The genome of another micro-organism which lives underextreme conditions has been sequenced. Scientists at the Department ofMembrane Biochemistry at the Max Planck Institute of Biochemistry haveanalysed the genome of Natronomonas pharaonis and uncovered thesurvival strategies with which the archaeon can best thrive in deadlyenvironmental conditions. In the latest edition of the internationaljournal Genome Research, Professor Dieter Oesterhelt and his colleaguespresent their research (Genome Research, October, 2005).
Archaea,small single-celled organisms, are particularly interesting forscientists because they are able to live under extreme environmentalconditions, for instance under high salt concentrations, highpH-values, or high temperatures. Nature’s masters of adaptation, theyare model organisms from which researchers can draw conclusions aboutthe first organisms on earth. The scientists studied mechanisms thatmake survival possible for the single-celled organisms, which arerod-shaped and are only five hundredths of a millimetre in size. At theDepartment of Membrane Biochemistry, led by Professor DieterOesterhelt, Max Planck researchers have shown, using genomic andproteomic methods combined with physiological experiments, how toexplain the amazing abilities of these extreme organisms.
FriedhelmPfeiffer, the research group’s bioinformatics expert, created adatabase for halophile (Greek "salt-lovers") archaea, called HaloLex(see link below). Using the database, genetic and protein data aboutthe organisms is tied to information about their structure andfunction. The newest genome on HaloLex is now that of Natronomonaspharaonis, whose genetic information was made available by MichaelaFalb, Friedhelm Pfeiffer, Peter Palm, Karin Rodewald, Volker Hickmann,Jörg Tittor and Dieter Oesterhelt. This information is made of some 2.6million base pairs (about one thousandth of the human genome), andencodes the synthesis of 2,843 proteins.
Natronomonas pharaonishas to deal with two different kinds of life-threatening conditions. Itwas found in pools which are strongly alkaline (pH-value of about 11)with an extremely high salt concentration (over 300 grams of salt perlitre of water). The high pH-values are about the same as lye soap andthe salt content that of the Dead Sea. As far as the salt content isconcerned, Natronomonas pharaonis behaves like closely relatedorganisms - for example, Halobacterium salinarum, the "house pet" ofDieter Oesterhelt’s department. In contrast to other salt-tolerantorganisms, halophile archaea have an extremely high salt concentrationinside of their cells. These levels of salt concentration cannotusually support proteins, the critical functional components of livingcells. But the greater portion of amino-acid building blocks in theproteomes of halophile archaea make it possible for the proteins toremain stabile, even in high salt concentrations. To survive among theextremely high pH-values, Natronomonas pharaonis also has a moderatelyincreased pH-value inside its cells.
The cellular components thatare in direct contact with the brine around them need their ownadaptation strategies. These components are the cell membrane and theproteins that have to function outside the cell. Michaela Falbdiscovered, using theoretical analysis as part of her doctoral thesis,that Natronomonas pharaonis has a particularly large number of proteinsattached to lipid molecules, anchoring it to the cell membrane.
Importantfunctions of the energy metabolism - for example, the respiratory chain- are embedded in the cell membrane and have to be adapted to theadverse external conditions. Despite a detailed bioinformatic analysisof the genome, it was still unclear whether Natronomonas pharaonis hasa respiratory chain and which ions would play a role in itsfunctioning. The bioinformatics expert Michaela Falb and biochemistJörg Tittor thus designed additional experimental studies which showedthat Natronomonas pharaonis does indeed have a functioning respiratorychain, which amazingly, and in contrast to other organisms that grow inalkaline conditions, functions with a "normal" proton. The Max Planckresearchers could thus refute the paradigm, dominant until now, thatorganisms in alkaline conditions have to switch to other ions (forexample, sodium, Na+).
A higher pH-value leads to thedepletion of ammonium. Because ammonium nitrate is a key building blockof amino acids, the tiny organism should have problems synthesising it.Michaela Falb discovered in the genome a number of ways thatNatronomonas pharaonis can take optimal advantage of the low incidenceof nitrogen: through the uptake and metabolism of nitrate and urea, aswell as the efficient uptake of ammonia.
The co-operation oftheoretically and experimentally-oriented researchers shed light onother questions. The bioinformatics experts were able to predict thatNatronomonas pharaonis can by itself produce vitamins and amino acids.Thus, the growth medium for the culture of the single-celled organismcould be significantly simplified.
Dieter Oesterhelt explainsthat "the comparison with other halophile archaea we have studied showsthat these organisms have a high plasticity with which they can adaptto the varying, extreme environmental conditions. The frugality ofNatronomonas pharaonis, with the possibility of simplifying thenutrient solution, opens new possibilities for experimentallyinvestigating the metabolic network. The data we thus acquire make upan important foundation for developing and testing metabolic models inthe framework of systemic biological studies and in interdisciplinaryco-operation with mathematicians."
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