Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:


Baker’s yeast rises from genome duplication


In work that may lead to better understanding of genetic diseases, researchers at the Broad Institute of MIT and Harvard show that baker’s yeast was created hundreds of millions of years ago when its ancestor temporarily became a kind of super-organism with twice the usual number of chromosomes and an increased potential to evolve.

The study is by postdoctoral fellow and lead author Manolis Kellis of the Broad (rhymes with "code") Institute; Eric S. Lander, Broad director; and Bruce W. Birren, co-director of the Broad’s sequencing and analysis program. It will be published online by Nature on March 7.

Scientists have postulated that in a handful of instances in evolutionary history, cells may have replicated their entire genomes in events called whole genome duplication, but no definitive proof existed. The Broad Institute work shows conclusively for the first time that the well-studied organism baker’s yeast originated through this little-understood phenomenon, resolving a long-standing controversy on the ancestry of the yeast genome.

Whole genome duplication (WGD) may have occurred when a cell replicated its DNA normally, as it does every time it divides, but did not split it between two resulting cells, or two cells may have fused. The result is that a yeast cell with around 5,700 genes suddenly had more than 11,000. In this scenario, while one copy of the gene performs its designated function, the other is free to perform a new and potentially valuable use. In addition, the organism is able to evolve more rapidly with natural selection acting on thousands of duplicated genes simultaneously, allowing for large-scale adaptation to new environments.

This super-organism doesn’t come without drawbacks. The excess genes cause instability in the genome and are deleted through mutation, gene loss and genomic rearrangement. As a result, millennia after the event, very few duplicated genes remain.

"This is the first time we actually see that an organism underwent complete genome duplication and went back to a single-copy state," Kellis said. In the case of baker’s yeast, roughly 90 percent of its duplicated genes were lost. The organism returned to having one gene per function for the vast majority of its genome, ending up with only 457 additional genes.

What’s the advantage to replicating the entire genome and then losing half the genes? According to one theory, by replicating the whole genome, entire systems (networks and pathways) within the organism can evolve together and take on new functions. Yeast, which metabolizes sugar and causes fermentation, apparently evolved to fill an evolutionary niche around the time that fruit-bearing plants appeared, creating an abundance of sugar in the environment.

"It’s the best fermenter out there," Kellis said of Saccharomyces cerevisiae, the species that the group studied. Many of its surviving 457 genes are devoted to sugar metabolism.

If incremental evolution over millennia is like a landscape changing through erosion, whole genome duplication is like an earthquake. "Direct study of such a cataclysmic event may provide major insights into the dynamics of genome evolution and the emergence of new functions," the authors wrote.

Uncovering the original

Given the massive gene loss and hundreds of rearrangements, little evidence of WGD remains within the genome of baker’s yeast. Tracing the development of a genome over billions of years is like printing a 5,000-page book twice without page numbers, throwing away most of the duplicate pages, shuffling both copies and binding them into a single book. Uncovering the ancestral gene order, Kellis said, would be like happening upon the original book in a hidden library.

The authors found the missing link by sequencing a yeast species whose evolutionary divergence preceded the duplication. They showed that each region of this pre-duplication relative corresponds to exactly two regions of baker’s yeast, providing definitive proof of duplication.

Researchers speculate that vertebrates, including human ancestors, may have undergone two rounds of complete duplication, but the evidence remains weak without comparison to a pre-duplication relative. Broad researchers used a new method to compare the complete genomes of each of the duplicated and pre-duplication yeast species, and they plan to apply this method to more species. Typical methods of genome comparison would "miss the genome duplication event if they focus on solely the best match for every gene and every region," Kellis said.

Genomic research is leading to new understanding of the connections between different types of genetic functions and which genes were paired in our ancestors to work together. For example, uncovering the duplication event provided a new link between gene silencing and the binding of DNA-replication origins.

Similarly, understanding the dynamics of genome duplication has implications in understanding disease. In certain types of cancer, for instance, cells have twice as many chromosomes as they should, and there are many other diseases linked to gene dosage and misregulation. "These processes are not much different from what happened in yeast," Kellis said.

Whole genome duplication may have allowed other organisms besides yeast to achieve evolutionary innovations in one giant leap instead of baby steps. It may account for up to 80 percent of flowering plant species and could explain why fish are the most diverse of all vertebrates.

"The results here suggest that it may also be fruitful to search for similar genomic signatures of WGD in other organisms. It will be interesting to see just how far such distant echoes of genomic upheaval may be traced," the authors said.

Kellis is also part of the MIT Computer Science and Artificial Intelligence Laboratory, and Lander is a professor of biology at MIT and a member of the Whitehead Institute for Biomedical Research.

The Broad Institute, known officially as the Eli and Edythe L. Broad Institute, is a research collaboration of MIT, Harvard University and the Whitehead Institute. The Broad’s mission is to fulfill the promise of genomics for medicine.

Scott Turner | EurekAlert!
Further information:

More articles from Life Sciences:

nachricht Novel mechanisms of action discovered for the skin cancer medication Imiquimod
21.10.2016 | Technische Universität München

nachricht Second research flight into zero gravity
21.10.2016 | Universität Zürich

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: New 3-D wiring technique brings scalable quantum computers closer to reality

Researchers from the Institute for Quantum Computing (IQC) at the University of Waterloo led the development of a new extensible wiring technique capable of controlling superconducting quantum bits, representing a significant step towards to the realization of a scalable quantum computer.

"The quantum socket is a wiring method that uses three-dimensional wires based on spring-loaded pins to address individual qubits," said Jeremy Béjanin, a PhD...

Im Focus: Scientists develop a semiconductor nanocomposite material that moves in response to light

In a paper in Scientific Reports, a research team at Worcester Polytechnic Institute describes a novel light-activated phenomenon that could become the basis for applications as diverse as microscopic robotic grippers and more efficient solar cells.

A research team at Worcester Polytechnic Institute (WPI) has developed a revolutionary, light-activated semiconductor nanocomposite material that can be used...

Im Focus: Diamonds aren't forever: Sandia, Harvard team create first quantum computer bridge

By forcefully embedding two silicon atoms in a diamond matrix, Sandia researchers have demonstrated for the first time on a single chip all the components needed to create a quantum bridge to link quantum computers together.

"People have already built small quantum computers," says Sandia researcher Ryan Camacho. "Maybe the first useful one won't be a single giant quantum computer...

Im Focus: New Products - Highlights of COMPAMED 2016

COMPAMED has become the leading international marketplace for suppliers of medical manufacturing. The trade fair, which takes place every November and is co-located to MEDICA in Dusseldorf, has been steadily growing over the past years and shows that medical technology remains a rapidly growing market.

In 2016, the joint pavilion by the IVAM Microtechnology Network, the Product Market “High-tech for Medical Devices”, will be located in Hall 8a again and will...

Im Focus: Ultra-thin ferroelectric material for next-generation electronics

'Ferroelectric' materials can switch between different states of electrical polarization in response to an external electric field. This flexibility means they show promise for many applications, for example in electronic devices and computer memory. Current ferroelectric materials are highly valued for their thermal and chemical stability and rapid electro-mechanical responses, but creating a material that is scalable down to the tiny sizes needed for technologies like silicon-based semiconductors (Si-based CMOS) has proven challenging.

Now, Hiroshi Funakubo and co-workers at the Tokyo Institute of Technology, in collaboration with researchers across Japan, have conducted experiments to...

All Focus news of the innovation-report >>>



Event News

#IC2S2: When Social Science meets Computer Science - GESIS will host the IC2S2 conference 2017

14.10.2016 | Event News

Agricultural Trade Developments and Potentials in Central Asia and the South Caucasus

14.10.2016 | Event News

World Health Summit – Day Three: A Call to Action

12.10.2016 | Event News

Latest News

Resolving the mystery of preeclampsia

21.10.2016 | Health and Medicine

Stanford researchers create new special-purpose computer that may someday save us billions

21.10.2016 | Information Technology

From ancient fossils to future cars

21.10.2016 | Materials Sciences

More VideoLinks >>>