Sunday, 20 December 2015

8th genome of Christmas: the greatest chemists in the world.

You might think that the best chemists on earth are humans, living perhaps in Cambridge, Heidelberg, Paris, Tokyo or Shenzhen, beavering away in laboratories filled with glassware, extraction hoods and other human-made things. But then you would be discounting a multitude of bacteria that have cracked all sorts of chemistry problems over the course of their long evolution, and that still harbour secrets about how they manipulate molecules. One inventive clade of bacteria, the cyanobacteria, quite literally changed the world, and built the foundations of modern life.

Some 2.5 billion years ago, the ancestor of present-day cyanobacteria made a radical chemical innovation to improve the way they supplied the electrons that feed through various photosynthetic systems. Rather than drawing on more exotic sources of electrons, they used the ubiquitous water molecule. Stripping out the electrons and hydrogens from water could release molecular oxygen: a powerful, reactive molecule, which of course drifted away as a gas. For the first 200 million years or so after this innovation, this gas reacted with reduced inorganic things, for example iron deposits. We can see the resulting change in earth's oxidation state today by drilling down through sediments. But eventually all those sinks were used up, and oxygen started to accumulate in the atmosphere.

This was a massive change to our planet. Molecular oxygen (O2) is thermodynamically unstable; the vast majority of the time it wants to form molecules with other atoms (though the kinetics of these processes gave some opportunities). As oxygen built up in the atmosphere, pumped out by cyanobacteria, every other living organism had to either adapt to cope with (and often exploit) this radical new oxidising agent, or hide itself away in any anaerobic place it could find, which was usually deep inside the Earth. There was no middle ground.

Most life forms adapted. Indeed, they exploited the presence of this oxygen, particularly when it let them control the oxidation of other molecules (such as carbon) to capture energy. Cyanobacteria brought about the source of energy for most living organisms, by enabling carbon capture in combination with various creative uses of oxygen.

The cyanobacteria themselves had to adapt. It’s quite possible, too, that this oxygen crisis triggered some of the most successful collaborations on the planet: alphaproteobacteria worked out how to use oxygen productively, only to be engulfed by the bigger, more motile archaea-like proto-eukaryotes, emerging as mitochondria. Then, these eukaryotes joined forces with ancestors of cyanobacteria to form algae and plants, with the ancestral cyanobacteria becoming the chloroplast, which collects light energy and fixes CO2 for growth.

There is pretty much nothing in our current world, from the diversity of life through the energy we use every day, that is not dependent on cyanobacteria's great innovation.

This is just one of many chemical innovations brought to us by bacteria. Billions of years before Fritz Haber worked out how to capture gaseous molecular nitrogen and convert it into the very useful ammonia, bacteria had worked out how to crack into the kinetically resistant N2 gas. Interestingly, even after intense, concerted efforts we still don’t understand how bacteria pull this off at room temperature. (Many scientists are still at work to crack this; we know the genes involved and have some sense of the awesome redox potentially needed, but how it actually works is still a mystery.) Some bacteria produce hydrogen, which is consumed by other bacteria; some bacteria eke energy out of the redox shifts between the oxidation of metals - everything from iron through to uranium. Bacteria can live in the weirdest environments, from the “hot smokers” of volcanoes underground to the clouds drifting above us.

Bacteria are usually pretty efficient organisms. They live life close to the margin, and every carbon they don't spend on growth is considered a carbon wasted. They have far smaller genomes than the sloppy, energy-rich eukaryotes - and these days it is almost a trivial task to sequence bacterial genomes.But the challenge is neither the size nor the complexity of each genome, but rather simple incredible diversity of bacteria. They are everywhere, finding any possible option for growth. The first bacteria sequenced for the purpose of understanding its chemistry (rather than its laboratory behaviour, or to target it as an infectious agent against humans) was probably Synechocystis in 1997 by a Japanese group. But so many more have sequenced: - over 10,000 - that it is impossible even for the naming systems to keep up. 


Bacterial genomes don't magically tell us how they perform such innovative chemistry, but they do give us the building blocks of the proteins involved, and allow us to start to study them - and sometimes use them - separately. And we have only really started to explore bacterial diversity.

We often consider ourselves and our mammalian cousins as the apogee of evolution, but really the greatest success stories on this planet belong to bacteria, which have radically changed the world.