Baker’s yeast (Saccharomyces cerevisiae) is one of the best studied eukaryotes. Its genome is just slightly larger than the largest bacterial genome and it was the first eukaryotic genome to be sequenced (Mewes at al., 1997). It has about 7000 genes in total and 6,604 of these genes are protein-coding genes but only 280 of these genes contain introns.1 The rest have lost their introns over the course of several hundred million years of evolution (Hooks et al., 2014).
We know that introns have been lost in yeast because the genes of related species have lots of introns. The common ancestor of all fungi undoubtedly had genes with multiple introns because the available evidence indicates that introns invaded eukarotic genes very early in the evolution of eukaryotes. The fact that most introns have been purged from the yeast genome suggests that introns are not essential for gene function. In other words, introns are mostly junk.2
What about the remaining introns? There’s an ongoing attempt to build a completely synthetic yeast genome by synthesizing artificial chromosomes and part of the process is to eliminate all the junk DNA by cutting out all unnecessary introns (Richardson et al. 2017). So far it looks like most of the introns can be removed without any obvious effect on the viability of the cells but there are a few introns that are essential and others that affect growth under certain conditions (Parenteau et al., 2008; Parenteau et al., 2011). Some of the essential introns contain genes for small noncoding RNAs (e.g. snoRNA) and that’s why they can’t be deleted but the role of other essential introns is still a mystery. The nonessential introns that affect growth appear to be required to regulate growth under starvation conditions (Morgan et al., 2019; Parenteau et al., 2019).
If we assume that the common ancestor of yeast and other fungi had three introns in every protein-coding gene then there would have been about 18,000 introns in the common ancestor. Most of them (>98%) have been eliminated by evolution without serious consequences but these results indicate that some of them have secondarily acquired an important role in gene expression.
I'm writing this post because of two recent Nature papers on the function of some of the remaining introns in yeast genes (Morgan et al., 2019; Parenteau et al., 2019). The important lesson is that >98% of the ancestral yeast introns have been eliminated by evolution, which is clear evidence that the vast majority of introns are junk. They have no function. The Nature papers confirm a previous observation that a subset (~30) of the remaining introns in yeast produce an RNA that confers a growth advantage on yeast cells under limiting growth conditions. This result has been widely misinterpreted by the legitimate media and by creationists who claim that it cast doubt on junk DNA.
Here's a video from the Nature website that ignores the big picture (introns are junk) and gives the impression that while the role of introns is a mystery there are, nevertheless, several adaptationist explanations that may account for their existence. The Nature video focuses on the new function of a small number of yeast introns and suggests that it can account for the prevalence of introns in humans and the incredible complexity of life. I contacted the author of the video and he declared that he was not an expert on the subject but simply reporting on what the two Nature articles said. When I asked him where he got the information for context—information that was not in the papers—he declined to comment. He also did not respond to my request to discuss this with me on my blog. That's too bad because I think it's important to try and understand how misinformation gets propagated by one of the leading science journals in the world.
Here's a link to an Intelligent Design Creationist blog post: As Predicted by Intelligent Design, “Junk” Introns Are Actually Functional. Again, the author of this blog post ignores the big picture; namely, that 98% of the yeast introns have been removed without affecting the viability of the cells. Instead, the anonymous author says,
We know that introns have been lost in yeast because the genes of related species have lots of introns. The common ancestor of all fungi undoubtedly had genes with multiple introns because the available evidence indicates that introns invaded eukarotic genes very early in the evolution of eukaryotes. The fact that most introns have been purged from the yeast genome suggests that introns are not essential for gene function. In other words, introns are mostly junk.2
What about the remaining introns? There’s an ongoing attempt to build a completely synthetic yeast genome by synthesizing artificial chromosomes and part of the process is to eliminate all the junk DNA by cutting out all unnecessary introns (Richardson et al. 2017). So far it looks like most of the introns can be removed without any obvious effect on the viability of the cells but there are a few introns that are essential and others that affect growth under certain conditions (Parenteau et al., 2008; Parenteau et al., 2011). Some of the essential introns contain genes for small noncoding RNAs (e.g. snoRNA) and that’s why they can’t be deleted but the role of other essential introns is still a mystery. The nonessential introns that affect growth appear to be required to regulate growth under starvation conditions (Morgan et al., 2019; Parenteau et al., 2019).
If we assume that the common ancestor of yeast and other fungi had three introns in every protein-coding gene then there would have been about 18,000 introns in the common ancestor. Most of them (>98%) have been eliminated by evolution without serious consequences but these results indicate that some of them have secondarily acquired an important role in gene expression.
I'm writing this post because of two recent Nature papers on the function of some of the remaining introns in yeast genes (Morgan et al., 2019; Parenteau et al., 2019). The important lesson is that >98% of the ancestral yeast introns have been eliminated by evolution, which is clear evidence that the vast majority of introns are junk. They have no function. The Nature papers confirm a previous observation that a subset (~30) of the remaining introns in yeast produce an RNA that confers a growth advantage on yeast cells under limiting growth conditions. This result has been widely misinterpreted by the legitimate media and by creationists who claim that it cast doubt on junk DNA.
Here's a video from the Nature website that ignores the big picture (introns are junk) and gives the impression that while the role of introns is a mystery there are, nevertheless, several adaptationist explanations that may account for their existence. The Nature video focuses on the new function of a small number of yeast introns and suggests that it can account for the prevalence of introns in humans and the incredible complexity of life. I contacted the author of the video and he declared that he was not an expert on the subject but simply reporting on what the two Nature articles said. When I asked him where he got the information for context—information that was not in the papers—he declined to comment. He also did not respond to my request to discuss this with me on my blog. That's too bad because I think it's important to try and understand how misinformation gets propagated by one of the leading science journals in the world.
Here's a link to an Intelligent Design Creationist blog post: As Predicted by Intelligent Design, “Junk” Introns Are Actually Functional. Again, the author of this blog post ignores the big picture; namely, that 98% of the yeast introns have been removed without affecting the viability of the cells. Instead, the anonymous author says,
ID proponents have long predicted that functions would be uncovered for such non-coding DNA. In The Myth of Junk DNA, Jonathan Wells reviews various functions discovered for introns. He points out that introns play vital roles in alternative splicing, where exons of a single gene can be mixed and matched such that one gene can give rise to many different proteins ...Actually, the Nature papers strongly imply that functions for introns are just anomalies in a sea of junk but you have to understand the big picture in order to see this!
Wells cites many studies that provide strong evidence that introns are involved in alternative splicing, helping to create diverse proteins required by cells.
It’s very difficult to argue that functions for introns are just anomalies in a sea of junk. These new Nature papers further confirm that this is the case.
Image credit: Differential interference contrast image of yeast cells from Wikipedia.
1. Most genes have only one intron but some have two for a total of 295 introns in the yeast genome.
2. Introns take up about 23% of the human genome. If they are mostly junk as all the evidence suggests then this is a significant contribution to the total amount of junk DNA in our genome. The fact that some organisms can get along without most of their introns (e.g. yeast) plus the fact that some species have much smaller introns (e.g. pufferfish) strongly supports the idea that introns are mostly junk.
Hooks, K.B., Delneri, D., and Griffiths-Jones, S. (2014) Intron Evolution in Saccharomycetaceae. Genome Biology and Evolution 6:2543-2556. [doi: 10.1093/gbe/evu196]
Mewes, H., Albermann, K., Bähr, M., Frishman, D., Gleissner, A., Hani, J., Heumann, K., Kleine, K., Maierl, A., and Oliver, S. (1997) Overview of the yeast genome. Nature, 387:7-8. [doi: 10.1038/42755]
Morgan, J.T., Fink, G.R., and Bartel, D.P. (2019) Excised linear introns regulate growth in yeast. Nature [doi: 10.1038/s41586-018-0828-1]
Parenteau, J., Durand, M., Véronneau, S., Lacombe, A.-A., Morin, G., Guérin, V., Cecez, B., Gervais-Bird, J., Koh, C.-S., and Brunelle, D. (2008) Deletion of many yeast introns reveals a minority of genes that require splicing for function. Molecular biology of the cell, 19:1932-1941. [doi: 10.1091/mbc.E07-12-1254]
Parenteau, J., Durand, M., Morin, G., Gagnon, J., Lucier, J.-F., Wellinger, R.J., Chabot, B., and Elela, S.A. (2011) Introns within ribosomal protein genes regulate the production and function of yeast ribosomes. Cell, 147:320-331. [doi: 10.1016/j.cell.2011.08.044]
Parenteau, J., Maignon, L., Berthoumieux, M., Catala, M., Gagnon, V., and Elela, S.A. (2019) Introns are mediators of cell response to starvation. Nature. [doi: 10.1038/s41586-018-0859-1]
Richardson, S.M., Mitchell, L.A., Stracquadanio, G., Yang, K., Dymond, J.S., DiCarlo, J.E., Lee, D., Huang, C.L. V., Chandrasegaran, S., and Cai, Y. (2017) Design of a synthetic yeast genome. Science, 355:1040-1044. [doi: 10.1126/science.aaf4557]
