Does porcupine scat contain the secret to transform the pulp and paper industry’s cellulose waste into a profitable biofuel on a commercial scale?
“It’s definitely possible,” says Mackenzie Thornbury, a synthetic biology buff and microbiology and immunology student at Dalhousie University.
In preparation for the 2017 Internationally Genetically Engineered Machine Competition (iGEM), Nov. 9-13 in Boston, Massachusetts, Thornbury and her 23 Dalhousie teammates are probing one of the newest and hottest scientific fields to show how synthesized enzymes from the porcupine gut could be harnessed for bioremediation. Long-term, commercial feasibility is in their sights.
As iGEM competitors, she explains,“ We’re using synthetic biology to make microorganisms do useful work for us.” In essence that is what the term, genetically engineered machine, means.
Going for gold
Dr. Craig McCormick, the team’s faculty advisor, a professor in the Department of Microbiology and Immunology, confidently declares, “we’re going for gold this year. Even though the Dalhousie team is only in its third year,” he says, “it has already competed at the Giant Jamboree in Boston twice, earning a bronze medal last year. Our students stood shoulder to shoulder with top Ivy League teams and told the story of their unique research.”
The competition is the world’s premier synthetic biology event for students. Synthetic biology, also known as synbio, is so new, formal training is hard to find. No university in Atlantic Canada offers it, but the field is surging because of its practical problem-solving potential.
Synthetic biology focuses on re-designing biological systems, including microbial components and genetic circuitry, to do useful work. Current synbio advances include new ‘green chemistry’ technology to produce useful compounds, and novel data-encryption platforms using microbial DNA. The same synbio techniques can be applied to long-term goals including the development of synthetic tissues and organs.
Genome Atlantic a sponsor
According to recent reports, McCormick says synthetic biology is on track to become a $26 billion global industry by 2025. That projected economic impact is one reason Genome Atlantic is a sponsor this year, says Dr. Kristin Tweel, the not-for-profit corporation’s business development officer. Besides financial aid, Genome Atlantic is introducing the team to some relevant industry contacts and scientific experts.
“Synthetic biology is an emerging area of genomics that holds a lot of promise for greener, more sustainable products,” says Tweel. “Genome Atlantic is proud to sponsor the Dalhousie iGEM team because these students will be tomorrow’s scientists who are leading innovation in this new field. Also, their project is entrepreneurial in nature, in an area that’s relevant to the forestry and pulp and paper industries which are important sectors for Atlantic Canada.”
For the second year running, Dalhousie entrants are probing the porcupine microbiome for cellulose-degrading enzymes. As a well-known fancier of tree bark, a substance rich in cellulose and difficult to digest, the porcupine is proving a savvy choice for attention.
In the papermaking process, the industry relies on chemicals, water or fire to separate unwanted cellulose from wood fibre. The Dalhousie team is searching the porcupine gut for a more environmentally friendly way to do the separating and turn the cellulose-laden waste into a sustainable source of energy.
Deeper data dive
Determined not to be outdone by last year’s iGEM crew, Thornbury says the 2017 team is starting with a deeper data dive.
Metagenomic sequencing has been completed using the same porcupine fecal samples subjected to standard 16S rRNA sequencing last year to detect the microbial diversity in the mammal’s gut. This latest action means the entire porcupine microbiome – all the DNA in the scat – has now been sequenced.
The enriched data makes it possible to identify the enzymes encoded in the bacterial sequences. This year the team is looking for two enzymes that can break down the main cellulose molecule and seven enzymes to degrade complex forms such as hemicellulose, found in tree bark.
As enzyme candidates are pinpointed, the plan is to chemically synthesize them at Integrated DNA Technologies Inc., another iGEM Dalhousie team sponsor, and then test the synthesized enzymes in E. coli for their cellulose degrading ability. In combination with enzymes, E. coli can transform cellulose and hemicellulose into glucose.
From there, it is a short step with a yeast silo reactor to creating a biofuel. “Our idea is to put yeast into the mixture to take the glucose and create ethanol,” says Thornbury. The same principle is used in wine- and beer-making when yeast converts the sugar in grapes and malted barley into alcohol.
In theory, there is plenty of commercial potential here. Thornbury points to BioVectra in Charlottetown, a company that already does microfermentation for the pharmaceutical industry and notes that a bioreactor for large-scale ethanol production is not a new concept. However, at this stage, she concedes,“ it would be a big jump from where we are now.”
Nevertheless, McCormick says, “I’d like to see the team engage with the Nova Scotia business community to explore the potential of synthetic biology to create new solutions for industry.” He points out that in 2015, the Dalhousie iGEM team cloned genes that make blueberries blue – and healthy.
This year’s Dalhousie iGEM contingent is more than triple the size of last year’s group. Disciplines as varied as computer science, management and engineering as well as the basic sciences are represented and Microbiology maintains a robust presence. Five grad students are acting as team mentors and students have run their own skill development workshops on gene cloning and bioinformatics.
What is the attraction? McCormick describes it as “ a unique educational experience. It’s student-led with hands-on training in an emerging area of science, the opportunity to communicate findings to an international conference and the opportunity to publish.”
The first team-produced scientific manuscript from Dalhousie’s iGEM experience, based on work with the porcupine gut, is due out this year in PLOS ONE, a peer-reviewed, open access scientific journal published by the Public Library of Science.