New & Noteworthy

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.

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

Autophagy’s (Atg)9th Symphony

January 17, 2013

(Please click the musical note and listen to the music while reading.) The music you’re listening to starts off with a marimba. Then a flute joins in and as the marimba fades, in comes a shamisen. The piece progresses similarly with a harp, and then ends with the reappearance of the marimba. A nice, jaunty little piece of music.

This song is actually a tool for learning about autophagy in the yeast S. cerevisiae. Autophagy is a way to break down damaged or no longer useful proteins and recycle their components for later use. It is a very important pathway in keeping starving yeast alive. Many of the proteins involved in autophagy are highly conserved, and autophagy defects are implicated in several kinds of human disease.

As described in a recent paper, Takahashi and coworkers converted the sequences of four proteins involved in a step in autophagy – Atg9, Sso1, Sec9, and Sec22 – into pieces of music using UCLA’s Gene2Music program. Each protein was then assigned a musical instrument. Atg9 was played with the marimba, Sso1 with the flute, Sec9 with the shamisen, and Sec22 with the harp. The orchestrated piece of music reflects how each protein interacts with the others in the autophagy pathway.

Atg9 is a transmembrane protein that is key to making the vesicles that carry the damaged or unused proteins to the lysosome for destruction. But it, like the marimba, is not enough. Atg9 is recruited into service by at least three other proteins, Sso1, Sec9, and Sec22. These appear in succession in the musical piece as a flute, shamisen, and harp. Just like all four are needed for the orchestral piece, all four are also needed for successful autophagy.

Now listen to the music again. With this background, did you find the piece more illuminating? If you didn’t, it may simply be because it doesn’t fit your learning style, or match the type of intelligence that is your strength. Some people may respond to music better than they do to pictures of pathways or memorizing the steps involved. It may be that these people’s understanding of complicated pathways is enhanced with a musical component.

There will need to be more research on musical representation of complex pathways to see if they actually help students and even the public better understand science. If they do, I am looking forward to hearing the Krebs Cycle put to music. Or the assembly of the RNA polymerase II preinitiation complex. Which pathways do you want put to music?

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

P is for Protection (not Processing)

January 11, 2013

Growing and dividing are dangerous work for a cell. Making all that energy throws off free radicals that mutate DNA and wreak havoc with delicate intracellular machinery. Given this it might seem surprising that just sitting there, not growing, is dangerous too. And yet it looks like it is.

When a cell runs out of food and goes into a quiescent state, it creates ribonucleoprotein (RNP) complexes called processing bodies (P bodies). In a new study out in GENETICS, Shah and colleagues were able to control how well yeast cells could make these P bodies. What they found was that cells that had trouble making P bodies didn’t survive the quiescent state as well as those cells that were great P body makers. It looked like P bodies were doing something to protect the cell when it wasn’t growing. In other words, being quiescent is dangerous too.

The key discovery made by the authors that allowed them to do these experiments was the fact that the Ras/PKA signaling system works specifically through the Pat1 protein to make P bodies. So by controlling the sensitivity of Pat1p to the signaling system, they could control the number of P bodies in the cell.

The Ras/PKA pathway phosphorylates two serine residues on Pat1p. When they are phosphorylated, P bodies are disrupted and/or are prevented from forming. The Pat1-EE mutation replaces the serine residues with glutamic acids, mimicking the phosphorylated state. The authors found that yeast cells carrying Pat1-EE produced fewer, smaller P bodies than did yeast carrying the wild type version of Pat1.

The authors then used this constitutively active mutant to ask whether P bodies helped cells survive the quiescent state. They compared the survival rate of cells carrying either the wild type version or the Pat1-EE protein and found that cells carrying the wild type version of Pat1 were more likely to survive after quiescence than were those cells carrying the constitutive form. More P bodies led to better survival.

The authors don’t yet know why this is, but one idea is that proteins and RNAs critical for survival after quiescence are stored in these particles. The idea would be that cells that have these key components squirreled away and protected survive better than those cells where these proteins and RNAs have degraded.

As a final point, it is important to mention why this matters (besides the excitement of figuring out how things work). Quiescent yeast cells are used as models for aging in higher eukaryotes like us. Perhaps by understanding how to make a yeast cell better survive this non-growing state, we can learn something about how to make people live longer too.

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