New & Noteworthy

Holding Back the Translation Torrent

June 12, 2014

We all know the story of the little Dutch boy who stuck his finger into a hole in a dike to keep his village from being flooded.  Now, a new study out in Molecular Cell by Pircher and coworkers has identified a novel regulatory mechanism involving a small 18-nucleotide RNA that behaves similarly to this boy.

A big difference in our story is that unlike the broken dike, the “water flow” in yeast cells is usually a good thing.  It is the continuous stream of protein translation that goes through the ribosome. 

When it’s under stress, though, yeast needs to slow down translation in order to make sure that it is making and folding each protein correctly. This gives it a better shot at surviving the stress.  Once the stress is gone, translation can ramp up again. This is where that 18-nt RNA comes in.

This group identified this 18-nt RNA as a ribosome binding RNA in a previous study. Because there are only a couple of known cases where a noncoding RNA (ncRNA) regulates the ribosome directly, Zywicki and colleagues had wanted to see whether this happens in yeast.  They found about 20 ncRNAs that bound to the ribosome, with the most abundant being an 18-nt fragment that corresponded to part of the coding sequence of the TRM10 gene that encodes a tRNA methyltransferase.

In the current study Pircher and coworkers reconfirmed that in yeast cells about 80% of this 18-nt RNA is associated with ribosomes. To verify whether it really bound to the ribosome rather than to the mRNA being translated, they broke apart polysomes with the chelating agent EDTA. This separated the large and small ribosomal subunits from each other and from mRNA.

All of the 18-mer stayed with the large subunit, showing that it really does interact with the ribosome. The researchers also found that under normal conditions it is bound to nontranslating ribosomes, while in stressed cells it shifts to actively translating polysomes.

The mutant phenotype of the trm10 null mutant suggested that the 18-mer might have a role in adapting to stress conditions. This mutant looks normal under standard conditions, but grows slower than wild type when under osmotic stress.

Pircher and colleagues used a clever strategy to find out whether this phenotype was due to the absence of Trm10p or to the absence of the 18-mer. First, they added a stop codon into the TRM10 gene, outside the region encoding the 18-mer. This mutation blocked production of Trm10p, but didn’t affect the 18-mer. The mutant looked just like wild type under osmotic stress conditions, showing that Trm10p isn’t involved in the stress response.

Second, to see directly whether the 18-mer is important, they mutated its sequence by changing some of the codons within it to other, synonymous codons encoding the same amino acid. So the Trm10p derived from this gene was wild-type, although the 18-mer sequence was different.

A couple of mutants of this type both showed the same phenotype of slow growth under osmotic stress. So production of the 18-mer is in fact important for maintaining growth rate under stress conditions. These mutant 18-mers also failed to bind to ribosomes. 

To find out what this little RNA actually does, they used electroporation to load up each cell with about 200,000 molecules of the 18-mer. This was about the same as the number of ribosomes per cell. Translation was almost completely inhibited. When they did the same experiment with an 18-mer with a scrambled sequence, it had no effect.

Further in vitro experiments confirmed the inhibitory effect of the 18-mer on translation, and showed that the inhibited step is translation initiation. It’s not completely clear why slowing down translation promotes cell growth during stress, but the authors speculate that it leads to more accurate translation and protein folding, which improves protein homeostasis and adaptation to stress. It also remains to be determined whether the 18-mer is created by processing of the TRM10 mRNA or is transcribed independently.

This regulatory mechanism is surprising and relatively novel: there are just a couple of known cases of ncRNAs regulating the ribosome directly. But it makes sense that regulating translation in this way allows the cell to react very quickly to changing environmental conditions, without needing to synthesize any new molecules.

Small ncRNAs like microRNAs or small interfering RNAs are emerging as big players in regulation in many organisms. However, miRNAs and siRNAs are not found in S. cerevisiae. But as this study shows, this does not mean that yeast doesn’t use small RNAs for regulation.  And one of the most surprising things about this story is that such a tiny scrap of RNA can regulate the ribosome, with its 5.5 kb of rRNA and 80 proteins. The little Dutch boy’s finger is immense by comparison!

by Maria Costanzo, Ph.D., Senior Biocurator, SGD

Categories: Research Spotlight

Tags: ncRNA, osmotic stress, Saccharomyces cerevisiae, translation

Proteins Hate Crowds Too

May 29, 2013

A goldfish will swim faster through water than it will through gravy or Jell-O. And according to the results of a new study by Miermont and coworkers, it looks like the same may be true for proteins in a yeast cell.

Now obviously the authors didn’t replace the insides of a yeast cell with gravy or Jell-O. Instead, they used severe osmotic stress to remove water from the cell, making the interior more viscous and the proteins more crowded.

The movement of a wide range of proteins within the cell slowed to a crawl in these shrunken cells. In fact, if the cell was subjected to enough stress, the proteins in the cell essentially stopped moving at all. This lack of movement wasn’t because the high osmotic stress had killed the yeast…they recovered just fine when put back into a more osmotically friendly environment.

The first case the authors looked at was the pathway that helps yeast respond to osmotic stress, the HOG pathway. Once a cell is subjected to osmotic stress, Hog1p is phosphorylated and translocated into the nucleus where it can then turn on the genes needed to respond to this environmental insult.

Miermont and coworkers traced the movement of Hog1p using a Hog1p-GFP fusion protein. At 1 M sorbitol, which subjects the cell to mild osmotic stress, this fusion protein was phosphorylated within two minutes and had reached the nucleus within five.  There were already signs of cell shrinkage even under these mild conditions.

As sorbitol concentrations increased, the phosphorylation and nuclear localization took longer and longer to happen. At 1.8 M sorbitol, Hog1p-GFP didn’t reach maximum fluorescence in the nucleus until 55 minutes. At 2 M sorbitol and above, the cells were shrunken down to their minimal volume, which was 40% of their original size. Under those conditions, only 25% of cells had any nuclear fluorescence even after several hours.

The authors used fluorescence recovery after photobleaching (FRAP) to confirm that these effects were due to slowed protein movement. Basically they zapped a small portion of a cell to burn out the fluorescence of the Hog1p-GFP in that region and then timed how long it took fluorescing Hog1p-GFP from other parts of the cytoplasm to diffuse into that area. To prevent the complication of nuclear translocation in these experiments, they used a pbs2 mutant strain, in which the HOG pathway is blocked and Hog1p stays in the cytoplasm.

They found that fluorescence recovery took less than one second in normal media, about five seconds in 1 M sorbitol, and never happened at 2 M sorbitol. Clearly the protein’s movement was slowed with increasing osmotic pressure. But the effects weren’t permanent: once the cells were put back into normal media, the protein returned to its original kinetics.

The authors expanded their studies to look at proteins that shuttle between the nucleus and cytoplasm in other pathways, including Msn2p, Yap1p, Crz1p, and Mig1p, and obtained similar results. All four proteins took longer to reach the nucleus after being exposed to high osmotic stress. They also looked at other cellular processes where protein movement is critical, such as endocytosis, and again found that increased osmotic stress led to slower moving proteins.

So it looks like molecular crowding can definitely slow down protein movement and affect how a cell functions. For example, the time it takes to respond to environmental stimuli could be significantly slowed, affecting the cell’s chances for survival.  Since yeast cells in the wild encounter high-sugar environments (like rotting grapes), their protein density must be regulated so that they can get through stresses like this. They are ultimately much better adapted than that goldfish in the bowl of Jell-O.

by D. Barry Starr, Ph.D., Director of Outreach Activities, Stanford Genetics

Categories: Research Spotlight

Tags: osmotic stress, protein crowding, Saccharomyces cerevisiae

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