New & Noteworthy

Seminal Yeast Literature

August 27, 2013

SGD has compiled a selection of seminal yeast literature, comprising landmark papers in yeast biology. The list is available on the SGD Wiki and includes important publications on cell biology, early genetic maps and genome surveys, and the original S288C sequencing consortium. Also listed are key papers describing the genomes of other sequenced strains of S. cerevisiae.

This new page is just one of the many resources already available on the SGD Wiki, such as What are Yeast?, Protocols, and Job listings. We encourage you to add additional information to any of the SGD Wiki pages. If you don’t already have an SGD Wiki account, please contact the SGD Help Desk to request one.

See You at Yeast 2013!

August 26, 2013

SGD staff will be attending the 26^th International Conference on Yeast Genetics and Molecular Biology, which will be held at Frankfurt University, Germany, from Thursday August 29th – Tuesday September 3rd. We will be available at a table at the poster sessions to answer all your questions about SGD, give one-on-one tutorials, listen to your ideas about what you’d like to see in SGD, and demonstrate some exciting new features. We will also be presenting talks and having an open discussion at the SGD Workshop (#7) on Saturday from 4:30 – 7 PM. Please stop by to say hello!

 

Smoothing Over an Extra Chromosome

August 22, 2013

Let’s say you had a rock you had to move that was way too heavy for you to lift. You could either start lifting weights until you could move it yourself or get someone to help you. Most of us would start texting our friends pretty quick.

Turns out our friend S. cerevisiae can be the same way. Many strains of this yeast can exist as either a fluffy colony or a smooth one. In a new study, Tan and coworkers show that some of these strains switch between the two by gaining or losing one of their chromosomes. They’d rather “get” an extra chromosome than try to gain a mutation that activates the necessary gene(s).

In this study, the authors found a strain where around one in a thousand yeast switched between fluffy and smooth colonies. As the smooth colonies grew, they developed “blebs” – little bumps on the smooth colonies.  Turns out these were yeast that switched back to the fluffy morphology.  The authors set out to explore why this strain switches at such a high rate and why it would want to. 

A first look showed that when this yeast strain went from fluffy to smooth, it gained an extra copy of chromosome XVI.  When the new smoother yeast lost this extra chromosome, it reverted back to its fluffy look.  A harder look showed that an extra chromosome XVI wasn’t the only way to a smoother yeast.  Occasionally the fluffy to smooth change could be caused by an extra copy of chromosome III, X, or XV, and an extra copy of V caused a slightly smoother colony.

These results suggest a couple of different ways that an extra chromosome might be leading to a smooth colony.  One is that just having extra DNA around causes the change.  The other is that a variety of genes can cause the change when present in higher than normal doses.  The researchers show pretty convincingly that the second reason is probably the right mechanism.

First off they show that not all extra chromosomes are created equal.  Some lead to a very sickly yeast while others have no effect on fluffiness.  Just having extra DNA around is probably not the culprit.

The authors next set out to figure out exactly what was going on with chromosome XVI.  Through a series of deletion studies, they found a single gene responsible for the fluffy to smooth shift – DIG1.  Overexpression of this single gene caused fluffy colonies to turn smooth.  Presumably there are other genes on some of the other chromosomes that serve a similar function.

They next set out to determine why yeast would ever want to do this.  Turns out that, as you might expect, each phenotype has an advantage in a different situation.  On a solid surface the fluffy strain did better, while the smooth one did better in liquid media.  

The “extra chromosome option” is actually a great way for a sedentary beast like yeast to quickly deal with a new situation.  Gaining an extra chromosome is much simpler than gaining a new mutation that up-regulates a gene under certain situations.

Figuring out this mechanism of fluffy to smooth transitions isn’t just fun biology either.  It may also point us in new directions for treatments for a variety of diseases, including drug-resistant cancers and microbial infections. 

In many cases, these cells become resistant because their chromosome number has changed from what is considered the norm.  If we could find a way to force cells to maintain the correct number of chromosomes, we might be able to make them more susceptible to drugs.  As usual, yeast studies are much more than fluff…they smooth the way to the future.

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

New data tracks added to GBrowse

August 20, 2013

SGD has added new data tracks to the GBrowse genome viewer covering differential expression RNA-seq data from Waern & Snyder (2013) and Transcript Leader RNA-seq data from Arribere & Gilbert (2013).

Download data tracks, metadata and supplementary data by clicking on the ‘?’ icon on each data track within GBrowse or directly from the SGD Downloads site. We welcome new data submissions pre- or post-publication and invite authors to work with us to integrate their data into our GBrowse and PBrowse viewers. Please contact us if you are interested in participating or have questions and comments. Happy browsing!