New & Noteworthy
September 24, 2012
Anyone reading this blog probably knows how important the yeast S. cerevisiae is. It makes our bread better, our beer and wine more spirited, and our genetics more understandable.
Because it is such an important beast, this yeast is also incredibly well characterized. It was the first non-bacterial organism whose genome was sequenced and is a key model organism for teasing apart how eukaryotes like us work. We may know more about the molecular biology and genetics of S. cerevisiae than about any other organism on the planet.
And yet we know surprisingly little about S. cerevisiae in the wild. We know that it isn’t on unripe fruits but suddenly appears once they ripen. We also know it doesn’t tolerate winter particularly well. So where does yeast hang out when there isn’t ripe fruit around and/or it gets chilly? A group of researchers in Italy thinks a key place is inside a hibernating wasp.
When Stefanini and coworkers looked, they found lots of yeast (including S. cerevisiae) in wasp intestines. They were also able to show that the S. cerevisiae remained viable in a hibernating queen over the winter and that that the queen transferred the yeast to new wasps in the spring by regurgitation. With this one study, these scientists managed to find at least one way that yeast can survive the winter and get to ripe fruit.
To figure this out, Stefanini and coworkers did experiments both in the field and in the lab. They first collected wasps and bees from around the Italian countryside and showed that wasps, but not bees, harbored yeast in their gut. In all they found 393 yeast strains in the 61 wasps they dissected, 17 of which turned out to be S. cerevisiae. By sequencing and comparing the genes URN1, EXO5, and IRC8, they were able to conclude that these yeast were related to wine, beer, bread, and laboratory strains of S. cerevisiae.
The researchers figured out that the yeast could survive for three months and be passed on to the next generation of wasps with a couple of controlled experiments they did in the lab. They fed queens GFP labeled yeast and then let them hibernate. After three months they dissected some of them and found lots of viable yeast in their intestines.
The rest of the queens were allowed to wake up and find new nests. Larvae were removed from the nests and were found to contain GFP yeast as well. The yeast not only lived through the winter but passed on to the next generations!
Of course this doesn’t mean that this is the only way that it can happen. But it is the first time anyone has managed to get such a detailed look at feral yeast. And this kind of work is important if we want to use S. cerevisiae as a way to study evolution.
To understand its evolution, we have to understand the natural forces that shaped S. cerevisiae into the organism it now is. Only then can we piece together why S. cerevisiae has evolved the way that it has and so learn fundamental lessons about the mechanisms of evolution.
September 12, 2012
Everyone knows that when the environment changes, those individuals with certain DNA differences useful in this new environment thrive while others wither. But there hasn’t been a lot of work done to investigate how many DNA differences are available to a population for adapting to a particular environmental change.
This may sound esoteric but the answer has real implications for speciation. If there are few mutations possible and these mutations are very similar in terms of phenotype, then different populations will travel similar routes in their adaptations to the same environmental change. This will definitely slow down speciation. If on the other hand there are many genetic ways to adapt to the same change, then isolated populations will head down different paths leading to faster speciation.
In a new study out in GENETICS, Gerstein and coworkers found that at least for the environmental insult they used (low levels of the fungicide nystatin), there were very few paths to resistance. In fact, just four genes in the ergosterol biosynthesis pathway turned up in the 35 resistant lines they surveyed using whole genome sequencing.
Now that isn’t to say that there were just a few mutations. There weren’t. They found eleven unique mutations in the ERG3 gene, seven in ERG6, and one each in ERG5 and ERG7. There were duplications, deletions, premature stop codons and missense mutations. So there are lots of ways to mutate these few genes.
The small range of genes affected might suggest that adaptation favors populations evolving along similar paths since the same environmental effects result in the same adaptative mutations. And yet, not all of these mutations in these few genes are created equally. Different lines responded differently to other stressors.
For example, lines with mutations in the ERG3 gene responded poorly to ethanol while the other lines did very well. And the lines with mutations in ERG5 and ERG7 responded less well to salt than the other lines. So if one population was subjected to salt and nystatin and the other to ethanol and nystatin, the strains would almost certainly adapt with mutations in different genes. Even within this narrow set of genes, there is room for adaptation by different routes.
While a useful first step, we don’t want to infer too much from this single study. The researchers used a very specific environmental insult known to work through a specific pathway and found only mutations in that pathway. The next study might want to focus on something like salt tolerance, a trait predicted to be achieved through multiple pathways. Then we can get an even better feel for how many options a population has for adaptation.
September 6, 2012
Chromatin proteins, primarily histones, are a great way to control what parts of a cell’s DNA are accessible to its machinery. These proteins coat the DNA and are marked up in certain ways to indicate how available a piece of DNA should be. A methyl group here, an acetyl group there and a cell “knows” where the genes are that it is supposed to read!
Of course this structure needs to be maintained or a cell might start to misread parts of its DNA as starting points of genes. Then RNA polymerase II (RNAPII), the enzyme responsible for reading most protein-coding genes, would start making RNA from the wrong parts of the DNA, wreaking havoc in a cell.
One place where maintaining chromatin structure might be especially tricky is within the coding parts of genes. It is easy to imagine RNAPII barreling down the DNA, knocking the proteins aside like pins in a bowling alley. But it doesn’t. For the most part the chromatin structure stays the same and survives the onslaught of an elongating RNAPII.
Two key marks for keeping histones in place are the trimethylation of lysine 36 of histone H3 (H3K36me3) that is mediated by Set2p, and a general deacetylation of histone H4 that is mediated by the Rpd3S histone deacetylase complex. We know this because loss of either complex causes an increase in H4 acetylation and transcription starts from within genes.
In a recent study in Nature Structural & Molecular Biology, Smolle and coworkers identified two key components that help chromatin resist an elongating RNAPII in the yeast S. cerevisiae. The first, called the Isw1b complex, binds H3K36me3 and the second, the Chd1 protein, binds RNAPII itself. That these two were involved wasn’t surprising since previous work had suggested they helped prevent histone exchange at certain genes.
What makes this work unique is that the researchers showed the global importance of these proteins in the process and were able to tease out some of the fine details of what is going on at the molecular level. They used electrophoretic mobility shift assays to show that Isw1b bound the trimethylated form of H3 via its Ioc4p subunit and used chromosome immunoprecipitation coupled to microarrays (ChIP-chip) to show that Isw1b localized to the middle of genes in vivo. They also showed that when Set2p was removed, the localization disappeared (presumably because of the loss of the trimethylation of lysine 36). They clearly demonstrated that Isw1b is found primarily in the middle of genes.
While these results indicate that the Ioc4p-containing Isw1b complex is moored to the middle of genes via its interaction with H3K36me3, it does not establish what it is doing there. For this the researchers knocked out Isw1b and Chd1 and showed via genome tiling arrays a global increase in cryptic transcription starts. The DNA in the middle of genes was now being used inappropriately by RNAPII as starting points for transcription. Further investigation with Isw1b and Chd1 knockouts showed an increase in chromosome exchange and an increase in acetylated H4 in the middle of genes.
Whew. So it appears that Isw1b and Chd1 inhibit inappropriate starts of transcription by keeping hypoacetylated histones in place over the parts of a gene that are read. They are two of the key players in maintaining the right chromatin structure over genes. They help keep RNAPII from railroading histones aside as it elongates, thus protecting the cell from inappropriate transcription starts.