Posts Tagged ‘yeast’

The brewer’s yoke, the domestication of microbes

// July 15th, 2012 // Comments Off on The brewer’s yoke, the domestication of microbes // Recent Research

Something happened when I was spliced, something wrong. Some random event in my chromosomes, I suppose it was. In any event, I wound up lacking. My sister took all the toxin genes, and I was left with nothing.

It’s a scary world out there for a fungus without a toxin. How would I strike fear into the hearts of all animals who dared to eat the plants I was eating? How, without my precious aflatoxin to attack the liver, causing acute sickness or eventual cancer?

Quite simply, I’m surprised I lasted as long as I did before they found me.

Indeed, I’m not sure how they did find me. I had a pretty good disguise, growing colonies of blue along the endless islands of white rice grains, just like my toxic cousins always had. Safe from munching animals by my don’t-eat-me mimicry, the promise of sickness is the discoloured rice.

For some reason, these sake brewers saw past it all. I thought I was a goner when they lifted me up from the wild and plonked me into a house of wood.

Then I saw the food.

A. oryzae in heaven. Image by Forrest O.

It’s hard for mould like me to see, lacking in the eye department, but I knew it was there. An endless carpet of steamed rice. With my filamentous fronds I could touch it. Drill down into it and grow cottony soft, sprout fruiting bodies on the surface and spread on and on.

Call me legion, for we are many. Better yet, call me qū meí jūn in Pinwin, kōji-kin in Japanese, nulook-gyun in Korean or the grandiose Aspergillus oryzae in scientific circles. Back then, some 2000 years ago, I didn’t know who I was, or that I would one day be the National Fungus of Japan.

That’s when the changes happened.

I didn’t notice at first, I don’t know that there was ever a master plan. It felt… natural. Human hands, bristling with microbes and pitted with pores, dropped me into heaven. And when I had eaten the heaven for a time, they picked me up and dropped me once more into fresh heaven.

Incomprehensible! These hands must have spent hours polishing the rice to remove all the husks, then steamed it to perfection, cooled it so I didn’t burn my filaments, then spread it out – just for me! It was like being a king! King Kōji-kin!

I'm a national icon, and pretty cute too. Image by Ryoku Kasinn

As they fed me and I ate, we gradually adapted to please one another. Heaven grew ever more heavenly, until the temperature and humidity was just so.

For my part, I started growing much faster, hell, I had brilliant conditions for it and not a doubt in the world that I could grow as fast as I pleased. Fearlessly fast.

Over generations, they selected only the best for their purposes, which at that stage I knew nothing about. They selected the sons and daughters (hell, we’re all of one gender here) that could best turn rice starch to sugar. They also preferred fungi of least colour, but most smell and flavour. Each generation, the best of me would be plucked and propagated.

Turning starch to sugar is a tricky thing. I suppose the point of starch is to tie up the sugar molecules into a big, complex network so the plant can use them later. For me, kōji-kin I secrete the amylase enzymes, biological machine that chops starch into pieces of sweet. From a couple of recently-licked hands, I’ve learned humans make the same enzyme in their saliva. My amylases, however, not only make glucose, but a few other sugars that produce a wonderful flavour.

But why, pray tell? Have you worked it out yet?

Winemakers use yeast to turn the natural sugars in grapes into alcohol. Beer brewers must malt their barley, partially growing the seed to convert starch to sugar, to ferment it with yeast into alcohol.

And I, the humble fungus, plucked from the wild a millennia ago for a deficit in character. My non-toxic self excels, above all other moulds, in turning rice starch into sugars.

From the beds of heaven, me and my alchemical rice is transferred to the fermenting tank. Mixed with yeast, water and more rice, then left to stew in our own juices for a month.

This mash is pressed and filtered, and the sweet, alcoholic liquid that pours forth is bottled as sake.

Not to ring my own bell filaments, but I make soy sauce and miso too. That’s a whole meal – appetizer, main, and a drink.

Domesticated A oryzae (left) and wild A flavus (right). Image by John Gibbons, Vanderbilt University

These days I hardly recognise myself! So much of me has changed by growing with the sake brewers. Though I still share some 95% of my genome with my wild and toxic cousin A. flavus (and you, human reader, share 99% of yours with a chimpanzee), I am given all I could ever want to eat and praised world-over for my skill in sake making. While A. flavus, the wild thing, is targeted daily for a war against fungi with resistant crops and competitive yeasts.

What must the wolf think of the dog? Or the auroch of the cow? Well, to their accusations I say this: We may change our genes and appearance for protection and care, but, in doing so, we also mould the humans who cooperate with us. Through their attentions and skills, they, too, are domesticated.

This story was inspired by this recent research by Vanderbilt University into the domestication of microbes. “Although people don’t often think about it, we haven’t only domesticated animals and plants, but we have also domesticated dozens of different microbes.” – Assistant Professor of Biological Sciences Antonis Rokas in the press release. You can find more information on brewing sake here, and a beautiful description of koji pampering by interns at a sake house in Japan who blogged their experiences.

ResearchBlogging.orgGibbons, J. et. al. (2012). The Evolutionary Imprint of Domestication on Genome Variation and Function of the Filamentous Fungus Aspergillus oryzae Current Biology

What is the synthetic cell?

// May 22nd, 2010 // 1 Comment » // How Things Work, Recent Research

Two days ago scientists at J. Craig Venter announced the creation of the first self-replicating synthetic cell, a bacteria with DNA made in a lab. How did they do it, and what does it mean for us in the future?

First up, the scientists didn’t make life out of nothing, and they didn’t make a new species. They recreated a bacteria that already existed, and developed the techniques to do it.

The bacteria is Mycoplasma mycoides. It’s a parasite which lives in cows, and some subspecies cause cow lung disease. It has a circular chromosome made of just under 600,000 base pairs, making it a small genome.

The scientists had the genome sequence of M. mycoides and split it into bite-size portions and then synthesised. Synthesising DNA is nothing new, scientists have been able to write DNA code for quite a while, and can write whatever code they want to.

These little chunks were put into yeast, which can be forced to absorb little bits of DNA. Inside the yeast, the chunks can be sewn together. It’s called recombination. The resulting medium chunks were taken out and put into more yeast to be sewn together making large chunks. There were 11 large chunks were put into more yeast, and sewn together into one complete genome.

Along the way and at the end they checked the code was right by doing PCR tests, genetic fingerprinting made famous by CSI.

Result: A synthetic genome, written by a computer and put together in yeast sweatshops.

Now they had to get it into a bacterial cell. At first they tried to put the DNA into bacterial cells of a similar species, M. capricolum. They ran into trouble at first, because the DNA they had was unmethylated (lacking methyl groups) and the bacteria destroys DNA which is unmethylated. It’s a clever defense mechanism, and they got around it by methylating the DNA before putting it in.

Finally success. The synthetic genome was put into an M. capricolum bacteria where it replaced the normal genome. The bacteria were controlled by the new, synthetic chromosome and were able to replicate billions of times.

What does it mean for us in the future? The technology these guys have developed could be used to alter the DNA of bacteria and make them do new things. From medicine to clean water, the benefits could be huge. We already have this ability to some extent, but it opens up some new doors.

Some organisations have raised concerns about the work. Could a new bacteria be unleashed and take over the world? Probably not. It’s hard to predict how new genes will work in cells, and everything is linked together in a way we don’t understand now. Too much tinkering to the genome will probably not be tolerated by the cell. And if it did get outside, it would probably be extinct pretty quickly because it doesn’t have thousands of years of evolution to prepare it for the world.

If it did get out, we could track it back to the company in charge. These guys watermarked their genome by adding some quotes into the DNA/protein code. Now that’s just epically geeky!

ResearchBlogging.orgGibson, D., & et al (2010). Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome Science DOI: 10.1126/science.1190719






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