Life on earth exhibits an enormous adaptive capacity and living organisms can be found even in extreme environments. The halophilic archea are a group of microorganisms that grow best in highly salted lakes (with KCl concentrations between 2 and 6 molar). To avoid osmotic shock, halophilic archea have the same ionic strength inside their cells as outside. All their macromolecules, including the proteins, have therefore adapted to remain folded and functional under such ionic strength conditions. As a result, the amino acid composition of proteins adapted to a hypersaline environment is very characteristic: they have an abundance of negatively charged residues combined with a low frequency of lysines.
A new study provides an explanation at the molecular level for the adaptation of these salt-loving microorganisms to their extreme environments. The findings reveal that the peculiar amino acid composition found in the proteins of halophilic archea results in a reduction in the contact surface with the solvent, and that this is the key mechanism by which they are adapted to life in high-salt environments. Bacteria can thrive even in the harshest conditions. In salt flats and salt lakes, halophilic archea survive the osmotic shock induced by a high salt concentration outside their cells by accumulating salt in the interior of their cytoplasm. However, such a high intracellular salt concentration can seriously alter the normal functioning of the cellular machinery. The proteins from these organisms have therefore evolved with a very biased amino acid composition: some amino acids, like aspartic acid, prevail, whereas others, like lysine, are almost absent. The study makes apparent that the reason the short aspartate side chain is preferred to the long lysine residue is because it minimizes interactions with the surrounding water molecules.
Three different protein domains were included in the study: a domain from a halophilic enzyme, its mesophilic counterpart (preferring moderate conditions), and a totally unrelated model protein. Site-directed mutagenesis was used to modify the surfaces of the proteins and progressively to transform the mesophilic domains into halophilic ones, and vice versa. After measuring the stability for all of the mutant proteins, nuclear magnetic resonance spectroscopy (NMR) was used to obtain high resolution structures for several of the modified proteins. The NMR structures are key to accurately determining the contacts with the solvent. This study provides insight into how high salt concentrations modulate protein stability, and paves the way for understanding the effect of salt on the catalytic activity of certain enzymes. A medium with high salt concentration is somewhat similar to the conditions found in bioreactors, and the biased amino acid composition found in halophilic archea could perhaps be helpful in redesigning enzymes for use in industrial biocatalysis.
Structural Basis for the Aminoacid Composition of Proteins from Halophilic Archea. 2009 PLoS Biol 7(12): e1000257. doi:10.1371/journal.pbio.1000257
Proteins from halophilic organisms, which live in extreme saline conditions, have evolved to remain folded at very high ionic strengths. The surfaces of halophilic proteins show a biased amino acid composition with a high prevalence of aspartic and glutamic acids, a low frequency of lysine, and a high occurrence of amino acids with a low hydrophobic character. Using extensive mutational studies on the protein surfaces, we show that it is possible to decrease the salt dependence of a typical halophilic protein to the level of a mesophilic form and engineer a protein from a mesophilic organism into an obligate halophilic form. NMR studies demonstrate complete preservation of the three-dimensional structure of extreme mutants and confirm that salt dependency is conferred exclusively by surface residues. In spite of the statistically established fact that most halophilic proteins are strongly acidic, analysis of a very large number of mutants showed that the effect of salt on protein stability is largely independent of the total protein charge. Conversely, we quantitatively demonstrate that halophilicity is directly related to a decrease in the accessible surface area.