Hydrothermal vents are home to microbes that are adapted to living in extreme environments


The tree of life: the 3-domain system replaced the 5-kingdom system


Archaea look very similar to bacteria, but are more genetically similar to us

December 2008

Brona McVittie reports

One of the world's smallest organisms may hold clues about how the cell nucleus evolved. Nanoarchaeum equitans is a species of tiny microbe, discovered in 2002 in a hydrothermal vent off the coast of Iceland. It grows in temperatures close to boiling ontop of another single-celled creature called Ignicoccus hospitalis, which provides it with essential nutrients.

Many such members of the Archaea domain live in extreme environments. However, they've also been found in less extreme contexts: soils, marshland and oceans. In fact, they may be one of the most abundant groups of organisms on the planet. Scientists believe they play an important role in both the carbon and nitrogen cycles, so understanding how they work is of considerable benefit.

One of the consequences of the DNA sequencing revolution involved a revision of the tree of life. It became clear that even though certain organisms look like each other, their DNA could be quite different. So Carl Woese proposed that life be organised into 3 domains (Bacteria, Archaea and Eukarya) rather than the traditional 5-kingdom model.

The five kingdoms were generally grouped into Eukarya or Prokarya. Eukaryotes (animals, plants, protists and fungi) are defined by their possession of a cell nucleus. The cells of prokaryotes (principally bacteria) on the other hand, lack this nuclear membrane. Archaea seem to be a half-way house: superficially they look like bacteria, but their DNA is more similar to that of eukaryotes.

Despite having the smallest non-viral genome ever sequenced, N. equitans has proteins that are strikingly similar to the histone proteins within eukaryotic cells. Scientists at the University of Regensburg in Germany have been studying one such protein in this parasitic microbe. It is most similar to histone H3: one of the five kinds of histone protein involved in the structure of chromatin in eukaryotic cells.

Within the eukaryotic nucleus, histones form the scaffold around which the double helix is wound. These proteins spontaneously pair together (H3 with H4; H2A with H2B), which keeps them stable. The pairs then bundle together to form a block of 8 proteins: the nucleosome. H1 histones link these nucleosome bundles together forming a chain around which DNA winds itself in a very specific manner inside the nucleus.

Not only does this compact 2m of DNA into a microscopic nucleus, but the biochemical state of these histones affects the way our genes get expressed. Ulrike Friedrich-Jahn and colleagues, who recently published an article in the Journal of Bacteriology, experimented with archael histones from N. equitans. NEQ288, which is similar to our histone H3, binds DNA on its own, but needs to pair up with another (NEQ288) to compact the DNA.

Understanding how histones interact with DNA in simpler organisms - and there are some 50 known archaeal genes that encode histones - could cast light on the way our own nucleus evolved its complex infrastructure. We are more closely related genetically to Archaea than Bacteria, so this tiny parasitic microbe could represent an evolutionary step from Archaea towards the eukaryotic state.

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