Bubbles, Bread and Beer

And now, evolutionary biologist Olivia Judson talks about yeast, which makes the world go ’round. From The New York Times, June 23, 2010.

Bubbles, Bread and Beer

A couple of teaspoons of dried yeast. A pinch of sugar. A cup of warm water. And a few minutes later, you’ll have a foamy, bubbly brew of lively yeast cells, ready to be added to a bowl of flour and turned into bread.

London.

Saccharomyces cerevisiae, also known as baker’s yeast, is one of the most useful beings known to humans. We rely on it for making bread and beer; but it is also a denizen of the laboratory, one of the most studied organisms on the planet. Which is why I’m nominating it for Life-form of the Month: June.

But what is it? Yeasts are fungi — so they are related to mushrooms. And fungi are, strangely, quite close relations of ours. Or at least, they are more closely related to animals than they are to plants. Like animals, they digest their food — though fungi do it not by swallowing, but by releasing chemicals into the environment. The chemicals break down the food — like rotting wood — into smaller molecules, and the fungus then imports these smaller molecules into its cells.

Sometimes this takes on sinister dimensions. For example, if you are nematode worm crawling through the soil, you may get stuck in a sticky web. But in this web there is no spider. The web itself is alive: it is not made of silk, but of the filaments of a fungus. The web itself will digest you. Other fungi set snares — they produce rings of cells that swell up when a worm passes through, catching it round the middle. The fungus then digests the worm at its leisure.

Fungi hold several world records. Some species can live in drier environments than any other organisms, including bacteria. Some species have huge numbers of sexes — the mushroom Schizophyllum commune is estimated to have as many as 20,000. (This doesn’t mean that 20,000 individuals must assemble for some sort of shroomed-out orgy; sexes are a set of genetic rules for which pairs of individuals can swap genes with each other. Members of the same sex do not swap genes.)

Further accomplishments: the first “tree” appears to have been a fungus of some sort — it lived in the Devonian period, around 400 million years ago — and sometimes stood as tall as nine meters (almost 30 feet). And although today’s fungi don’t stretch towards the skies, some of them are massive. Single individuals of the species Armillaria bulbosa have been estimated to cover 15 hectares (37 acres) and weigh 10,000 kilograms (22,000 pounds). Funky.

Fungi are also famous for evolving associations with other organisms. Some are parasitic, like the smuts that attack our crops. But many are beneficial. Lichens are associations between fungi and algae or certain bacteria; and many plants depend on fungi to provide them with nutrients from the soil. Humans depend on certain fungi for penicillin, and for foods like truffles. And bread.

Which brings me back to yeast. Yeasts are lowly beings: they have but a single cell. But that doesn’t mean they aren’t mighty. Baker’s yeast, in particular, has proven to have some powerful attributes. Especially in the laboratory. For one thing, it grows easily and fast — it can go through several generations between the time you have your morning toast and your evening beer.

Compared to us, Saccharomyces cerevisiae has few genes — it has around 6,500, while we have more than three times that many. All the same, the study of this organism has illuminated many aspects of human biology. It is, for example, an important tool for studying diseases of the nervous system like Friedreich’s ataxia, an inherited condition that inflicts, among other things, slurred speech and stumbling gaits on those who have it.

This may seem bizarre. How can an organism with one cell — and no nervous system — be useful for studying the degeneration of the human nervous system? There are a couple of parts to the answer.

The first is that humans and yeast have many genes in common: about 60 percent of yeast genes are known to have human equivalents, and almost a quarter of human disease-causing genes have equivalents in yeast. Studying yeast genes thus gives us a window into what some of our most essential genes are doing. Indeed, suppose you create a yeast “knock out” — you remove one of the yeast genes. Often, this will have a clear and detrimental impact on how the organism grows. Now, replace the knocked-out gene with the human version — and like as not, you will have restored the yeast to its former frothy self.

Moreover, many degenerative diseases are due to mutated genes that cause the build up of misshapen proteins inside cells. Looking at the appropriate mutations in yeast can thus help us to discover what is going wrong, and why it is that our nerve cells begin to die.

All in all, it’s quite a set of accomplishments for a being that has only one cell. And with that in mind (picture the thought bubbles over my head), I think I’ll go and loaf about with a beer.

NOTES

Nice general introductions to fungi can be found in the relevant chapters of Dawkins, R. 2004. “The Ancestor’s Tale: A Pilgrimage to the Dawn of Life.” Weidenfeld and Nicolson; and Margulis, L. and Schwartz, K. V. 1998. “Five Kingdoms: an Illustrated Guide to the Phyla of Life on Earth.” W. H. Freeman. Both also give accounts of how fungi are more closely related to animals rather than plants, and give descriptions of how fungi secrete enzymes into the environment. The role of Saccharomyces in brewing and baking is well known. Ditto, the fact that some fungi form lichens, others associate with the roots of plants, and still others cause nasty diseases. However, an interesting and concise review of the variety of fungal lifestyles can be found in McLaughlin, D. J. et al. 2009. “The search for the fungal tree of life.” Trends in Microbiology 17: 488-497.

For an overview of the fungi that capture nematodes, and the variety of ways they do it, see Yang, Y. et al. 2007. “Evolution of nematode-trapping cells of predatory fungi of the Orbiliaceae based on evidence from rRNA-encoding DNA and multiprotein sequences.” Proceedings of the National Academy of Sciences USA 104: 8379-8384.

For some fungi tolerating some of the driest environments on the planet see, for example, Williams, J. P. and Hallsworth, J. E. 2009. “Limits of life in hostile environments: no barriers to biosphere function?” Environmental Microbiology 11: 3292-3308; and Onofri, S. et al. 2004. “Antarctic microfungi as models for exobiology.” Planetary and Space Science 52: 229-237. For 20,000 sexes in Schizophyllum, and for a general discussion of how such complex mating systems work, see Kothe, E. 1996. “Tetrapolar fungal mating types: sexes by the thousands.” FEMS Microbiology Reviews 18: 65-87.

For the first “tree” being a fungus, see Hueber, F. M. 2001. “Rotted wood-alga-fungus: the history and life of Prototaxites Dawson 1859.” Review of Palaeobotany and Palynology 116: 123-158; and Boyce, C. K. et al. 2007. “Devonian landscape heterogeneity recorded by a giant fungus.” Geology 35: 399-402. Some authors argue that Prototaxites is in fact a lichen (though this still makes it a fungus in part): see Selosse, M.-A. 2002. “Prototaxites: a 400 MYR old giant fossil, a saprophytic holobasidiomycete, or a lichen?” Mycological Research News 106: 642-644. For the huge size of Armillaria bulbosa, see Smith, M. L., Bruhn, J. N., and Anderson, J. B. 1992. “The fungus Armillaria bulbosa is among the largest and oldest living organisms.” Nature 356: 428-431.

The role of baker’s yeast as a laboratory organism is well known. Its potential for helping elucidate human diseases was pointed out some time ago — see, for example, Bassett, D. E. Jr., Boguski, M. S. and Hieter, P. 1996. “Yeast genes and human disease.” Nature 379: 589-590; and Botstein, D., Chervitz, S. A. and Cherry, J. M. 1997. “Yeast as a model organism.” Science 277: 1259-1260. For my discussion of yeast and degenerative diseases, I drew heavily on two papers: Knight, S. A. B. et al. 1999. “The yeast connection to Friedrich ataxia.” American Journal of Human Genetics 64: 365-371; and especially Khurana, V. and Lindquist, S. 2010. “Modelling neurodegeneration in Saccharomyces cerevisiae: why cook with baker’s yeast.” Nature Reviews Neuroscience 11: 436-449. For anyone interested in this subject, this last paper contains a wealth of useful information, and was part of what inspired me to write this article.

Many thanks to Oliver Morton and Jonathan Swire for insights, comments and suggestions. This column is dedicated to my late mother who, when I was a child, taught me to make bread.

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