Grants and Contributions:

Grant or Award spanning more than one fiscal year. (2017-2018 to 2022-2023)

An amazing diversity of life has evolved on Earth over some 3.5 billion years. Evolution by natural selection acts on the genetic variation within a population of life forms, such that individuals with advantageous genetic traits are more likely to survive and pass on their genes to the next generation. Much of this genetic variation occurs in the form of mutations, which are changes to the information coding content of DNA. Mutations occur all the time at a very low "background" frequency, but these mutations are so rare that their origins are difficult to study and not well understood.

There are many molecules within cells that potentially can damage DNA, leading to mutations. We will investigate the roles of two interrelated processes that can create reactive molecules which can damage DNA: oxygen metabolism and foodstuff utilization. Our highly sensitive baker's yeast model system generates long stretches of single stranded DNA, which is about 100 to 1,000 times more susceptible to being mutated than the usual double stranded DNA found in cells. In fact, damage to the exposed single stranded DNA often yields clusters of closely spaced mutations. This is ideal for generating large numbers of mutations, which we will analyze computationally to infer the characteristic mutation signatures. A mutation signature is a molecular fingerprint due to 1) preferential targeting (or avoidance) of specific DNA sequence contexts and 2) distinctive patterns of substitutions in the DNA base sequence, which can be some combination of C to A, C to G, C to T, T to A, T to C, or T to G. We will comprehensively characterize the mutation signatures of oxygen metabolism and foodstuff utilization under different conditions using the yeast system. We will then check various databases to look for these same signatures and infer the role of these processes in shaping the genomes of humans and many other species over the course of evolution.

The theory of evolution presupposes that there is genetic variation for natural selection to act upon, but says nothing about where the genetic variation comes from in the first place. Our program seeks to answer the longstanding, fundamental question of the origins of genetic variation that enables life to evolve. In addition to yielding important insights into the ultimate basis for biodiversity on Earth, there are potential applications for facile engineering of microbes with desirable properties, including for biofuel or pharmaceutical production; bioremediation; or synthetic biology. Using mutation clusters, we can easily create many variants of a specific target gene of interest in living microbes, without the drawback of introducing many other mutations throughout the microbes' genomes. Success in our program can therefore accelerate progress in these other fields as well. This program will bolster Canada's status as a leader in impactful pure and applied scientific research.