New & Noteworthy
May 16, 2013
When a gene is duplicated, one copy usually dies. It is battered by harmful mutations until it eventually just fades into background DNA.
But this isn’t the fate of all duplicated genes. Sometimes they can survive by gaining new, useful functions. The genes responsible for snake venom proteins are a great example of this.
Another way for a duplicated gene to live on is when both copies get different mutations that confer different functions, so that a cell needs both to survive. Two examples of this type of codependent gene survival are highlighted in a new study by Marshall and coworkers. They compared various fungal species and identified cases where two functions were carried out by either one gene or by two separate genes. Surprisingly, these cases involve alternative mRNA splicing, which is a rare process in fungi.
The first gene pair they focused on was SKI7 and HBS1 from Saccharomyces cerevisiae. In this yeast these two genes exist as separate entities, but in other yeasts like Lachancea kluyveri they exist as a single gene which the authors have called SKI7/HBS1.
The SKI7/HBS1 gene makes two differently spliced mRNAs, each of which encodes a protein that matches up with either Ski7p or Hbs1p. In addition, the SKI7/HBS1 gene can rescue a S. cerevisiae strain missing either or both the SKI7 and HBS1 genes. Taken together, this is compelling evidence that SKI7 and HBS1 existed as a single gene in the ancestor of these two fungal species. In S. cerevisiae, after this gene was duplicated each copy lost the ability to produce one spliced form.
The second gene Marshall and coworkers looked at experienced the reverse situation during evolution. PTC7 exists as a single gene that makes two mRNA isoforms in S. cerevisiae: an unspliced form that generates a nuclear-localized protein, and a spliced form that produces a mitochondrial protein.
But in Tetrapisispara blattae, these two forms exist as separate genes. The PTC7a gene is similar to the unspliced form in S. cerevisiae and the protein ends up in the nucleus, while the PTC7b gene is similar to the spliced S. cerevisiae version and its product is mitochondrial.
Because an ancestor of S. cerevisiae had every one of its genes duplicated about 100 million years ago, yeasts have been a great system to study the fate of duplicated genes. This study shows that even though gene duplication is widespread in fungi and alternative splicing is rare, these mechanisms are actually interrelated and each can increase the diversity of the proteins produced by a species.
Fun fact: 544 genes survived duplication in S. cerevisiae. That is around 10%.
May 8, 2013
When you get down to a single cell, things can get really noisy. Instead of the nice, smoothed over data that you see in populations, you see some variation from cell to cell. This is even if all the cells are identical genetically.
Of course this makes perfect sense if you think about it. Part of the variation comes from slightly different environments. Conditions at the bottom of the flask are bound to be different from those at the top! This goes by the name of extrinsic noise.
Another source of variation has to do with levels of reactants within the cell and the chances that they encounter each other so they can react. These effects can be especially pronounced when there aren’t a lot of reactants around. This goes by the name intrinsic noise.
One process with a lot of noise is gene regulation. It is often affected by minor fluctuations in the environment and there are usually just one or two copies of the gene itself. This is the perfect recipe for noise.
The noisiness of gene expression can be split into two steps. One, called burst frequency, reflects how often RNA polymerase sits down and starts transcribing a gene. The second, burst size, has to do with how many proteins are produced each time a gene is turned on.
Of these two processes, the most sensitive to noise is usually burst frequency. A transcription factor (TF) has to find the promoter of the gene it is supposed to turn on and then bring the polymerase over to that gene. This is dependent on the amount of TF in a cell and the number of TF binding sites on the DNA. What this means is that most of the time, genes with low levels of expression tend to be very noisy.
There are some situations, though, where it is very important to have low expression and low noise: for example, where a cell needs at least a few copies of a protein, but can’t tolerate too many. For most promoters, low levels of expression mean high noise, which in turn means there will be some cells that lack this key protein entirely. But a new study out in PLOS Biology shows one way that a promoter can have the best of both worlds.
In this study, Carey and coworkers examined the noisiness of sixteen different naturally occurring promoters in the yeast S. cerevisiae, controlled by the TF Zap1p. This is a great system because the activity of Zap1p is determined by the concentration of zinc in the medium. This means the authors were able to look at the noisiness of these promoters under a broad range of gene activities.
Their research yields a treasure trove of information about the noisiness of these promoters at varying levels of expression. As we might predict, noise decreased at most (11/13) of the reporter genes as more active Zap1p was around. This makes sense, as cell to cell variability will decrease as genes are turned on more often. Higher burst frequency means less noise.
The opposite was true for most (2/3) of the reporters repressed by Zap1p. As more Zap1p was around, transcription of the reporter gene became less frequent, which meant that the noise effects became more prominent.
One of the more interesting findings in this study focused on an exception to this rule. The ZRT2 promoter showed a bimodal expression pattern, as it was activated at low levels of zinc and repressed at high levels. What makes it so interesting is that its noise level stays fairly constant.
As the zinc concentration increases and activity goes up, the noise goes down. This is what we would expect. But when zinc levels get high enough so that the gene is repressed, the noise levels do not increase. They stay similar to the levels seen with the activated gene.
The authors show that this promoter is repressed differently than the other two repressed promoters, ADH1 and ADH3. These promoters are repressed by decreasing the burst frequency: they fire less often when repressed. In contrast, the ZRT2 promoter fires at the same activated rate when repressed, but yields less protein with each firing: repression decreases burst size.
So this is how a cell can manage to get a gene turned on at low levels more or less uniformly through a cell’s population. If it can create a situation where the gene fires a lot but very little protein is made with each firing, then the cell will have relatively constant but low levels of that protein.
This study also provides a new tool for dissecting how a TF affects the expression of a gene. If a repressor decreases expression without an increase in noise, then it is probably affecting burst size. If on the other hand the noise goes up as expression goes down, then the repressor is affecting burst frequency.
May 1, 2013
When a cell goes cancerous, its chromosomes get seriously messed up. Pieces get deleted, duplicated, mixed and matched. One of the worst things that can happen, in terms of a cell keeping its chromosomes together, is that a chromosome ends up with two centromeres.
A centromere is the part of a chromosome that gets attached to the spindle so it can be moved to the right place during cell division. When there are two centromeres, both get attached and something has to give if the chromosome is pulled in two different directions. Often this means that the DNA of the chromosome breaks between the two centromeres.
This isn’t as simple as the rope breaking during a tug-of-war, though. A chromosome can withstand around 480 piconewtons of force before breaking, but the force exerted by the spindle that breaks the chromosome between the centromeres is just one piconewton or less. Clearly something else is going on to create those breaks!
In a new study out in GENETICS, Song and coworkers looked more closely at what happens when a dicentric chromosome breaks. They used a diploid strain of S. cerevisiae to show that where the DNA breaks is not random. In their experiments, the break tended to happen within 10 kilobases (kb) of the “foreign” centromere.
They used a previously described system where a conditional centromere was placed 50 kb from the normal centromere on chromosome III. This conditional centromere is only turned on in the absence of galactose. They then mated this strain to an unrelated one, resulting in a diploid with a high degree of heterozygosity. In other words, the chromosomes from each strain were different at lots of different places.
Song and coworkers streaked diploids from isolated colonies to a plate lacking galactose and then investigated how the yeast managed to resolve its double centromere issue. Two key ways that the yeast could eliminate the additional centromere involve crossing over between sister chromatids or break-induced repair. They focused on these as it is relatively easy to identify the DNA breakpoint. Because the two chromosomes in each pair are so different, they just needed to look for a loss of heterozygosity. In other words, where did the chromosomes become the same?
When they looked through 27 colonies, they found that the breaks weren’t randomly spread between the centromeres. Surprisingly, about half of them happened very near the conditional centromere. To make sure that there wasn’t something special about these sequences, they looked at two different strains with the conditional centromere located in different places on chromosome V instead of III. They obtained similar results.
Since the force exerted by the spindle isn’t enough to break the chromosome, there must be enzymes involved in creating the DNA breaks. But why do they prefer the region near the conditional centromere? One possibility is that the DNA there is stretched and is more open to enzymes. As the chromosome is being pulled apart, an enzyme gets into this region and manages to cut the DNA.
Although we don’t have time to go into it here, the paper also has a lot to say about the variety of ways that a diploid cell resolves its extra centromere in a way that allows it to survive. And that will inform the study of chromosome dynamics in all kinds of cells.
April 18, 2013
One of the ways you can tell a human cell is cancerous is by taking a peek at its genome. Instead of the orderly 23 pairs of chromosomes seen in a normal cell, the cancerous one has a jumbled mess of a genome. There are extra chunks sticking here and there, chunks missing, and lots of other oddities.
Besides looking untidy, this sort of chaos also causes something called copy number variation (CNV). In CNV, there are either more or less than the usual two copies of some genes. Having the wrong number of copies of certain genes can definitely cause problems.
There is some debate out there about whether CNV causes a cell to go cancerous or if it is just an effect of the cancer. In a new study, de Clare and coworkers provide strong evidence that for many genes in the yeast Saccharomyces cerevisiae, having just one copy in a diploid background leads to faster growth, poor cell cycle control, and an aversion to apoptosis (programmed cell death). This argues strongly that CNV can actually cause a cell to go cancerous. This suggestion is strengthened further by the fact that many of the genes they identified are orthologs of human genes that exist as single copies in certain cancers.
Earlier studies from this group looked at the growth rates of over 5,800 heterozygous diploid yeast mutants, each missing one copy of a particular gene, and found around 600 that actually grew faster than wild type. You might not expect such a high number at first blush, since it seems like a single celled organism would have evolved to grow as fast as it can. The authors hypothesized that there must be a strong selective advantage to having these genes, outweighing the fact that they slow down growth.
Looking more closely, they found that the genes in this set were significantly more likely than the average gene to have functions that keep the genome stable, such as DNA damage repair. They were also highly conserved across the Ascomycete fungi, confirming their importance.
The next step was to see whether there might be any connection to human cancer. They took a subset of these genes – 30 genes involved in DNA repair and sister chromatid segregation – and compared them to human genes. Nineteen of the yeast genes had a human ortholog, and 17 of those human genes exist as a single copy in many cancers, suggesting that having only one copy of these genes may contribute to a cell’s cancer phenotype.
If copy number variation of those genes contributes to cancer in human cells, does it confer a cancer-like phenotype on yeast? The researchers found that the heterozygous yeast mutants showed characteristics of cancer cells such as altered cell cycle, a decrease in apoptosis, and lowered sensitivity to anti-cancer drugs. So the increased growth conferred by the mutations comes with a high cost: increased genome instability and cancer-like symptoms.
Because this cancer-like phenotype occurs in yeast, it will be an excellent model to study exactly how particular genes contribute to it. But these findings could also have a more immediate impact on cancer treatment. Certain experimental cancer treatments work by decreasing the activity of the proteins produced by some of these genes. If a treatment only partly knocks down the activity, then it may actually encourage cancer growth. It would mimic the effects of having a single copy of a gene. The authors actually show that this is the case in yeast for some of the drugs they tested.
And this isn’t a worry just for the drug targets themselves. The drugs aren’t completely specific…they can affect other genes too, again mimicking the effects of having a single copy of one of these other genes. Add to this the fact that each genomically jumbled cancer cell may have different proportions of genes, and you have quite a mess. As usual, yeast can swoop in and save the day.
Scientists may be able to use this and other yeast libraries to quickly screen varying amounts of potential new drugs for their effects on growth. Not only that, they’ll be able to identify what pathways these drugs are hitting in addition to the one(s) that are targeted. This should make the process of drug optimization move ahead much more quickly. Thanks yeast!
April 15, 2013
Anyone reading the SGD blog knows that the yeast Saccharomyces cerevisiae is an amazing little organism. Not only does it give us bread, wine and beer, but it also is an invaluable tool in understanding human biology. It has helped us better understand cancer, Alzheimer’s, and lots of other diseases, not to mention basic biological processes like gene regulation and cell cycle control. This little one celled beast is the rock star of biology!
And now, finally, government is starting to take notice. In a 58-0 vote, the Oregon House recently decided that yeast should be the official state microbe. If the Senate and the governor agree, then yeast will be getting the recognition it deserves. Take that, C. elegans, Drosophila, and all of you other model organisms!
Unfortunately, this recognition is not for yeast’s scientific value. Craft beer making is huge in Oregon, and designating yeast as the official state microbe is a way of celebrating this important state industry. Given all of yeast’s other important contributions to the well-being of us all, this feels a bit like celebrating Hugh Jackman for his role as Wolverine in X-Men while ignoring his roles on Broadway or his role as Jean Valjean in Les Miserables. Yes, he was great in X-Men, but that is an incomplete picture of him as an actor. Same thing with yeast.
Yeast should be celebrated for wine and bread, for medicines like anti-malarials and antifungals, for the deep biological understanding it has given us, and even for its possible future as a source for biofuels. Still, this honor is way better than nothing, and at least yeast will be the first microbe officially recognized by a state. Well, it will be if Oregon hurries.
Hawaii is voting on an official state microbe too, Flavobacterium akiainvivens. This bacterium was discovered by a high school student during a science fair project and is only found in the state of Hawaii. The Oregon senate should vote soon, or yeast will be the second officially recognized microbe.
Of course, the bill could die in the Senate. This is what happened in Wisconsin back in 2009 when their House passed a bill making Lactococcus lactis the official state microbe. This bacterium is important for making Wisconsin’s famous cheese but it wasn’t important enough for the Senate to approve it as Wisconsin’s official state microbe. Hopefully Oregon won’t make the same mistake with yeast.