Rime of the Ancient Parasite

Biologists these days can paint many different portraits of the same organism. They can follow the tried and true style of Aristotle and paint with a broad brush, describing what they can see with the naked eye–number of legs, color of hair, live young or eggs. Or they can paint a creature at the cellular level–the twist and turns of collagen fibers in a horse hoof or the poison-producing organelles of a rattlesnake. In the past few years a new kind of portrait has been hung in the biological museum: a portrait of the genome. In the thousands or millions of DNA base pairs, genomes can reveal secrets not only about an organism’s natural history, but its ancient history as well.

Some genomes are big (ours is over 3 billion base pairs). Others are small. Today saw the unveiling of the portrait of the smallest genome of a cellular organism ever sequenced. At only 490,000 base pairs, the genome of the microbe Nanoarchaeum equitans is less than a thousandth the size of the human genome. It’s a portrait in miniature, but like all great miniatures, it is packed with exquisite details.

N. equitans is new to science. In 2002, explorers searching the hydrothermal vents off the coast of Iceland discovered microbes covered by tiny balls. On closer inspection, the balls turned out to be microbes themselves measuring just 400 nanometers across. At first glance, it looked as if N. equitans was a parasite on the bigger microbe.

Parasites are nothing unusual, but when scientists studied how it fit into the tree of life, it became clear that N. equitans was certainly unusual. All living things belong to one of three great domains. We humans (along with plants, mushrooms, and amboebas) are eukaryotes. Most of the microbes we’re familiar with (particularly by making us sick) are bacteria. But there’s a third domain scientists have only recognized in recent years, called Archaea. Archaea can thrive in oxygen-starved swamps, salt flats, and other harsh environments. The deepest-branching lineages of the Archaea are generally found around hydrothermal vents. This may be because life got its start in the scorching waters at the seams of the Earth.

N. equitans, it turns out, is an Archaea–the first Archaean parasite ever found. But even more astonishingly, it sits on a branch that reaches down to the very base of the Archaea. It’s a relict of the earliest chapters of life, over three billion years ago.

It’s easy to prejudge the signficance of N. equitans. Its tiny genome might suggest that it is a degenerate that has lost most of its genes as it has enjoyed the decadence of the parasite’s life. On the other hand, its ancient heritage might suggest that its genome shows us what life was like in its earliest stages, before it had become very complex. If you chose either of these possibilities, you’d be wrong.

In a paper appearing this week in the online edition of the Proceedings of the National Academy of Sciences, a team of researchers show that N. equitans turns out to be something else altogether. Its genome is tight, efficient, and surprisingly complex. Our genomes may be big, but it’s full of junk. Only about 2% of it is actual genes; much of the rest of it is composed of defunct genes and virus-like sequences of DNA. N. equitans, on the other hand, has hardly any junk DNA at all. Almost its entire genome is made up by its 552 genes.

It’s also true that the genome of N. equitans lacks genes for basic jobs like synthesizing amino acids and lipids–stuff that it can steal from its host. But on the other hand, the microbe makes lots of enzymes involved in processing the information in its genome. It can even read out two parts of a gene located on different chromosomes and stitch the result together into a single protein.

It will take a lot of research figure out the full significance of this new portrait, but I think it already shows something very important about biology–something I stressed in my book Parasite Rex: the genomes of parasites are not the dustbins of history but the jewels of evolution.