New Insights Into Microbial Adaptation To Extreme Saline .

EPOV 2012understand the drivers of changes leading to an obligatory lifestyle associated with a specificharsh environment and its fluctuations.3 Halophiles: model organisms in exobiology and environmentalmicrobiologySaline environments are of important environmental significance. About one quarter of the landmass contains salt deposits and saline lakes and seas and oceans represent a large part of theearth’s surface (27). Halophilic microbes thrive in nearly saturated brines. They are remarkablytolerant to multiple stresses such as desiccation, temperature, toxic metals, radiation etc (28-32).Halophilic strains have even been shown to survive space conditions (33,34). Extreme halophilesare extremely robust when trapped in fluid inclusions within salt crystals (35,36) and cultures canbe inoculated from this material many years after the water evaporated away. Moreover, severalstudies have reported the existence of viable cells from salt deposits hundreds of million yearsold (37-39). We have shown that halophilic proteins or RNA embedded in salt crystals wereprotected from heat denaturation (40). Hypersaline conditions exist in other planets of our solarsystem. Salt deposits have been formed by evaporation of the primitive oceans on Mars and theoceans lying just beneath the frozen surfaces of Europa and Enceladus, the moons of Jupiter andSaturn are believed to be hypersaline (9,41-44). Terrestrial environments can be quite similar tosuch planetary conditions. For instance, the Deep Halophilic Anoxic Lakes (DHAL’s) located inthe depths of the Mediterranean sea combine hypersalinity, anoxia, darkness and high pressuresimilar to the ones expected bellow the surface of Europa (45). Interestingly, diverse, abundantand metabolically active microbial communities of halophiles were identified in these DHALbrines (46,47). For these reasons, salt sediments or hypersaline waters represent interestingsampling areas in the quest for traces of life on other planets. For long periods, the earth’sprimitive oceans were also hypersaline (48) and it has been hypothesized that life started inhypersaline conditions. The stabilization of RNA molecules by hypersaline conditions couldindeed have played a role in the emergence of life in the "RNA world" scenario. However, it isimportant to bear in mind that the geological history of our planet is extremely chaotic and thatthe physico-chemical conditions of the oceans have changed a lot, accompanied by massivespecies extinctions followed by recolonizations. Moreover, phylogenomics studies of halophilicgenomes and the recent advances in understanding halophilic molecular adaptation describedbelow have suggested that salt adaptation could be a rapid, stepwise, process and that thecontemporary organisms that thrive in theses environments may have arisen from recentadaptations. Therefore, the statement consisting in saying that contemporary halophilicorganisms, or more generally "extremophiles", are "living fossils" is probably ill-suited. Itremains that halophilism is one of the most tractable types of adaptation to understand howevolution changes in depth the functional and biophysical properties of individual biologicalmolecules and whole cell metabolism to match environmental constraints. Halophilism representsa unique model to identify cellular mechanisms allowing cells to cope with a natural changingenvironment due to their unique robustness and their ability to cope with multiple stresses. Inorder to understand the adaptive strategies of halophilic microbes, it is important to specify thelimits of stability/solubility of their proteins and to determine their structural specificities.Unlike halotolerant microbes that counterbalance the difference in osmotic pressure byaccumulating compatible solutes in their cytosol, the extreme halophiles accumulate about 4MKCl as osmoprotectant (49-51). This concentration, close to the saturation of KCl, is similar tothe external NaCl concentration and allows to balance the osmotic pressure. As a consequence, inextreme halophiles, all biochemical processes need to function in close to saturated salt solutions,implying the development of specific adaptations. Indeed, hypersalinity represents a majorstressor for non-adapted organisms. Above the physical constraint on cellular ultrastructure dueto the osmotic pressure, hypersalinity induces aggregation in unadapted proteins and limitsenzyme activity. Protein solvation, i.e. the interaction of water molecules and ions with02001-p.3

BIO Web of Conferencespolypeptide chains in solution, is essential for protein folding and provides a lubricant formolecular dynamics necessary for activity (15). Liquid water is essential for life, and life cannotexists bellow a critical water activity (52). Halophiles are remarkable because they thrive on theedge of the know limits of water activity. In non-adapted systems, such conditions promoteproteins aggregation, precipitation, and denaturation, thus reducing the activity of most nonextremophile enzymes. On the contrary, most halophilic proteins display an obligatoryrequirement for the high salt conditions to be active and stable and, in many cases, low saltconditions result in enzyme inactivation and precipitation (53,54). It is assumed that it is for thisreason that the halophilic organisms must maintain a high cytoplasmic salt concentration.4 Water in cellsWater constitutes the intracellular matrix in which biological molecules interact and its dynamicstate in cells has been the subject of controversy until neutron scattering experiments provideddirect measurements of water diffusion on the atomic scale in living samples of different celltypes. Water dynamics on an atomic length scale has been measured in vivo in the cytoplasm ofEscherichia coli in experimental timescales covering motions from pure water to interfacialwater. In contrast to the widespread opinion that all cellular water is ‘tamed’ by macromolecularconfinement, the data established that water diffusion within the bacteria is similar to that of bulkwater at physiological temperature with an about 10% contribution from solvation shell water(55). A similar conclusion was reached from experiments on human red blood cells (56). Neutronscattering experiments on water diffusion in the extreme halophile Haloarcula marismortui, incontrast, revealed a water fraction with significantly slower diffusion even than solvation shellwater (57), while, as was shown by NMR it maintained bulk-like rotational diffusion (58). Themechanisms behind this slow fraction in the Dead Sea halophile are not yet understood. Aspeculation that it involves a strong and specific K ion/water interaction with macromolecularcarbonyl groups is currently being tested.5 Halophilic protein adaptationGenomic analyses were performed in order to probe the mechanisms of halophilic adaptation atthe molecular level (59). They confirmed that halophilic proteomes are dominated by highlyacidic proteins with an average pI of 4.2. The examination of available halophilic proteinstructures showed that the negatively charged residues are clustered on the protein surface (60).This observation is consistent with the solvation model proposed by Zaccai and co-workers inwhich surface bound hydrated salt ions contribute to protein stabilisation and solubility in thesupersaline conditions (54). In addition it has been proposed that strong inter-subunit and intraionic interactions also contribute importantly to the folding of halophilic proteins (61). Thus,both stabilizing interactions between salt ions and obligatory halophilic proteins behavior arebelieved to be mandatory to retain biochemical function in a salt saturated cytoplasm. This viewhas been challenged recently by the discovery of non-halophilic strains that possess acidicproteomes (62) and by the work comparing the enzymatic, biophysical and structural propertiesof the lactate-malate dehydrogenases enzymes from different halophilic strains. In particular, thestructural and enzymatic study of the MalDH enzyme from Salinibacter ruber, a halophilicbacterium (57), showed that an adapted enzyme that possesses high activity and solubility undermultimolar salt conditions can remain folded and active under low salt conditions (63,64). TheX-ray crystallographic structure of the protein revealed a reduced set of adaptive traits. Theprotein displays a typical acidic surface, solvent exposed and buried hydrophobic surfaces similarto typical halo-adapted enzymes, but it lacks intersubunit ion binding sites. This suggests astepwise evolutionary pathway characterized by the incremental addition of modifications thatlead to an obligatory salt dependence for protein folding and activity. In the case of halophiles,the environmental adaptation is therefore more subtle than the simple modification of the proteinsurface and is the consequence of an adaptive process from non-halophilic to halophilicorganisms.02001-p.4

EPOV 20126 Cellular responses to fluctuating salt environmentsHalophilic microbes stop growing when the environmental conditions drop bellow a specific saltconcentration. This concentration varies from one strain to another. For the extreme halophilicarchaea H. salinarum and H. marismortui that possess cultivation salt optima above 4M NaCl thelower limit is around 2.5M. Below this value the cell mortality rate increases rapidly, probablydue to the effect of osmotic pressure on membranes and because of a low intracellular saltconcentration, which is believed to be incompatible with the salt-dependent protein stabilizationprocess that we described for the halophilic lactate-malate deshydrogenase enzyme from H.marismortui, an extreme halophilic archaeon from the Dead Sea (65). However, low salt stressesoccur frequently in the natural environment in which halophiles thrive. Rain, flooding,evaporation and tidal effects often modify drastically the environmental salt concentration. Saltdependent microbes must therefore have developed survival strategies to cope with thischallenge.In order to identifiy the cytosolic perturbations associated with low salt stress, we first studied themodifications of the internal salt concentration after moderately low salt stress in H. salinarum, amodel extreme halophilic archaeon. The study showed that the high internal K and Na concentrations cannot be maintained for long periods. For example, a low salt shock from 4.2 to2.5 M the internal K concentration dropped down to 1.75M after a 15 min lag period (Marty etal, unpublished). Since significant amounts of K still remained accumulated in the cytosol, onecan assume that the energy-dependent Na/K pumps are still active and that the cells maintained aminimal metabolic activity. This is surprising since according to the in vitro data obtained onhalophilic enzymes the measured intracellular salt concentration after a low salt stress is notcompatible with a long-term stability and functioning of the proteins.As for other types of extreme adaptation, the salt-dependent stability of a specific protein canvary a lot from one protein to the other. It all depends on the types of molecular interactions thatone protein uses to adopt and stabilize its 3D fold and to maintain a flexibility to allow itsfunction. In addition, the cytosolic conditions are far different from the one used in vitro to studyprotein activity and stability. Proteins are not randomly distributed within the cells, they displayextensive physical interactions with partners and the natural ligands and products of theenzymatic reactions influences a lot the stability of the proteins. Also, the intracellular proteinconcentration has been estimated to be 360mg/ml in the cytosol of E. coli. Such molecularcro

halophilic organisms deserve special attention in the search for traces of life on other planets. . The extremophiles often rely on geo-chemical resources as electron donors for their energy metabolisms and represent the core of rich ecosystems (7,8). . microorganism to extreme condition cou