New & Noteworthy
Harvesting Until the Last Minute
April 15, 2015
In the Dune universe, carryalls allow for the precious commodity spice to be harvested for as long as possible. In a yeast cell, it is Rio1 that allows Pol I to generate rRNAs for the precious commodity ribosomes for as long as possible. Photo by Barry Starr
In the science fiction novel Dune, the most precious thing in the universe is spice. It is harvested from the sands of the planet Dune under very dangerous conditions—every time people start to mine it, a gigantic worm comes to kill them. The spice is so valuable, though, that the miners harvest it until the very last second. As time runs out, a carryall whisks them away as the worm rises out of the desert.
While nothing quite so exciting happens in the nucleus of a yeast cell, one of the closest situations may be at the rDNA locus. Here the precious commodity is ribosomes and yeast cells need them to be made almost constantly. The only pauses in production are when this part of the genome needs to be replicated and when it needs to be segregated into a daughter cell. In both cases, as something akin to giant sandworms comes crashing onto the scene, harvesting stops and the machinery is removed with a cellular carryall.
Of course there aren’t harvesters extracting whole ribosomes from the yeast nucleus! Instead, it is RNA polymerase I (Pol I) and RNA polymerase III (Pol III) making the raw stuff of ribosomes, the 35S and 5S rRNAs, respectively. These polymerases need to stop transcribing and clear the way for the rDNA replicating replisome during S phase and for condensins at the end of anaphase. If they don’t, the rDNA locus becomes unstable, resulting in the mother yeast cell living a shorter life and in its daughter not getting the rDNA locus (and the rest of the chromosome it is on) at all.
In a new study in Nature Communications, Iacovella and coworkers have identified the carryall that helps to remove Pol I from the rDNA locus. Surprisingly, it is a kinase, named Rio1, that was previously known to be involved in rRNA processing and building ribosomes in the cytoplasm.
Rio1 does not physically remove Pol I from the 35S gene. What this study suggests is that it phosphorylates one of the 14 subunits of Pol I, Rpa43, so that Pol I no longer interacts as strongly with the transcription factor Rrn3. The end result is the untethering of the polymerase and its release from the DNA. Now condensins can glom onto the rDNA locus at the end of anaphase and DNA polymerase can barrel through the region in S phase without wreaking genomic havoc.
The first key finding in this study was that Rio1 isn’t just active in the cytoplasm, but also in the nucleus. In fact, it was most active in the nucleolus, a small moon shaped section of the nucleus that is formed around the rDNA locus.
The researchers went on to show that Rio1 is present in the nucleolus only at certain times in the cell cycle (S phase and anaphase). Using chromatin immunoprecipitation (ChIP) assays, they were able to show that Rio1 was enriched specifically at the rDNA’s 35S promoter and coding sequence.
They next created a conditional Rio1 mutant that could not enter the nucleus in the presence of galactose. When Rio1 was kept out of the nucleus, nucleoli became fragmented, there were no condensins on the rDNA locus at anaphase, and the mother yeast did not pass the replicated nucleolus to her daughter. Obviously Rio1 is a critical housekeeper for the rDNA locus!
They next used ChIP assays to show that when Rio1 was kept out of the nucleus, there was around 3-fold more Pol I at the 35S promoter and gene during anaphase than when Rio1 was allowed to go nuclear. This resulted in a 5-8 fold increase in 35S rRNA levels—implying that Pol I was still there cranking out rRNA.
The most likely explanation is that all the hyperactive Pol I transcribing the rDNA locus prevents condensins from binding the DNA and that removal of Pol I by Rio1 allows the condensins to bind. The condensins then shrink the rDNA region such that it can move though the tiny bud opening into the daughter.
They got similar results in S phase, where lack of nuclear Rio1 caused an increase in Pol I occupancy at the rDNA and an increase in 35S transcription as well. Here the lack of Rio1 has more devastating consequences to the genome. Its absence most likely causes the replisome to collide head-on with the transcribing Pol I, resulting in double strand DNA breaks. Because the rDNA locus is such a repetitive region, the cell makes mistakes when it repairs the break using homologous recombination. The end result is nucleolar fragmentation and a shorter life span.
The final set of experiments showed that Rio1 most likely affects Pol I occupancy by phosphorylating one of its subunits, Rpa43. First the authors used Western blot analysis to show that Rpa43 is less phosphorylated when Rio1 is kept out of the nucleus and when a mutant version of Rio1 lacking its kinase function is used. They also showed that Rio1 could phosphorylate Rpa43 in vitro.
They postulate that this phosphorylation causes the interaction between Pol I and the transcription factor Rrn3 to weaken, allowing Pol I release. Alternatively, Rpa43 phosphorylation could lead to the disintegration of the Pol I enzyme itself. Confirmation of one or the other will require more research.
Taken together, these studies paint a fascinating picture of the rDNA locus. Here Pol I is frenetically transcribing as much 35S rRNA as it possibly can to keep up with the yeast cell’s unquenchable thirst for ribosomes. The only time it stops is when continuing could harm the cell, during DNA replication in S phase and DNA transmission in anaphase. And even then, like spice hunters on Dune, they stay until the very last minute. A spicy tale, indeed.
by D. Barry Starr, Ph.D., Director of Outreach Activities, Stanford Genetics
Rise, replisome, rise!
Categories: Research Spotlight