes” and not by shedding the introns.

Think of it this way. This ancient eukaryotic lineage went to all the trouble of acquiring a massive influx of introns (starting from an original genome devoid of introns) and evolved a complex, sophisticated machine to process all the introns. Then afterwards, descendent after descendent shed their introns, but when it came time for metaozoans to emerge, all that shedding slowed and/or stopped.

Move along people, move along, no rabbit prints here.

1. Collins L, Penny D. 2005. Complex spliceosomal organization ancestral to extant eukaryotes. Mol Biol Evol. 22:1053-66.

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2 responses to “More Intron-Shaped Bunny Prints

  1. GringoRoyale

    Mike, don’t mean to put this here.
    I’m talking about the movie “Splice” with some friends and they’re talking about genetic hybrids – a creature that is half one thing/half another by virtue of the different genes.
    But I thought you had an article a while back about how this is impossible. How a movie like “The Fly” would not happen, because if you take a gene for something like a fly’s eye & swap that gene for a human’s eye gene – the result would still be a human’s eye, not a fly’s eye.
    Could you point my in the direction to some articles covering this?

  2. Here’s one paper where they took the squid gene and expressed it in the fruit fly:

    Figure 4 shows little fly eyes, not squid eyes, popping up on the wings.

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