Anuj Kumar Featured in Genomic Technology Magazine

March 15, 2005

Model Organism Marathon

If you've been in this field long enough, you've probably heard -- or perhaps contributed to -- the grumbling by now. Researchers who traffic in plant and animal genomics say they often feel like second-hand citizens in the broader genomics community, arguing that human genome researchers get all the glory.

That's obviously a matter of judgment. But what is clearly true, no matter which side of the line you're on, is that scientists working on plant and animal genomes have been responsible for some of the biggest breakthroughs -- technological or otherwise -- in the community. RNAi, as you'll recall, was first recognized in petunias. And of course, the many technological insights coming out of comparative genomics, such as CGH and ROMA, wouldn't be possible without model organism genomes to compare.

In the following pages, Genome Technology pays tribute to the plant and animal genomics folks with a look at scientists involved in some of today's most compelling research and innovations. These are mostly in the early stages now, but will one day likely be adopted -- as have so many advances from plant and animal researchers -- by the human genome field as well. And in an attempt to let you in on what's next, we also included, where possible, research topics that these scientists consider particularly intriguing.

With more than 2,000 people attending the community's biggest meeting, Plant & Animal Genome XIII in San Diego this January, there's obviously far too much fascinating work going on to be able to cover it all here. We narrowed our universe by looking only at research in model organisms. The science presented here is meant to be a sampling, rather than a comprehensive view, of the field.

—Meredith W. Salisbury

Yeast: Anuj Kumar, Life Sciences Institute, The University of Michigan - Ann Arbor
Colocalization to track down protein-protein interactions

Somewhere between the false positives of the yeast two-hybrid method and the false negatives of FRET lie the true answers about protein-protein interaction - or so goes the theory behind Anuj Kumar's yeast research

The germs of Kumar's current work came up while he was a postdoc studying protein localization in Mike Snyder's Yale lab, he says. Now a research assistant professor at the Life Sciences Insitute in Michigan, Kumar has spent the past year getting started on his work. He's still very much "in the pilot stages," he says, adding that for now his group has "cloned 60 genes...obviously we'd like to do a whole lot more than that."

Kumar's approach to understanding multiple proteins' localizations--a good indicator of function and potential to interact - begins with building a collection of yeast genes that have been fused to a fluorescent protein, he says. That's accomplished using "a recombination-based cloning strategy that's commercially available" that avoids the use of restriction enzymes or ligases. "We're making these plasmids so that the yeast genes are under the control of their own promoters," he says.

Working with protein pairs, the fluorescent protein is fused to the C terminus of the yeast gene. Using pairs of proteins enables Kumar to co-localize the proteins - "we're trying to determine if two proteins have the potential to interact," he says. Existing strategies for looking at protein-protein interactions have known problems, Kumar says. The yeast two-hybrid approach leads to "a lot of false positives" - generating what may be a comprehensive list, but includes too much garbage to be of real use. "You can also use FRET," he adds, but, "this method is prone to false negatives." The results from a FRET experiment tend to be high-confidence, but far from comprehensive.

Currently, Kumar's progress has extended to designing the vectors for the cloning, used for some 60 genes. Studies are stilll in the earliest phases - to some extent, Kumar is still settling into his post at Michigan's LSI and gearing up his lab. He'll be collaborating with Michigan colleagues Bob Fuller, Joel Swanson, and Adam Hoppe on the FRET-based part of his research.

Ultimately, he hopes his work will generate "a high-confidence protein-protein interaction data set," he says. "The idea there is to complement the other protein-protein interaction data sets which exist in yeast which may be prone to more false positives." After that, Kumar anticipates applying the same concept to studying pathways in yeast.

Yeast is the chosen vehicle for Kumar's work partly because of how easy it is to manipulate and how well its genetics are understood, he says. "It's quite similar to a single human cell," he adds. "Two-thirds of the genes in humans that have been implicated in diseases have an ortholog in yeast." Yeast is also stable in both haploid and diploid form, and when DNA is introduced into it, "it goes where it should," Kumar says. "That's a pretty powerful tool for a lot of applications." Still, he notes there's nothing specific about colocalizing proteins in yeast, so that type of research could certainly be done on other organisms.

On His Radar

• Protein Arrays
• Advances in mass spectroscopy to measure protein abundance
• Large-scale applications of RNAi
• Methods of studying post-translational modification