October 11, 2016
As anyone who has tinkered with the inside of a living cell or looked at one of those daunting and overwhelming biochemistry poster knows, life is complicated. Like thousands of gears all interconnected in some vast steampunk machine, a cell has thousands of genes making thousands of proteins that come in a variety of flavors all interacting in overlapping, complicated ways to keep the cell alive. Toss in those important RNAs and a few other bells and whistles and you begin to understand why scientists have had to just focus in on individual parts of the machine to study.
Until now that is. In a new study out in Science led by University of Toronto Professors Brenda Andrews and Charles Boone, and Professor Chad Myers of the University of Minnesota-Twin Cities, Costanzo and coworkers were able to get a first approximation of how all those genes are connected in a yeast cell. And it is as complicated as you imagined.
This was a daunting undertaking that took over 15 years to pull off but it looks like it was well worth it. They have already learned an incredible amount and people will continue to learn more and more as scientists mine this treasure trove of data for a long time to come (Stay tuned for the data to be available here at SGD). This is the sort of study that will provide an invaluable reference guide that will keep giving year after year after year.
And it isn’t just a tour de force of basic biology either. This study will, among other things, reveal what genes of unknown function are actually doing in cells, identify new targets to go after in diseases like cancer and may even help geneticists find that “missing heritability” in their genome-wide association studies (GWAS). Given that these three examples are just a subset of what we’ll get out of this study, I think you can see why it is such a game changer.
It would not have been possible without all of the yeast work that has been done and carefully curated over the years. And there is no way it could have been done in another organism, like humans. Human cells are simply too complicated, we don’t yet have the necessary tools, and we don’t have as deep a knowledge as we do with yeast. It is only in yeast that we could begin to get this amazing peek at life happening inside of a cell.
Yeast as a model organism is alive and well and helping us better understand life and ourselves. This sort of study drives that point home in a way that benefits many, many scientists and, eventually, patients the world over.
When 1+1 Does Not Equal 2
So how did these researchers pull this off? They basically looked at what happens when they knock out two genes at once in yeast. They did this for every possible gene pair for 5416 out of the 6,000 or so yeast genes.
Of course this strategy won’t work with the 1000 or so yeast genes that are essential—the yeast dies when these are knocked out. For these genes, the researchers used temperature sensitive mutations under conditions where the gene is tweaked but not dead.
What they were looking for were combinations that did either better or worse than you might predict based upon each individual deletion on its own. And they found plenty.
They generated 23 million of these double knockout yeast (Yes, you read that right!) and found ~550,000 negative interactions and ~350,000 positive interactions—a huge amount of data about the inner workings of a cell. The next step was to take all of this data and try to make sense of it.
They did this by clustering the genes together based on who was interacting with whom. If deleting gene A with either gene B or gene C had a larger negative effect than expected, then these three genes were clustered together. And if deleting gene A had an effect on gene D, but deleting gene B or C did not have an effect on D, then A was involved in both a cluster with B and C as well as a separate cluster with D. Now repeat this over and over thousands and thousands of times.
When they did this, many things about living cells quickly came into focus. I only have the space to touch on a few.
First off, while negative interactions usually happened between genes in the same biological processes or in the same subcellular compartments, the same was not true for the positive interactions. These were much more spread out and often genes like chaperones.
They also found about 1000 genes that weren’t involved with many other genes at all. These are most likely genes that would show more interactions under different growth conditions. For example, deleting a gene critical for utilizing galactose might not show a lot of interactions if a cell is grown in glucose. Repeating this experiment under different conditions will probably uncover where these genes fit in.
This is just a taste of what they found and of what is to come in the next few years. Here is a bit more:
Finding Out What a Gene Does
You’d think having a genome sequence for over 20 years might mean you’d pretty much know what all those genes are doing, but you’d be wrong.
There are still plenty of genes in yeast with unknown function. This kind of study can help uncover what a gene might be doing by seeing which genes it clusters together with. If gene X is clustered with known DNA repair genes, it is probably involved in something to do with DNA.
One such gene they looked at in this study was YJR141W. Not a lot was known about this gene other than it was essential.
What they found was that this gene clustered with genes in the cleavage polyadenylation factor (CPF) and cleavage factor 1A (CF1A) protein complexes suggesting this gene might have a role in mRNA 3’-end processing and polyadenylation. After showing experimentally that the protein from this gene physically interacted with CPF complex members Mpe1p and Ysh1p and that the temperature sensitive mutant had trouble processing mRNA in vitro, the researchers felt confident enough to give this gene a name based on its function. They named it IPA1 (Important for cleavage and PolyAdenylation 1).
Helping Find New Cancer Treatments
This study also has important implications for human health in lots of different ways. For example, it might help scientists find better cancer treatments.
Cancer happens when mutations in key genes cause cells to grow uncontrollably or to refuse to die. In an ideal world we’d treat these cancers by going after these genes directly. Unfortunately many of them are not particularly great targets to go after with pharmaceuticals.
This is where synthetic lethals can help. A synthetic lethal is when mutations in two separate genes do not kill a cell on their own, but they do when a single cell has both mutant genes.
The idea then is to find a pair of mutant genes that kills a cell with one of the genes being involved in cancer and the second one some other gene. You can go after the second gene and by affecting its activity kill the cancer cells that have the other gene in this pair mutated.
And of course noncancerous cells are fine with you targeting that second gene—mutating only that gene isn’t lethal. Chemotherapy with many fewer side effects!
If you think this sounds like something this study might uncover, you’d be right. This study found around 10,000 or so double knockouts that were lethal which might provide a lot of possibilities for cancer researchers.
Cancer is almost certainly just one of many possible applications to human health. And we will learn so much about the basic biology of a cell from such an exhaustive and detailed analysis of the inner workings of a cell.
This holistic portrait of the genetic interactions of a yeast cell is elegant, beautiful and useful. Not bad for the beast that gives us bread and booze.
by Barry Starr, Ph.D., Director of Outreach Activities, Stanford Genetics
Categories: Research Spotlight