|
Friedhelm Pfeiffer, the research group's
bioinformatics expert, created a database for halophile (Greek "salt-lovers")
archaea, called HaloLex (see link below). Using the database, genetic
and protein data about the organisms is tied to information about
their structure and function. The newest genome on HaloLex is now that
of Natronomonas pharaonis, whose genetic information was made
available by Michaela Falb, Friedhelm Pfeiffer, Peter Palm, Karin
Rodewald, Volker Hickmann, Jörg Tittor and Dieter Oesterhelt. This
information is made of some 2.6 million base pairs (about one
thousandth of the human genome), and encodes the synthesis of 2,843
proteins.
Natronomonas pharaonis has to deal with two
different kinds of life-threatening conditions. It was found in pools
which are strongly alkaline (pH-value of about 11) with an extremely
high salt concentration (over 300 grams of salt per litre of water).
The high pH-values are about the same as lye soap and the salt content
that of the Dead Sea. As far as the salt content is concerned,
Natronomonas pharaonis behaves like closely related organisms - for
example, Halobacterium salinarum, the "house pet" of Dieter
Oesterhelt's department. In contrast to other salt-tolerant organisms,
halophile archaea have an extremely high salt concentration inside of
their cells. These levels of salt concentration cannot usually support
proteins, the critical functional components of living cells. But the
greater portion of amino-acid building blocks in the proteomes of
halophile archaea make it possible for the proteins to remain stabile,
even in high salt concentrations. To survive among the extremely high
pH-values, Natronomonas pharaonis also has a moderately increased
pH-value inside its cells.
The cellular components that are in direct contact
with the brine around them need their own adaptation strategies. These
components are the cell membrane and the proteins that have to
function outside the cell. Michaela Falb discovered, using theoretical
analysis as part of her doctoral thesis, that Natronomonas pharaonis
has a particularly large number of proteins attached to lipid
molecules, anchoring it to the cell membrane.
Important functions of the energy metabolism - for
example, the respiratory chain - are embedded in the cell membrane and
have to be adapted to the adverse external conditions. Despite a
detailed bioinformatic analysis of the genome, it was still unclear
whether Natronomonas pharaonis has a respiratory chain and which ions
would play a role in its functioning. The bioinformatics expert
Michaela Falb and biochemist Jörg Tittor thus designed additional
experimental studies which showed that Natronomonas pharaonis does
indeed have a functioning respiratory chain, which amazingly, and in
contrast to other organisms that grow in alkaline conditions,
functions with a "normal" proton. The Max Planck researchers could
thus refute the paradigm, dominant until now, that organisms in
alkaline conditions have to switch to other ions (for example, sodium,
Na+).
A higher pH-value leads to the depletion of
ammonium. Because ammonium nitrate is a key building block of amino
acids, the tiny organism should have problems synthesising it.
Michaela Falb discovered in the genome a number of ways that
Natronomonas pharaonis can take optimal advantage of the low incidence
of nitrogen: through the uptake and metabolism of nitrate and urea, as
well as the efficient uptake of ammonia.
The co-operation of theoretically and
experimentally-oriented researchers shed light on other questions. The
bioinformatics experts were able to predict that Natronomonas
pharaonis can by itself produce vitamins and amino acids. Thus, the
growth medium for the culture of the single-celled organism could be
significantly simplified.
Dieter Oesterhelt explains that "the comparison
with other halophile archaea we have studied shows that these
organisms have a high plasticity with which they can adapt to the
varying, extreme environmental conditions. The frugality of
Natronomonas pharaonis, with the possibility of simplifying the
nutrient solution, opens new possibilities for experimentally
investigating the metabolic network. The data we thus acquire make up
an important foundation for developing and testing metabolic models in
the framework of systemic biological studies and in interdisciplinary
co-operation with mathematicians." |
