Nobody At The Vault But Yeast
A Flame-Side Chat, with Dr Anna Fijarczyk
Dear Brew Enthusiasts,
You may remember a post from The Beerologist that dealt with the archaeology of beer yeast. In that post, I described the work done by the group of Prof Christian Landry, that aimed to identify the source and use of the Jean-Talon yeast strain in Quebec.
I am delighted to report on a flame-side chat I had with one of the main authors of that work, Dr Anna Fijarczyk. Anna is a postdoctoral researcher in the Landry group, responsible for the bulk of computational analyses and interpretation that underpinned this exciting piece of work.
Let’s get stuck in!
Edgar: Could you tell me what your reasons were to start looking into the Quebec brewery and Jean-Talon?
Anna: There is always interest in new and original strains in the brewing industry. One of the microbreweries in Québec City became interested in an archaeological location known to be the first brewery in Nouvelle France, founded by Jean Talon who was the first Intendant appointed by King Louis XIV. This place has a rich history, as it started as the first Canadian brewery in the XVIIth century, later was turned into a Palace, a powder storage facility and then became one of the biggest breweries in Canada in the XIXth century, and was eventually closed in the 60s.
This last brewery, Boswell/Dow, strongly alluded to the times of Jean Talon and the old brewery when marketing their beer. The name of Jean Talon became a recognized mark, even though the first brewery was short-lived. With finding yeast strains in the vaults, an exciting question had arisen; where did the strain originate from? Was the strain used in the first or the second brewery? The strain arrived in the laboratory of Christian Landry and that’s how I got involved in this project.
Edgar: Could you describe the condition of the vaults? Is it an environment where you would expect yeast to thrive (in the absence of a substrate?)
Anna: Although the original building from the XVIIIth century, which served as the Intendant’s Palace, has been destroyed, the vaults stayed intact and were accustomed by Boswell/Dow brewery for storing beer and afterwards served as a location for the brewery's pub. Strains were sampled by Bruno Blais from one of the microbreweries in Quebec City, La Barberie, in 2010, long after the Boswell/Dow brewery was closed and the vaults were emptied. It is definitely not an ideal place for yeast to thrive, because S. cerevisiae is not found naturally at this latitude, and without an abundance of proper substrate yeast may have a hard time surviving for a long time. In that sense, it was surprising to find living yeast in this location.
Edgar: You used genome-wide genotype dissimilarities to investigate relatedness or relationships between strains. Did you identify any regions or genes between strains that define groups of sub-types? If so, what separates strains from each other?
Anna: One type of genetic variation we looked at to place the “Jean-Talon” yeast strain among existing genomes of S. cerevisiae was a change in the number of copies of genes involved in maltose metabolism. These genes are known to have varying numbers of copies depending on, for example, the source of fermentation. In this study, we also see that yeast strains used in some styles or types of beer, such as wheat, alt, Kolsch or Hefeweizen from Germany have a distinct profile of copy number changes from other beer styles.
Jean-Talon has a profile closest to Belgian and English ales. In fact, Jean-Talon is very similar in genomic sequence to other commercially available beer strains that you can buy nowadays so it does not comprise a distinct genetic group. The Jean-Talon strain has a number of mutations scattered all over the genome, but the most striking differences are unique large-scale copy number changes that span large parts of its chromosomes. These large-scale copy number changes influence gene copy numbers, such as the gene responsible for resistance to cobalt. We suspect that an additional copy of this gene gives Jean-Talon an advantage in a cobalt-rich environment.
Edgar: Given that you find varying degrees of gene copy number, is there any evidence that copy number influences gene evolution?
Anna: I think this would be really interesting to study! We looked at very recent cases of gains or losses of gene copy numbers, where we expect no or very little changes in the gene sequence. With time, it’s possible that some of these copies will evolve independently and diverge on the sequence or even functional level. Frequent copy changes in, e.g. genes responsible for maltose metabolism could be a good starting point for new genetic innovations in yeast.
Edgar: You found quite a number of structural variations when looking at the Jean-Talon strains and S288c. Do you think this is simply a result of chance and propagation (generation number) or do you think there is a biological reason (e.g. selection) for the SVs you identified?
Anna: In brewing yeast structural variants, copy number changes, aneuploidies or whole-genome duplications occur quite often. The fact that yeast is grown in large populations in a rich substrate probably helps these events to become apparent.
It’s therefore tricky to determine whether the change is established in a population as a response to environmental change or simply by chance and subsequent propagation. We suspect that at least one large duplication which is unique to the Jean-Talon strain is maintained or was maintained in the past by selection. As mentioned before, an additional copy of a large genomic segment provides Jean-Talon with 5 copies of a cobalt-resistance gene. Given that Jean-Talon is indeed more resistant to cobalt than other related beer strains, and that the Boswell/Dow brewery was known for using cobalt in their beer production, this duplication could have given our Jean-Talon strain a unique growth advantage under these local brewing conditions.
Edgar: What did you find were the major problems or bottlenecks that hampered your work?
Anna: The fact that the true source of the strain was unknown increases the uncertainty as to its origin. Since the samples were collected directly in the vaults and not from the bottles, we did not know for how long the strains actually occupied the vaults. Independent pieces of evidence such as sequence divergence with other beer strains and the fact that they are more resistant to cobalt led us to conclude that they are descendants of beer strains used in the Boswell/Dow brewery.
Another level of complexity is added by the fact that the strain is tetraploid. Tetraploid genomes are quite difficult to unphase (i.e. to read the complete sequence of each of the four genomes), and knowing the sequence of each genomic copy would allow us to make more inferences, i.e. about the past size changes of a population from which the strain was derived.
Edgar: What do you think the interesting questions are from this work, that you are now pursuing?
Anna: I think one of the interesting aspects of the evolution of beer yeast is the fact that they are often polyploid and carry a lot of structural and copy number variations, which may have something to do with their mixed ancestry. Gains and losses of genes can be potent drivers of species adaptation to new environments not only in yeast but in other species as well, including plant pathogens.
Large populations maintained during the brewing process, combined with a high rate of large genetic changes, provides an environment that allows species to survive despite the accumulation of some deleterious mutations, which can turn out to be useful when the environment changes. It would be very interesting to tease those factors apart and gain clarity.
Edgar: If the readers are interested in the Jean-Talon strain, could they obtain a culture and if so, how?
Anna: The strain is currently maintained by the Lallemand institute in Montréal and it can be ordered via Montréal-based Siebel Institute of Technology. Questions about orders, storage or propagation can be directed to Rodd Seher (yeast.genetics@siebelinstitute.com).
I hope (and I am sure) that this Flame-Side Chat and our post will have convinced you on how genomics and phenotypic analyses can help us establish both provenance and attributes of brew yeasts. A heartfelt thanks to Anna for her thoughtful and insightful answers. Any More questions about this or related work? Get in touch.
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