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Past Winner
2004 E.W.R. Steacie Memorial Fellowship

Patrick Keeling

Botany

The University of British Columbia


Patrick Keeling
Patrick Keeling

The notion that large-scale evolutionary change occurs through gradual adaptations is part of biology's bread and butter. Animals and plants don't suddenly alter fundamental characteristics from one generation to the next. There aren't big genetic jumps. Certainly not burps. Or are there?

A Canadian researcher is leading biologists to rethink the range of evolutionary possibilities that have shaped and continue to shape life, and he's doing it through the detailed study of some of the world's tiniest, usually overlooked, creatures: the protists.

"If you're interested in studying the really huge transitions in evolution, you really need to look at the microbial world, because that's where all the action was," says Dr. Patrick Keeling, a Canadian Institute for Advanced Research scholar at the University of British Columbia, and one of six 2004 NSERC E.W.R. Steacie Memorial Fellows.

In the world of eukaryotes – creatures with cells that have a nucleus, unlike the bacteria that don't have a nucleus – protists are the "other" group. The eukaryotes that get most of the press are furry (the animals), flower (the plants), or are at least sometimes edible (the fungi). But what protists, which are mostly single-celled micro-organisms, lack in size, they make up in numbers. They are by far the largest and most diverse group of eukaryotes on the planet, ranging from marine photosynthesizers to the malaria-causing parasite Plasmodium.

The diversity of protists provides an amazing avenue for studying the molecular evolution of eukaryotes, says Dr. Keeling, and the range of his research reflects this diversity. He has discovered two of only five cases in eukaryotes of deviations from the standard genetic code, the rules guiding the translation of DNA into amino acids. His lab group is also contributing to an international effort to build an accurate tree of eukaryotic life.

But what really gets Dr. Keeling excited about protists is endosymbiosis. This is the process in which one cell eats another, but rather than digesting its meal, incorporates the ingested cell into its own cellular machinery. It's literally a case of evolution by eating.

Research by Dr. Keeling and many others indicates that this is how plastids developed in early eukaryotes. Just like larger organisms, single-celled creatures have organs, called organelles, that are responsible for basic life processes, from energy conversion to reproduction. The plastids are the organelle for photosynthesis in plants and some algae, and the mitochondria, the cellular powerhouses responsible for most of the sugar metabolism in all eukaryotic cells. It's believed that both plastids have their origins in ancient eukaryotes gulping, and keeping, bacteria.

With multicellular creatures, this evolution by eating is largely relegated to our primordial past. If we eat a burger and fries, any DNA that enters our gut cells has zero chance of making it into a sperm or egg cell. But protists reproduce by dividing, so there isn't a reproductive-body barrier.

"If a protist gets a new gene, all its kids do too," says Dr. Keeling.

So just how prevalent is this gustatory genetics? Earlier this year, Dr. Keeling reported the first evidence of widespread and substantial eukaryotic lateral gene transfer – the movement of genes from one species to another, and it appears that eating could be one mechanism.

His lab group studied the nuclear genes that make plastid-targeted proteins in the tropical marine alga Bigalowiella natans. The plastid is known to have originated from a green alga ingested into the protist via endosymbiosis, so all of the plastid genes should reflect this origin. However, about 20 percent of these genes came from other sources.

"They were phylogenetically all over the place," says Dr. Keeling.

To provide a point of comparison, Dr. Keeling's group compared these to the same genes from a green alga (Chlamydomonas) but found none of the unexpected discrepancies.

"One big difference between Chlamydomonas and Bigalowiella is that Chlamydomonas doesn't eat other organisms and Bigalowiella does," says Dr. Keeling. "So our impression is that the process of eating other organisms provides a fantastic source of genes from a variety of things. The combination of eating other organisms and being single-celled sets up an almost perfect machine for taking genes from your environment and integrating them into your genome."

The discovery indicated that lateral gene transfer, thought to be widespread among bacteria, is also at play in eukaryotes.

"Lateral gene transfer is fundamental to understanding how the eukaryote genome works. In practical terms, it matters because it means that an organism can evolve by leaps and bounds rather than by slow incremental changes," says Dr. Keeling.

As part of his NSERC Steacie research, Dr. Keeling will continue to work with Bigalowiella to see if the evidence of lateral gene transfer extends across the protist's entire genome and if other organisms are similarly affected. He'll also be working with organisms that use a variant genetic code to investigate how a genome adapts to a new genetic code, and what other factors are affected by this change.