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%.
Tags: alternative splicing > evolution > gene duplication > Saccharomyces cerevisiae
The Indulgent Chaperone
April 1, 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.
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.
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?
Tags: evolution > protein folding > ribosome > Saccharomyces cerevisiae > translation
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.
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.
Tags: centromeres > evolution > Saccharomyces cerevisiae > yeast model for human disease
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.
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!
