New & Noteworthy

Codependent Genes

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.

Genes can be codependent too. Sometimes this is what keeps a duplicated gene alive.

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%.

by D. Barry Starr, Ph.D., Director of Outreach Activities, Stanford Genetics

Categories: Research Spotlight

Tags: alternative splicing, gene duplication, evolution, Saccharomyces cerevisiae

The Indulgent Chaperone

April 01, 2013

When you think of a chaperone, you probably think of a strict adult at the prom who keeps a tight rein on the kids’ behavior.  Well, in nature, a chaperone sometimes has to do the opposite to help new genes form more quickly.  Sometimes the chaperone has to give the gene a longer leash to explore lots of different possibilities.


Nature’s chaperones will look the other way when kids spike the punch.

See, in theory, it is pretty easy to make a new gene.  A cell accidentally makes an extra copy of an existing gene and this gene is then free to mutate into something new.  A few mutations later and you have a new gene.

Turns out this is probably trickier than it sounds.  First off, having an extra copy of a gene can cause problems.  And second, getting to a new function is no walk in the park either.  It usually takes a few sequential mutations to get there and, with proteins being such persnickety things, many of the intermediates along the way end up being unstable. 

One way a cell might deal with these issues is to bring in a chaperone that lets the gene tolerate more mutations.  Chaperones are proteins that help stabilize other proteins, often under trying conditions like high temperature.  They coddle the protein and keep it stable so that it can still do its job.  In addition, chaperones can also cause a protein to relocate to different parts of the cell.

So the idea is that if a duplicated gene gains a mutation that lets its protein interact with a chaperone, the protein may get more stability from that interaction or may be rerouted to where it won’t do any harm. Because the chaperone buffers the possible harmful effects for the cell, the gene is free to explore more different intermediates on the way to its new function.

A new study out in GENETICS by Lachowiec and coworkers lends support to this “capacitor hypothesis.”  The authors used both Arabidopsis and Saccharomyces cerevisiae to show that genes whose proteins interact with the chaperone Hsp90 evolved more quickly than closely related genes that did not.  This strongly supports the idea that chaperones can encourage new functions in duplicated genes.

The authors first looked at a couple of closely related transcription factors from Arabidopsis, BES1 and BZR1.  Using a specific inhibitor of HSP90 called geldanamycin (GdA), they were able to show that BES1 was a client of HSP90 but BZR1 was not.  They then created a phylogenetic tree of Arabidopsis BZR/BEH gene family and, by determining the ratio of non-synonymous to synonymous changes, found that BES1 had a higher rate of mutation.  One explanation is that the stabilizing/relocalizing influence of HSP90 allowed BES1 to tolerate more mutations.

This result was an excellent first step in showing that the capacitor hypothesis may be true in some cases, but it is limited by being based on a single pair of proteins.  To broaden their findings, Lachowiec and coworkers took advantage of the vast knowledge about Hsp90 interactions in Saccharomyces cerevisiae to look at many more genes.

At first this didn’t work out that well.  The authors looked at a data set of yeast proteins that interacted with Hsp90 (encoded in yeast by the HSP82 and HSC82 genes) and, after removing any co-chaperones from the set, found no difference in the rate of evolution between those proteins that interacted with Hsp90 and those that did not.  But as the authors note, this isn’t surprising as so many other factors play a role in the rate of evolution too.

To refine their analysis, they mimicked their BES1/BZR1 study and focused on pairs of closely related proteins where one interacted with Hsp90 and the other did not.  They found that proteins that interacted with Hsp90 had a “longer branch length” than did their close relatives that did not interact.  In other words, Hsp90 appeared to help along the formation of a new gene.

The authors then went back to Arabidopsis and showed that BZR and BES1 were found in distinct but overlapping parts of the cell.  This lends credence to the idea that chaperones cause proteins to localize to different parts of the cell. 

So it looks like an important function of chaperones may be to shepherd new gene formation.  They are more like a 1960’s version of a chaperone…they let duplicated genes make lots of mistakes on their way to discovering who they really are.

by D. Barry Starr, Ph.D., Director of Outreach Activities, Stanford Genetics

Categories: Research Spotlight

Tags: Saccharomyces cerevisiae, evolution, chaperones

The Rhythm of Ribosomes

February 13, 2013

We all know that some people march to the beat of a different drummer. But now we’re finding out that mRNAs also have their own particular rhythms as they move along the ribosome.

Marching Band

For mRNAs, codon usage sets the beat.

It’s long been known that some codons just work better than others. They are translated faster and more accurately mostly because they interact more strongly with their tRNAs and because there are more of their specific tRNAs around. So why hasn’t evolution gotten rid of all the “slow” codons? With only optimal codons, translation could move at a marching beat all the time.

One idea has been that a few pauses every now and then are a good thing. For example, maybe slowing down translation at the end of a stretch coding for a discrete protein domain gives that domain time to fold properly. This would make it less likely for the polypeptide chain to end up tangled, or misfolded. Great thought, but even when researchers looked in multiple organisms, they couldn’t find a consistent correlation between codons used and protein structure. Until now, that is.

In a recent study published in Nature Structural and Molecular Biology, Pechmann and Frydman took a novel approach to this question. They derived a new formula to measure codon optimality. Using it they found that codon usage was highly conserved between even distantly related species, and that this conservation reflected the domain structure of the particular protein a ribosome was translating.

First, the authors came up with a more accurate way of classifying codons as optimal or non-optimal. They took advantage of the huge amount of data available for S. cerevisiae and included a lot more of it in the calculation, such as the abundance of hundreds of mRNAs and their level of ribosome association. They also took into account competition between tRNAs based on supply and demand, something that the previous studies had not done.

Once they developed this new translational efficiency scale, they applied it to ten other yeast species – from closely related budding yeasts all the way out to the evolutionarily distant Schizosaccharomyces pombe. The authors found that positions of optimal and non-optimal codons were indeed highly conserved across the yeasts. And codon optimality was highly correlated with protein structure.

One of the better examples of this is alpha helices. These protein domains form while still inside the ribosomal tunnel. The authors found that the mRNA regions coding alpha helices use a characteristic pattern of optimal and non-optimal codons to encode the first turn of the helix. They theorize that this sets the rhythm for folding the rest of the helix. Other structural elements are coded by distinct codon signatures too.

This isn’t just interesting basic research. It has some far-reaching practical implications too.

When using yeast to make some sort of industrial product, the thought has been to use as many optimal codons as possible. This has not always worked out, and now we may know why. A gene that tailors the codon usage to the rhythm of the protein structure is probably the best way to make a lot of correctly folded protein.

And the factory isn’t the only place where this kind of information will come in handy. Protein misfolding is the known or suspected culprit in a whole slew of human neurodegenerative diseases such as Alzheimer’s, ALS, Huntington’s chorea, and Parkinson’s disease. A better understanding of its causes might give us insights into managing those diseases.

Who knew in 1971 that translation actually is a rhythmic dance?

by Maria Costanzo, Ph.D., Senior Biocurator, SGD

Categories: Research Spotlight

Tags: Saccharomyces cerevisiae, protein folding, evolution, translation, ribosome

Ghosts of Centromeres Past

January 28, 2013

Every cell needs to correctly divvy up its chromosomes when it divides.  Otherwise one cell would end up with too many chromosomes, the other with too few and they’d both probably die.

The Ghost of Christmas Past

A different kind of ghost may be embedded in the yeast genome.

Cells have developed elaborate machinery to make sure each daughter gets the right chromosomes.  One key part of the machinery is the centromere.  This is the part of the chromosome that attaches to the mitotic spindle so the chromosome gets dragged to the right place. 

Given how precise this dance is, it is surprising how sloppy the underlying centromeric DNA tends to be in most eukaryotes.  It is very long with lots of repeated sequences which make it very tricky to figure out which DNA sequences really matter.  An exception to this is the centromeres found in some budding yeasts like Saccharomyces cerevisiae.  These centromeres are around 125 base pairs long with easily identifiable important DNA sequences.

The current thought is that budding yeast used to have the usual diffuse, regional centromeres but that over time, they evolved these newer, more compact centromeres.  Work in a new study published in PLOS Genetics by Lefrançois and coworkers lends support to this idea.

These authors found that when they overexpressed a key centromeric protein, Cse4p (or CenH3 in humans), new centromere complexes formed on DNA sequences near the true centromeres. The authors termed these sequences CLR’s or Centromere-Like Regions.  And they showed that these complexes are functional.

When Lefrançois and coworkers kept the true centromere from functioning on chromosome 3 in cells overexpressing Cse4p, 82% of the cells were able to properly segregate chromosome 3.  This compares to the 62% of cells that pull this off with normal levels of Cse4p.  The advantage disappeared when the CLR on chromosome 3 was deleted.

A close look at the CLRs showed that they had a lot in common with both types of centromeres.  They had an AT-rich 90 base pair sequence that looked an awful lot like the kind of sequence that Cse4p prefers to bind and a lot like the repeats found within more traditional centromeres.  They also tended to be in areas of open chromatin and close to true centromeres. The obvious conclusion is that these are remnants of the regional centromeres budding yeast used to have. 

The hope is that the yeast CLRs might make studying regional centromeres easier.  They are so long and complicated that it is very difficult to pick out which sequences matter and which don’t, but the yeast CLRs could be a simpler model system.  Even better, the CLRs might shed some light on the process of neocentromerization – the formation of new centromeres outside of centromeric regions, which happens a lot in cancer cells. Once again, simple little S. cerevisiae may hold the key to understanding what’s going on in much larger organisms.

by D. Barry Starr, Ph.D., Director of Outreach Activities, Stanford Genetics

Categories: Research Spotlight, Yeast and Human Disease

Tags: Saccharomyces cerevisiae, yeast model for human disease, evolution, centromeres

Be Good, For Adaptation’s Sake

December 17, 2012

You may never have herded cows. But in one way or another, you’ve certainly experienced the tragedy of the commons.

When herders get away with cheating, everyone loses. The same thing is often true for yeast.
Image from Wikimedia Commons

This happens when a village shares a pasture that can only feed a certain number of cows. For the system to work, everyone has to cooperate and keep the total number of cows under that limit. But inevitably, one cheater comes along and adds extra cows to his herd. At no immediate cost to himself, he gets all the benefits of the extra cows. But then tragedy kicks in as the pasture is overgrazed until no one can have any cows.

This doesn’t just happen out in the village. We can see it in the overfishing of the oceans, the production of carbon dioxide contributing to global warming, the milking of investors on Wall Street, and many other aspects of modern life. But perhaps surprisingly, we can even see it in cultures of the humble yeast S. cerevisiae.

In a recent issue of the Proceedings of the National Academy of Sciences, Waite and Shou set up a yeast system to look at the factors influencing the tragedy of the commons. In human society, sometimes cheaters cause a collapse, but other times, cooperators get together and exile the cheaters from the village. You might think that since yeast aren’t quite as smart as humans, in yeast “society” the cheaters would always win. However, Waite and Shou found that sometimes the cheaters were marginalized or even driven out, and the cooperators thrived!

To do these experiments, the researchers set up a very clever pasture in miniature. They engineered three strains, each marked with a different-colored fluorescent marker so they could be distinguished from each other.

The two “cooperator” strains needed each other to survive on minimal medium: one required lysine and produced excess adenine, while the other required adenine and produced excess lysine. The “cheater” strain required lysine but it didn’t provide any nutrients. So the cheater needed one of the cooperators to survive, but didn’t contribute anything to the common good.

As we might expect, being cooperative has a cost. The generous production of extra nutrients made the cooperator grow slower than the otherwise identical cheater strain. So you would predict that if you mixed the cooperators and the cheater in equal numbers and grew them together, the cheater would take over and collapse the culture every time.

However, when the researchers mixed all three strains in a 1:1:1 ratio and grew lots of replicate cultures, they found that cheaters didn’t always prosper. Sometimes the nice guys finished first.

Of course some of the cultures did collapse under the influence of the rapacious cheaters. After a while these cultures stopped growing and turned out to be made up of mostly dead or dying cheater cells. The cheaters had taken over the culture, selfishly using up the lysine until eventually there was not enough to continue growing.

But unexpectedly, other replicate cultures were growing much faster, at rates similar to cultures without any cheaters. In these cultures, the two cooperator strains had either dominated the culture or even driven the cheaters extinct!

To explain this, the researchers proposed that the intense selection pressure led to an adaptive race between cooperators and cheaters. In surviving cultures, the rare cooperator with a small advantage had outcompeted the cheaters.

To confirm this, they took a close look at the winning cooperators. They found that the fitness advantage could be inherited, so they used whole-genome resequencing to find out why the cooperators were outcompeting the cheaters. They kept finding mutations in the same five genes.

These genes all made sense, as mutating them would help in an environment with limited amounts of lysine. For example, most of the mutations were found in ECM21 and DOA4. Both of these gene products are important in pathways that break down proteins like permeases. Knocking them out would keep the permeases around longer, making for better lysine uptake. But this newfound advantage did not come without a price.

Dogs playing cards

While cheating is usually a good short term strategy, it doesn’t always work out so well in the long term.
Image from Wikimedia Commons

The researchers tested directly whether the adaptive mutations improved growth in limiting amounts of lysine. Without exception, they did. But almost all these strains grew more slowly in abundant lysine than did their ancestor strains. That explains why these mutant strains only became a significant proportion of the population late in the life of the culture, when lysine levels were very low.

The same mutations can arise in both cooperators and cheaters, of course. But when cheaters become better at growing in low lysine levels, they just become that much better at making themselves extinct. When cooperators get better at growing in low lysine levels, they are better able to keep growing and keep the cheaters at bay.

So the take-home lesson is that cooperation does pay, after all. Especially in a constantly changing environment, cooperators can often win the adaptive race and squelch the cheaters. Maybe we should take a hint from little S. cerevisiae that being kind to each other is not only a nice thing to do, it’s in all of our best interests!

by D. Barry Starr, Ph.D., Director of Outreach Activities, Stanford Genetics

Categories: Research Spotlight

Tags: Saccharomyces cerevisiae, evolution, adaptation

Wintering in a Wasp’s Gut

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. 

Social wasps are a natural reservoir for yeast

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. 

by D. Barry Starr, Ph.D., Director of Outreach Activities, Stanford Genetics

Categories: Research Spotlight

Tags: Saccharomyces cerevisiae, wild yeast, evolution

Few Genetic Paths From Here to There

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.

How many paths lead to adaptation?

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.

by D. Barry Starr, Ph.D., Director of Outreach Activities, Stanford Genetics

Categories: Research Spotlight

Tags: Saccharomyces cerevisiae, ergosterol biosynthesis, evolution, nystatin

Prions Let Yeast Take Traits for a Test Drive

August 27, 2012

For the most part, prions have a bad rep. They are the proverbial bad apple that spoils the whole bunch.

One bad apple can spoil the whole bunch...

A prion is a protein that misfolds in a certain way that creates a chain reaction to misfold many additional copies of that particular protein in a cell. This misfolding en masse can cause severe problems like mad cow disease or Alzheimer’s.

As if that weren’t bad enough, this misfoldedness can spread from one organism to another. Once a prion gets into a cell and/or a part of the body, it will cause many of its properly folded brethren to misfold too. This is true even though the prion gene in the new host is happily churning out properly folded protein.

These things look like a nightmare. Why on Earth are prions still around? Because in addition to their bad side, they can sometimes be an advantage too (at least in yeast).

In a study published in Nature in February 2012, Halfmann and coworkers provide compelling evidence that prions can help both laboratory and wild yeast strains to adapt rapidly to a changing environment, by unlocking survival traits hidden in yeast DNA. In other words, prions are a way for a yeast population to hedge its bets against a world of changing environments.

The authors focused on the most famous prion in yeast, the translation termination protein Sup35p. When Sup35p switches to prion mode ([PSI+]), it becomes bound up in insoluble fibers, causing translation termination to become leaky. Now normally untranslated parts of mRNAs become part of their respective proteins. And this can change these proteins’ functions.

Sure, most of this newfound variation will have no effect or maybe even be harmful, but occasionally the prion will reveal a beneficial trait. This yeast can then go on to survive and even thrive in this new environment.

This mechanism may apply to other prions in addition to Sup35p. Prions tend to come from proteins that are global regulators of transcription or translation. In the non-prion form, these proteins do their usual job making sure transcription and translation are following the rules. But when these proteins become misfolded into a prion, they can no longer perform their usual function. This uncovers previously silent bits of DNA or RNA for transcription or translation.

These authors also convincingly showed that prions are not some weird phenomenon found only in laboratory strains of yeast. They found evidence for prions in 255 out of the 690 wild strains they surveyed (although only ten had Sup35p based prions). Not only that, but many of these prions also conferred new traits on the yeast that could be beneficial in certain circumstances. It looks like prions may serve an important function in yeast.

A more surprising result from the study is that these prion-derived traits carry on in later generations even after the prion has been removed. For example, the authors looked at the wine yeast UCD978. They found that when Sup35p was in its prion form in this strain, UCD978 could effectively penetrate agar surfaces and that this trait was lost when the prion was cured, reverting Sup35p to its functional form.

They then took the study further and showed that after meiosis and sporulation, 5/30 haploid progeny of UCD978 retained the trait even after the prion was removed. These five had fixed the new trait and no longer required the prion to maintain it. They got all the benefits with none of the costs.

It isn’t obvious how this trait became independent of the original inducing prion. But that is for another study (or two or ten).

If the results of this study pan out, they show that prions are not just part of a disease but are really just another way to adapt to environmental changes and to pass them down to future generations. Maybe these apples aren’t so bad after all!

Prions allow yeast cells to take various traits out for a test drive.

by D. Barry Starr, Ph.D., Director of Outreach Activities, Stanford Genetics

Categories: Research Spotlight

Tags: S. cerevisiae, SUP35, evolution, variation, prions

Multicellularity a Snap? Maybe so…

February 10, 2012

It took just a few months to go from one cell to many. Image adapted from Ratcliff, et al (PMID: 22307617).

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.

by D. Barry Starr, Ph.D., Director of Outreach Activities, Stanford Genetics

Categories: Research Spotlight

Tags: Saccharomyces cerevisiae, evolution, multicellular, yeast

A Simpler Way to Evolve

February 06, 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

Proton pumps like this one may be easier to evolve than scientists first thought.

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.

by D. Barry Starr, Ph.D., Director of Outreach Activities, Stanford Genetics

Categories: Research Spotlight

Tags: ATPase, mutation, evolution, gain of function, proton pump, gene duplication, loss of function