Jack Greenblatt on the impact of the first genome-wide protein interaction network
“In the mid-1990’s I thought I knew the future of biology. It was an inspired guess.”
Three decades ago, the environment surrounding molecular biology was moving so quickly, University of Toronto Professor and Donnelly PI Jack Greenblatt could only keep up if he predicted its direction. After Genome Canada was created in 2000 to fund large scale genome research, Greenblatt pivoted his vision away from smaller hypothesis-driven projects and towards a difficult undertaking involving 6,000 yeast genes.
“Research was evolving,” says Greenblatt, “by the time we learned how to use a mass spectrometer to identify proteins, the yeast genome was sequenced.”
From 2001 to 2005, the Greenblatt Lab raced to create the first genome-wide protein interaction network for an entire organism: Saccharomyces cerevisiae. Also known as baker’s or brewer’s yeast, the same microorganism used to make bread and beer actually shares nearly half of its genes with the human genome. With proteins carrying out most cell processes, comprehending protein interactions was key to an improved understanding of everything from small-scale chemical reactions to targeted drug treatment for genetic diseases.
"We defined the composition of nearly a thousand different protein machines in yeast, belonging to every kind of process in the cell,” Greenblatt explains. “You learn which proteins are working together and all the fundamental processes in which proteins are involved. This project provided the first large-dose input into proteomic databases.”
"Global landscape of protein complexes in the yeast Saccharomyces cerevisiae" was published in Nature in March 2006, along with a comprehensive publicly available database. The lab used a method called tandem affinity purification to isolate the proteins, and discerned the identity of tagged proteins with mass spectrometry. While comparatively easy in the current day, to complete a project of this scale in the early 2000s was an incredible show of persistence and skill. It was a race at the end, to ensure their discoveries would be published alongside a private company’s research on the same topic; the first draft submitted for review was written entirely during the weekend before the winter break in 2005. Everything, from the bulk of the text to the figures and supplementary tables, was assembled in a handful of days to meet the deadline.
Leading up to the final publication, the four to five years of the paper’s development saw the Greenblatt Lab selecting some of the most interesting findings to do follow up experiments. Most of these experiments revolved around gene regulation and expression, a topic the lab is still researching in the current day.
“We would suddenly be faced with new pieces of information that told us the answers to molecular biology problems we hadn’t even thought of,” says Greenblatt. “We knew the answers; it was a question of filling in the experiments around it.”
Greenblatt considers the follow-up experiments, done by his own lab and many others, to be the major impact of the paper. The Greenblatt Lab's work created a wealth of data that was freely available to analyze. Greenblatt describes the project as an exercise in “rounding up collaborators,” and providing them with the starting points for interesting discoveries.
"There were all kinds of basic scientific information hidden in that data, which would lead hundreds, if not thousands of other people to interesting experiments,” says Greenblatt. “It inspired projects on human proteins, with functions similar to those of the yeast proteins; comprehensive interaction studies on the human proteins are much harder, because we have 20,000 proteins—not 6,000—and many kinds of cells.”
Since 2006, the Greenblatt Lab has studied protein-protein interactions for bacterial, yeast, and human proteins, with a particular focus on the regulation of human gene expression. Over those twenty years, the Greenblatt Lab has evolved in step with the changing research environment of molecular genetics and computational biology, largely shaped by their insights into the humble brewer’s yeast.
20th Anniversary Retrospective Series
This is the first instalment of a 10-part news series highlighting two decades of breakthroughs at the Donnelly Centre.
