Halotolerant or halophilic microorganisms, able to live in saline environments, offer a multitude of actual or potential applications in various fields of biotechnology. The technical applications of bacteriorhodopsin comprise holography, spatial light modulators, optical computing, and optical memories. Compatible solutes are useful as stabilizers of biomolecules and whole cells, salt antagonists, or stress-protective agents. Biopolymers, such as biosurfactants and exopolysaccharides, are of interest for microbially enhanced oil recovery. Other useful biosubstances are enzymes, such as new isomerases and hydrolases, that are active and stable at high salt contents. Halotolerant microorganisms play an essential role in food biotechnology for the production of fermented food and food supplements. The degradation or transformation of a range of organic pollutants and the production of alternative energy are other fields of applications of these groups of extremophiles.

Potential of halotolerant and halophilic microorganisms for biotechnology.

Extremophiles as a source for novel enzymes.

Intrinsically disordered proteins and intrinsically disordered protein regions are highly abundant in nature. However, the quantitative and qualitative measures of protein intrinsic disorder in species with known genomes are still not available. Furthermore, although the correlation between high fraction of disordered residues and advanced species has been reported, the details of this correlation and the connection between the disorder content and proteome complexity have not been reported as of yet. To fill this gap, we analysed entire proteomes of 3484 species from three domains of life (archaea, bacteria and eukaryotes) and from viruses. Our analysis revealed that the evolution process is characterized by distinctive patterns of changes in the protein intrinsic disorder content. We are showing here that viruses are characterized by the widest spread of the proteome disorder content (the percentage of disordered residues ranges from 7.3% in human coronavirus NL63 to 77.3% in Avian carcinoma virus). For several organisms, a clear correlation is seen between their disorder contents and habitats. In multicellular eukaryotes, there is a weak correlation between the complexity of an organism (evaluated as a number of different cell types) and its overall disorder content. For both the prokaryotes and eukaryotes, the disorder content is generally independent of the proteome size. However, disorder shows a sharp increase associated with the transition from prokaryotic to eukaryotic cells. This suggests that the increased disorder content in eukaryotic proteomes might be used by nature to deal with the increased cell complexity due to the appearance of the various cellular compartments.

Orderly order in protein intrinsic disorder distribution: disorder in 3500 proteomes from viruses and the three domains of life

Potassium is the major intracellular cation in bacteria as well as in eucaryotic cells Bacteria accumulate K+ by a number of different transport systems that vary in kinetics, energy coupling, and regulation The Trk and Kdp systems of enteric organisms have been well studied and are found in many distantly related species The Ktr system, resembling Trk in many ways, is also found in many bacteria In most species two or more independent saturable K(+)-transport systems are present The KefB and KefC type of system that is activated by treatment of cells with toxic electrophiles is the only specific K(+)-efflux system that has been well characterized Pressure-activated channels of at least three types are found in bacteria; these represent nonspecific paths of efflux when turgor pressure is dangerously high A close homolog of eucaryotic K+ channels is found in many bacteria, but its role remains obscure K+ transporters are regulated both by ion concentrations and turgor A very general property is activation of K+ uptake by an increase in medium osmolarity This response is modulated by both internal and external concentrations of K+ Kdp is the only K(+)-transport system whose expression is regulated by environmental conditions Decrease in turgor pressure and/or reduction in external K+ rapidly increase expression of Kdp The signal created by these changes, inferred to be reduced turgor, is transmitted by the KdpD sensor kinase to the KdpE-response regulator that in turn stimulates transcription of the kdp genes K+ acts as a cytoplasmic-signaling molecule, activating and/or inducing enzymes and transport systems that allow the cell to adapt to elevated osmolarity The signal could be ionic strength or specifically K+ This signaling response is probably mediated by a direct sensing of internal ionic strength by each particular system and not by a component or system that coordinates this response by different systems to elevated K+

The roles and regulation of potassium in bacteria.

The abundant existence of proteins and regions that possess specific functions without being uniquely folded into unique 3D structures has become accepted by a significant number of protein scientists. Sequences of these intrinsically disordered proteins (IDPs) and IDP regions (IDPRs) are characterized by a number of specific features, such as low overall hydrophobicity and high net charge which makes these proteins predictable. IDPs/IDPRs possess large hydrodynamic volumes, low contents of ordered secondary structure, and are characterized by high structural heterogeneity. They are very flexible, but some may undergo disorder to order transitions in the presence of natural ligands. The degree of these structural rearrangements varies over a very wide range. IDPs/IDPRs are tightly controlled under the normal conditions and have numerous specific functions that complement functions of ordered proteins and domains. When lacking proper control, they have multiple roles in pathogenesis of various human diseases. Gaining structural and functional information about these proteins is a challenge, since they do not typically “freeze” while their “pictures are taken.” However, despite or perhaps because of the experimental challenges, these fuzzy objects with fuzzy structures and fuzzy functions are among the most interesting targets for modern protein research. This review briefly summarizes some of the recent advances in this exciting field and considers some of the basic lessons learned from the analysis of physics, chemistry, and biology of IDPs.

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A decade and a half of protein intrinsic disorder: Biology still waits for physics

It is now clear that the understanding of halophilic adaptation at a molecular level requires a strategy of complementary experiments, combining molecular biology, biochemistry, and cellular approaches with physical chemistry and thermodynamics. In this review, after a discussion of the definition and composition of halophilic enzymes, the effects of salt on their activity, solubility, and stability are reviewed. We then describe how thermodynamic observations, such as parameters pertaining to solvent-protein interactions or enzyme-unfolding kinetics, depend strongly on solvent composition and reveal the important role played by water and ion binding to halophilic proteins. The three high-resolution crystal structures now available for halophilic proteins are analyzed in terms of haloadaptation, and finally cellular response to salt stress is discussed briefly.

Halophilic adaptation of enzymes.

l-Malate (MalDH) and l-lactate (LDH) dehydrogenases belong to the same family of NAD-dependent enzymes. To gain insight into molecular relationships within this family, we studied two hyperthermophilic (LDH-like) l-MalDH (proteins with LDH-like structure and MalDH enzymatic activity) from the archaea Archaeoglobus fulgidus (Af) and Mehanococcus jannaschii (Mj). The structural parameters of these enzymes determined by neutron scattering and analytical centrifugation showed that the Af (LDH-like) l-MalDH is a dimer whereas the Mj (LDH-like) l-MalDH is a tetramer. The effects of high temperature, cofactor binding, and high phosphate concentration were studied. They did not modify the oligomeric state of either enzyme. The enzymatic activity of the dimeric Af (LDH-like) l-MalDH is controlled by a pH-dependent transition at pH 7 without dissociation of the subunits. The data were analyzed in the light of the crystallographic structure of the LDH-like l-MalDH from Haloarcula marismortui. This showed that a spec...

C. Ebel

Papers

Halophilic adaptation of enzymes.

Differences in the oligomeric states of the LDH-like L-MalDH from the hyperthermophilic archaea Methanococcus jannaschii and Archaeoglobus fulgidus.