October 30, 2014
Halloween is the time of year when we are all reminded of vampires. And if our favorite yeast Saccharomyces cerevisiae isn’t careful, it might be a vampire’s next target.
Now of course the yeast aren’t pumping blood. Instead, hordes of proteins are pulsing from place to place within the cell. Dracula might be attracted by these pulses, but would be very disappointed indeed to find that there’s no blood involved…
It’s a pretty recent discovery that some proteins move around in a coordinated way. They come together in one location at the same time, and then later all move to another location in response to changes in environmental conditions, or even under constant conditions. This phenomenon of “pulsatile dynamics” has been seen in organisms ranging from bacteria to human.
Dalal and colleagues harnessed the awesome power of yeast genomics, in combination with sophisticated imaging equipment, to ask a question that was unthinkable before these resources were available. How many yeast proteins, out of the entire proteome, show pulsatile dynamics?
This was obviously an ambitious goal. The researchers started with a library of 4159 strains, each containing a different yeast open reading frame fused to the gene for green fluorescent protein. Rather than following the location of each protein over time in great detail, which would have been a huge amount of work, they devised an ingenious scheme to narrow down the possibilities and focus on potentially pulsing proteins.
In the first phase, they looked at the library at fairly low resolution, following individual cells by taking pictures once an hour over about 10 hours. This improved their focus right away: most proteins just stayed put, and only 170 showed any hint of pulsing.
In the next phase, Dalal and coworkers looked more closely at those 170 strains, taking a picture every 4 minutes over a 4-hour span. This eliminated another large group and left them with 64 proteins that still seemed to show pulsatile dynamics.
Another two steps cut the list of candidates way down. Other scientists had shown previously that some yeast proteins show cell cycle-dependent pulsatile movement. Since the researchers were less interested in these, they looked at protein movement during the cell cycle and eliminated 25 proteins whose movement followed it.
They also wondered whether some of the apparent movement they saw was simply due to small shifts in the focal plane during the experiment. To control for this, they examined their candidate proteins in three focal planes, spaced 0.5 um apart.
After all of these steps, Dalal and colleagues were left with just 9 proteins. All of the proteins showed pulsing into the nucleus; seven were known transcription factors, and two were subunits of the RPD3L histone deacetylase complex.
The researchers wondered whether they might have missed any other transcription factors because they hadn’t used the right conditions to see pulsing. So they looked specifically at 122 known transcription factors, testing each under conditions known to induce their activity. This analysis confirmed the previous 9 proteins found, and added just one more.
Interestingly, eight of the ten were members of paralog pairs. In three of these pairs, both members showed pulsing. Looking in detail at the MSN2-MSN4 paralog pair, the researchers found that the pulsing of Msn2p was correlated with that of Msn4p. It isn’t yet clear whether the pulsing phenomenon evolved before the whole-genome duplication that created the paralog pairs, or alternatively whether regulators shared between paralogs later became pulsatile.
Since all of the yeast pulsing proteins are involved in transcriptional regulation, and pulsing brings them into the nucleus where they are active, it’s very likely that the pulsing is an important part of their regulatory role. And since this regulatory mechanism is conserved across species, yeast will provide a great model for studying and understanding it. Dracula might be disappointed, but the rest of us will benefit.
by Maria Costanzo, Ph.D., Senior Biocurator, SGD
Categories: Research Spotlight