Manipulating microbes: Biology grad student joins research team’s efforts to turn a microbe into a genome engineering tool

Tuesday, January 31, 2017

Ola Matysiakiewicz holding a flask in the lab.

Byline: Emilie Spasov, Biology MSc. student

Sometimes life gives you unexpected opportunities. For University of Waterloo grad student Ola Matysiakiewicz, that opportunity was the chance to work on engineering a bacterium’s genome.

"I wasn’t planning on going to grad school” explained Matysiakiewicz, currently a new Biology Master’s student in Prof. Trevor Charles lab.

At the time, Matysiakiewicz was a Waterloo Biochemistry undergraduate, with a specialization in biotechnology. She had thought about teaching English abroad after she graduated, but then she heard about Prof. Charles’ search for Master’s students. She applied to be part of this project, a collaboration between Waterloo, Western and McMaster, which focusses on turning the soil bacterium Sinorhizobium meliloti into a genome engineering tool.

S. meliloti is a soil bacterium that lives with the roots of plants like alfalfa and converts nitrogen from air into ammonia, which plants need. The goal is to learn more about its genome, to be able to engineer the bacterium—modify its genes—in the future.

Synthetic biology involves designing and manipulating biological systems, for example, engineering organisms to produce proteins that they don’t naturally produce. The goal with S. meliloti is to modify its genetics so it is better at taking up DNA from other microbes so that DNA can be engineered more easily.

Getting a microbe to take up one small gene sequence of foreign DNA isn’t too difficult, but transferring large or multiple genes is. To get around this problem, scientists use ‘in vivo assembly of DNA.’ This method involves smaller pieces of DNA with overlapping regions that can get taken up by the bacteria, which then assembles it once inside.

"The aim is to turn S. meliloti into a tool to do genetic work in."

To do this, she first must determine the best way to move DNA from another organism into S. meliloti. This involves various methods such as heat shocking the cells, conjugation―where DNA is transferred from one bacterial cell to another, and electroporation, which involves using a pulse of electricity to open the pores of the cell membrane to move DNA inside.

While genetic manipulations can lead to many exciting avenues, Matysiakiewicz says that the project right now is not about the future applications.

"The end goal is to design a method to make genome changes rapidly and accurately."

This project is in collaboration with Dr. Bogumil Karas from Designer Microbes Inc. and Western University, and Prof. Turlough Finan from McMaster University.

NOTE: BIOL 690 Scientific Communication is a graduate course that helps students enhance their skills in the acquisition, organization and presentation of scientific information. Students in the course interviewed and wrote a news story about one of their classmates' research.