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Cracking the digital code of wine yeast
Anthony R. Borneman, Angus H. Forgan, Paul J. Chambers & Isak S. Pretorius
In a world first, scientists at The Australian Wine Research Institute have sequenced the genome of a wine yeast, characterising the 'recipes of life' that shape this winemaker's friend. This work paves the way for the development of new yeast strains, potentially leading to innovative solutions to the problem of stuck fermentations, and increasing winemakers' options to sculpt grape juice into wines with desired alcohol levels and flavour profiles.
Every four years the Olympic Games inspire the world with spectacular performances and feats of endurance, speed and grace. We marvel at the athletic performance of the competitors; most of us can only wonder how these champions reach the standards they do. What makes world record-breakers so profoundly different to the rest of us? Are we not the same species, and therefore shouldn’t we all have the same potential? Couldn’t we also win gold in swimming or running if we had the same training regimes, diet, lifestyle, etc?
The answer is no. Elite athletes are born with a potential that has ‘gold’ stamped all over it. They have muscle-types, physique, physiology and aptitude that, with training, can be honed for international success. Unfortunately, most of us would require a great deal more than honing to reach this elite level; until bionics is able to rebuild what we are born with, when it comes to athletics, most humans will have to settle for amateur league or less.
Genes are recipes for making proteins. For example, your cells carry a gene/recipe for making the protein insulin, which is a hormone that regulates blood sugar level. You also have genes/recipes that instruct your cells how to make proteins that control how tall you can grow, the colour of your eyes, the general shape of your body, etc. It is these recipes of life that dictate whether you will have athletic potential or not, and, because you inherited them from your parents you end up looking like them.
If genes are recipes then genomes are recipe books. The human genome carries all of the recipes required for making proteins to build a human body from conception to adulthood, and repair and defend that body during its life. All of our physiology and anatomy is shaped by a collection of 20,000 - 25,000 genes that comprise the human genome. And, unless you have an identical twin, your recipe book differs a little from everyone else's.
The language of the genes is very different the languages we use to communicate with each other. It is based on an alphabet of only four letters (A, T, G and C) and its lexicon is limited to three letter words, which means there are only 64 words in the genetic dictionary. However this is more than enough to string together sets of instructions for building all of the proteins (enzymes, hormones, muscles, antibodies, cartilage etc.) we require for life.
The 'paper' on which the words that make up the recipes of life is written is known as DNA, and when we read an entire recipe book of an organism, decoding what is recorded in its DNA, we say we are sequencing its genome. What we end up with in this process is a long sequence of millions of A, T, G, and Cs, with no spaces or obvious punctuation marks, that we have to decipher. Thankfully, sophisticated computational aids can do most of this for us.
This begs the question: What makes a wine yeast tick? What, in the inner workings of this elite athlete, enables it to grow in such an inhospitable environment and deliver gold medal wines when other S. cerevisiae strains don’t even leave the starting blocks? Research at the AWRI is beginning to unravel the mysteries of the variation across the S. cerevisiae species, and early results on what they tell us about wine yeast are tantalising.
The variation in performance that we see across strains of S. cerevisiae is inheritable; this means that it is genetically determined. The starting point for characterising this variation, therefore, should focus on yeast genetics. Fortunately, S. cerevisiae was the first organism of its type to have its genetic make-up (its genome) sequenced, and this was done over ten years ago on a strain, known as S288c, chosen for its ‘laboratory friendly’ characteristics (for more information on what genes and genomes are, see the breakout box). Scientists love this yeast because it is very easy to work with, but it would not win any medals in the winemaking arena; in fact, it is probably not even up to amateur status. Nevertheless, if you want to find out what makes wine yeast so different from other S. cerevisiae strains, you have to have something to compare it with, and S288c is a good starting point.
Another strain of S. cerevisiae, YJM789, recently had its genome sequenced. The genome of this yeast, an opportunistic pathogen isolated from the lungs of an AIDS patient, turned out to be quite different to that S288c. Thus we had two different versions of S. cerevisiae to compare a wine yeast against, and this is what we found.
It turns out that our wine yeast is a little more different to the two previously sequenced strains than they are to each other. About 0.6% of the letters of the wine yeast sequence are different to what is found in the laboratory strain. This might seem like a small difference, but if you consider that genetic differences between humans and chimpanzees amount to only about 1 - 2 %, it is really quite large.
Perhaps of greater interest, however, is that there are extra DNA sequences in the wine yeast; enough to carry at least 27 genes that are not present in the two yeasts it was compared against. In fact, some of the sequences in this extra DNA do not resemble anything found in other species of Saccharomyces; they appear to be more like genes found in very distant fungal relatives. We do not yet know how they got into the wine yeast genome, but we are curious to find out whether or not they play a part in distinguishing wine yeast from other S. cerevisiae, particularly in the winemaking stakes.
Some of the wine yeast-specific genes encode proteins that are probably associated with the cell wall, a feature of yeast that is undoubtedly important for resilience in inhospitable environments. We are curious to find out whether these genes impact on robustness of wine yeast, a feature that is crucial for completing fermentations. Do these genes, for example, make the yeast more or less vulnerable to becoming stuck or sluggish in a ferment?
We have also identified genes that probably encode proteins associated with amino acid uptake (a neutral amino acid transporter) and metabolism (an aspartate transaminase). Because amino acid metabolism is associated with flavour development, it is tempting to suggest that these genes will impact on sensory attributes in wine, but, of course, this will have to be tested.
Then there are lots of genes that we cannot guess the function(s) of yet, and these might turn out to be the most exciting of all; time and experimental work will tell.
Interestingly, we also found some sizeable rearrangements in the genome that we are also curious about, but cannot even guess what their significance will be.
What does the future hold now that we have this rich source of information on a wine yeast? We will, of course, ascertain as far as possible, which of the unique features of a wine yeast genome are important in a winemaking context. However, we also plan to build on data gathered from this project by sequencing and comparing the genomes of several other wine yeast strains that are known to have different winemaking properties. This will enable us to work out what is common to all wine yeasts (i.e. what constitutes the core requirements of a wine yeast) and what differences between them drive production of wines with differing qualities (e.g. different propensities to deliver fruity flavours and aromas).
Once we understand what makes a wine yeast tick, and the significance of variation among wine yeasts, we will be much better placed to develop strains of this microorganism that can complete the marathon of fermentation without becoming stuck or sluggish en route, while producing gold medal wines; and all of this should be possible without the need of performance enhancing additives.
Just like our Olympians at the Australian Institute of Sport, the wine sector has gold-medal aspirations. Backed by sound science and robust research it should be gold all of the way for Australian winemakers.
Acknowledgements
AWRI team members who were responsible for the unravelling of the genetic blueprint of wine yeast is are Drs Anthony Borneman, Angus Forgan, Paul Chambers and Sakkie Pretorius. The Australian Wine Research Institute, a member of the Wine Innovation Cluster in Adelaide, is supported by Australia's grapegrowers and winemakers through their investment body, the Grape and Wine Research and Development Corporation, with matching funds from the Australian Government. Systems biology research at the AWRI is performed using resources provided as part of the National Collaborative Research Infrastructure Strategy, an initiative of the Australian Government, in addition to funds from the South Australian State Government. We gratefully acknowledge the contribution of the Australian Genome Research Facility, a member of Bioplatforms Australia, where the actual sequencing of the wine yeast genome was carried out. We also thank Sharon Mascall and Rae Blair for editorial assistance, and Jeff Eglinton for the preparation of the illustrations. The detailed results of this work are published in the peer-reviewed journal FEMS Yeast Research.
Further reading
Borneman, A.R, Forgan, A., Chambers, P.J. & Pretorius, I.S. (2008) Comparative genome analysis of a Borneman, A.R., Forgan, A., Pretorius, I.S. & Chambers, P.J. (2008) Comparative genome analysis of a Saccharomyces cerevisiae wine strain. FEMS Yeast Research 8:1185-1195.
Borneman, A.R., A.H. Forgan, P.J. Chambers & I.S. Pretorius. 2008. Unravelling the genetic blueprint of wine yeast. Australian and New Zealand Wine Industry Journal 23:21-23.
Borneman, A.R., A.H. Forgan, P.J. Chambers & I.S. Pretorius. 2008. Cracking the genetic code of wine yeast. Wine Business Monthly October issue, pp. 41-43.
Borneman, A.R., Chambers, P.J. en Pretorius, I.S. (2007) Yeast Systems Biology: modelling the winemaker’s art. Trends in Biotechnology 25:349-355.
Goffeau, A, Barrell, B.G., Bussey, H., Davis, R.W., Dujon, B., Feldmann, H., Galibert, F., Hoheisel, J.D., Jacq, C., Johnston, M., Louis, E.J., Mewes, H.W., Murakami, Y., Philippsen, P., Tettelin, H. & Oliver, S.G. (1996) Life with 6000 genes. Science 274:563-567.
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