New & Noteworthy
February 22, 2012
As many of you know, Jonathan Widom died suddenly last summer. He was a Professor in the Department of Molecular Biosciences at Northwestern University. The beauty of Jon’s scientific research was more than matched by his surpassing intellectual brilliance and personal warmth, and he is deeply missed by those who knew and loved him. Jon’s family and colleagues have organized a symposium celebrating his life and work, which will be held at Northwestern’s Evanston campus on March 16, 2012. Information about this gathering, called “Unraveling the Mysteries of Life: Recognizing the Life and Work of Jon Widom”, can be found online here. All are welcome. Additionally, tributes to Jon that will be shared at the meeting (and afterward) can be contributed here.
February 17, 2012
Let’s face it: low alcohol beer just doesn’t taste that great. This is because the alcohol is either diluted or removed chemically after fermentation. Both methods wreak havoc with a beer’s flavor.
Dr. John Morrissey of University College Cork is trying to change this. His lab is working to generate a strain of yeast that turns some but not all of its sugar into alcohol. That way the beer process is the same, just with less alcohol at the end.
This is different from stopping fermentation early. In that case there are still sugars in the final product which ruin a beer’s taste even more than removing the alcohol! Here the same amount of sugars are used up, it is just that only part of that energy has gone into making the alcohol. Same sugar content, less alcohol.
Although we don’t have all the details because of intellectual property issues, what we do know is that he compared the genomes of yeast species that make a lot of alcohol and those that don’t. In an email he stated that he focused on genes that would affect carbon metabolism without perturbing redox balance in a significant way. Presumably he then swapped the appropriate genes between strains and created his low alcohol strain.
This is not only a godsend for low alcohol beer, but it may be useful for other fermentation processes as well. For example, maybe something similar can be done for low or no alcohol wines which, apparently, are even less tasty than low alcohol beer. Designated drivers everywhere will be thanking Dr. Morrissey profusely if he can make decent tasting, low alcohol drinks a reality.
And apparently it isn’t just designated drivers that want this stuff. Judging by recent upticks in sales of the relatively low quality low alcohol beers currently on the market, there is definitely a market out there for such beverages. A cool science project, decent low alcohol beer and nice profits to boot! Who could ask for more?
How beer is made, from Modern Marvels, www.history.com
February 14, 2012
RNA expression data that are included in SGD’s SPELL expression analysis tool are now available for download in the expression directory. Datasets have been grouped by publication and are in PCL format.
LiftOver files that allow conversion of chromosomal coordinates between different S. cerevisiae genome versions are also now available for download via the genome_releases link in the sequence directory.
February 10, 2012
Some people might think that the transition from single-celled creatures to multi-cellular ones must have been tough. After all, single celled organisms ruled the world for the first one or two billion years of life here on Earth.
And yet, all multi-celled beasts didn’t evolve from the same ancestor. Current theories are that multicellularity evolved dozens of times over the ages. In fact, all of the transitional stages of multicellular life can be seen in the volvocine green algae species around today. So maybe it isn’t so tricky after all.
Using a very clever screen in yeast, Ratcliff and coworkers have shown that they can get crude multicellular life to evolve in the lab. Basically they only let the yeast that settled easily to the bottom of a shaking flask go on to reproduce. Within 60 or so days, they had the beautiful, snowflake-like, multicellular beasts made up of multiple yeast cells shown in the image to the right.
Of course multicellular is more than having a bunch of cells stuck together. Heck, yeast do that now in something called flocs. No, to be multicellular, these yeast need to reproduce in a way that generates new multicellular yeast and to have specialized cells. The snowflake yeast from this experiment did both.
These yeast did not reproduce by creating sperm and eggs that combine to generate progeny. Instead they reproduced more like a lot of plants do. They produced smaller versions of themselves which then went on to grow to “adulthood.” Multicellular life gave birth to more multicellular life.
Cells within these snowflakes were also willing to die for the common good. For example, the cell where the juvenile snowflake was attached would undergo apoptosis so the juvenile could be released. No single-celled organism would willingly take that kind of hit for other cells.
So it looks like these researchers managed to evolve multicellular organisms from single-celled ones in just a few months. Pretty amazing what can be learned from yeast!
Of course some care is needed here. Yeast actually evolved from a multicellular ancestor so some sort of memory of multicellular life may still be lurking in its genes. If true, this might make the transition from one to many simpler in yeast than in other single-celled organisms.
This is why the researchers plan to try similar experiments with single celled organisms that have been single cells throughout their evolutionary life. Then they’ll have an even better idea about how easy the “one to many cells” transition is.
Multicellular yeast having babies.
February 6, 2012
As life evolves there is a tendency for increased complexity. Up until now, scientists have mostly focused on gain of function mutations as the motor for this change. This has proven fertile ground for evolution deniers who have claimed that life’s complexity could not have arisen from these rare, gain of function mutations alone.
A new study by Finnigan and coworkers provides an important counterpunch to this argument. These authors resurrected ancient proteins and showed that an increase in complexity can come from much more common, loss of function mutations. Time for the deniers to find a new argument…
Making Molecular Machines
Finnigan and coworkers focused on the evolution of a protein called vacuolar H+ -ATPase or V-ATPase for short. Like other molecular machines, this proton pump consists of many different proteins all working together in a coordinated fashion. One key part of this machine is a rotary ring called V0. (This would be the ring of C proteins in the image to the right.)
In most eukaryotes, V0 is made up of five identical subunits (called Vma3) and one subunit called Vma16. In fungi, a third protein, Vma11, has replaced one of the Vma3 subunits. In other words, the fungal version is a bit more complex than other eukaryotic versions.
Current theories are that these three proteins all arose through gene duplication. Duplication of the Vma3 gene first led to the Vma16 gene and then later in fungi, Vma3 duplicated again this time becoming Vma11. Yeast V-ATPase absolutely requires Vma11 to function and other eukaryotic Vma3 family members cannot replace Vma11.
Using the 139 family members of the Vma family available in GenBank, members of the Thornton and Stevens lab recreated the ancestral proteins that existed before and after the Vma11 gene duplication event. Before the arrival of Vma11, there were only two proteins which the authors have named Anc.3-11 and Anc.16. Anc.3-11 presumably has functions of both Vma3 and Vma11. After the gene duplication event, there were three ancient proteins: Anc.3, Anc.11, and Anc.16.
Using these ancient proteins, the authors first showed that Anc.3-11 could substitute for either Vma3 or Vma11 in yeast. It could even partially rescue a yeast strain that lacked both of the other genes. They then showed Anc.16 could replace Vma16 and most importantly, that the two ancient proteins could replace the three modern ones. They reconstructed an ancient molecular machine that works.
The next step was to figure out what happened after Anc.3-11 duplicated again and the two genes began to evolve into the separate proteins, Anc.3 and Anc.11. Again using the GenBank sequences, the authors predicted that two single mutations were an initial step on the way to the separation of Anc.3-11 activities into the Anc3 and the Anc11 proteins.
The authors engineered each mutation independently into the Anc.3-11 protein and found that one mutation made Anc.3-11 more like Anc.3 and the other made Anc.3-11 more like Anc.11. The complex now required all three Anc proteins instead of just the two for maximal activity. The authors had recapitulated the first evolutionary steps that led to the formation of the three subunit V0 rotary ring.
Finally the authors showed that each of these mutations were loss of function mutations. The Anc.3-11 protein has two different interfaces that interact with Anc.16. The first mutation weakened one interface on Anc.3 and the second mutation weakened the other interface on Anc.11 causing both proteins to now be required to reconstitute the ring. The added complexity arose from a combination of gene duplication and relatively common loss of function mutations.