“Junk DNA” Suffers a Blow as Nature Papers Find “Global Function” for Introns in Budding Yeast

Introns are segments of genes, found in eukaryotes, that do not code for proteins. Introns are removed from the pre-mRNA transcript by a protein complex called a spliceosome, and the protein-coding regions (called exons) are pasted together by another enzyme, RNA ligase. 

Introns were first identified in 1977 by the lab of Richard Roberts and Phil Sharp (Chow et al., 1977; Berk and Sharp, 1977; Berget and Sharp, 1977). The introns of higher eukaryotes can often be very long indeed — in many cases spanning hundreds of thousands or even millions of bases. Lower eukaryotes (for example, yeast) tend to have shorter and fewer introns. While they were once thought to be junk — genetic debris left over from millions of years of evolution — more recent evidence has revealed many important functions for these non-coding regions of genes. 

For example, it has been established that introns contain codes involved in the regulation of alternative splicing (e.g. Kabat et al., 2006). It has also been shown that the length of introns (and, consequently, the time taken to transcribe them) can contribute to timing mechanisms during development (Swinburne and Silver, 2010). Introns can also encode RNA molecules such as microRNAs (which are required for the expression of mRNAs during development) and small nucleolar RNAs (which play an important role in the processing of ribosomal RNAs) (e.g., Qi et al., 2010; Kiss and Filipowicz, 1995). Plenty of other functions of intronic sequences could be discussed.

Introns in Budding Yeast

Saccharomyces cerevisiae possesses a compact genome, containing only 295 introns which are found across 280 genes (Hooks et al., 2014; Neuvéglise et al., 2011). Most of these introns are shorter than 500 nucleotides in length and only nine yeast genes possess more than one intron (Neuvéglise et al., 2011; Spingola et al., 1999). 

The latest issue of Nature carries a paper on the functions of introns in budding yeast (Parenteau et al., 2019). Here is the Abstract:

Introns are ubiquitous features of all eukaryotic cells. Introns need to be removed from nascent messenger RNA through the process of splicing to produce functional proteins. Here we show that the physical presence of introns in the genome promotes cell survival under starvation conditions. A systematic deletion set of all known introns in budding yeast genes indicates that, in most cases, cells with an intron deletion are impaired when nutrients are depleted. This effect of introns on growth is not linked to the expression of the host gene, and was reproduced even when translation of the host mRNA was blocked. Transcriptomic and genetic analyses indicate that introns promote resistance to starvation by enhancing the repression of ribosomal protein genes that are downstream of the nutrient-sensing TORC1 and PKA pathways. Our results reveal functions of introns that may help to explain their evolutionary preservation in genes, and uncover regulatory mechanisms of cell adaptations to starvation. [Emphasis added.]

The paper further explains:

In this study, we present what is — to our knowledge — the first complete collection of yeast strains each with a deletion of a specific intron. The analyses of this collection provide direct evidence for global functions of introns that may explain their preservation during evolution, regardless of the function or expression of the host gene of the intron. 

A Library of Yeast Strains 

The researchers, led by Sherif Abou Elela of the University of Sherbrooke, systematically constructed a library of yeast strains, deleting a different intron from each of the 295 strains. The result of deleting introns was a stunting of the cell growth in nutrient-depleted environments, even though there was not much impact on the cells whose environment was not depleted of nutrients. Elela and his team determined that approximately 90 percent of introns across the genome of Saccharomyces had this result when removed. In their own words, “We conclude that introns are specifically required for growth in the stationary phase of the culture when nutrients are depleted.”

In their discussion, they note:

We have shown that introns affect cell growth in response to nutrient depletion, regardless of host-gene function. Deleting a single intron reduces the capacity of cells to withstand nutrient depletion or starvation (Figs. 1, 2). Notably, introns could independently rescue the defects caused by intron deletion, even when their host protein was not produced (Fig. 3). Transcriptome analyses indicate that introns promote resistance to nutrient depletion by inhibiting a common set of genes that are associated with translation and respiration (Fig. 5). These intron effects appear to couple the TOR and PKA pathways to the repression of ribosome biogenesis, on the basis of nutrient concentration (Fig. 6 and Extended Data Fig. 10b, c). Together, the data present a paradigm of intron function in which the presence of introns directly contributes to cell growth in a way that is independent of the function of their host gene.

In the same issue of Nature, a different team led, by RNA biologist David Bartel of the Massachusetts Institute of Technology, reported 34 introns in Saccharomyces cerevisiae that “accumulate as linear RNAs under either saturated-growth conditions or other stresses that cause prolonged inhibition of TORC1, which is a key integrator of growth signalling” (Morgan et al., 2019). Usually, cells have been assayed during log-phase growth where cell proliferation is not limited and division takes place at a constant rate. Since this doesn’t normally reflect the situation of budding yeast in a natural environment, the researchers sought to investigate its gene regulation in a context other than that of log-phase growth. 

The researchers deleted a subset of these introns from the Saccharomyces genome using CRISPR, and compared the resultant cells to wild-type cells in order to determine the effect on cell growth. Consistent with the results of Elela and his colleagues, they discovered that the wild-type cells performed well in nutrient-depleted environments but not so well when there was an abundance of resources. The altered cells (with introns deleted), by contrast, performed well when there was abundant resources, but not when resources were scarce.

Survival in Resource-Depleted Environments 

How do introns promote cell survival in conditions of depleted resources? A possibility, suggested by the researchers, is that spliceosomes are sequestered by stable introns. That is, the spliceosome apparatus is “cluttered up” by introns such that it is inhibited from splicing newly transcribed introns. The researchers proposed a model in which the TORC1 pathway, a signalling cascade responsible for regulating yeast cell growth in response to nutrient-availability, causes the build-up of introns in resource-depleted environments. This would be an advantage, since it would prevent energy from being wasted on attempting to grow in environments where resources are scarce. Indeed, TORC1 is already known to regulate, in a nutrient-dependent manner, the expression of ribosomal proteins (Li et al., 2006).

Elela’s team has performed further experiments to suggest that in nutrient-depleted cells, the expression of the ribosomal proteins needed for protein translation is suppressed by introns. This suggests that the introns are inhibiting splicing and translation, thereby reducing the rate of cell metabolism and energy consumption.

All of this calls to mind a comment from biologist John Mattick, a critic of the junk DNA paradigm. Back in 2003 in Scientific American (Gibbs, 2003), he wrote:

The failure to recognize the full implications of this — particularly the possibility that the intervening noncoding sequences may be transmitting parallel information in the form of RNA molecules — may well go down as one of the biggest mistakes in the history of molecular biology.

Quite so.

Literature Cited

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