Protein adaptations in archaeal extremophiles

Abstract

Extremophiles, especially those in Archaea, have a myriad of adaptations that keep their cellular proteins stable and active under the extreme conditions in which they live. Rather than having one basic set of adaptations that works for all environments, Archaea have evolved separate protein features that are customized for each environment. We categorized the Archaea into three general groups to describe what is known about their protein adaptations: thermophilic, psychrophilic, and halophilic. Thermophilic proteins tend to have a prominent hydrophobic core and increased electrostatic interactions to maintain activity at high temperatures. Psychrophilic proteins have a reduced hydrophobic core and a less charged protein surface to maintain flexibility and activity under cold temperatures. Halophilic proteins are characterized by increased negative surface charge due to increased acidic amino acid content and peptide insertions, which compensates for the extreme ionic conditions. While acidophiles, alkaliphiles, and piezophiles are their own class of Archaea, their protein adaptations toward pH and pressure are less discernible. By understanding the protein adaptations used by archaeal extremophiles, we hope to be able to engineer and utilize proteins for industrial, environmental, and biotechnological applications where function in extreme conditions is required for activity.

Figure 1

Graphical view of cysteinyl-tRNA synthetase with extremophilic protein adaptations. The homology models of Halobacterium salinarum (Hs), Pyrococcus furiosus (Pf), and Methanolobus psychrophilus (Mp) CysRS were generated based on the structure of Escherichia coli CysRS (see text for details). In the upper corner, the crystal structure of the Ec CysRS (PDB 1U0B, [10]) is provided for orientation and description of the enzyme's features. (a) and (c) Coulombic surface map of the models on the tRNA side and back of the molecule, respectively. The Coulombic surface maps the amino acid electrostatic potential (according to Coulomb's law) on surface residues: red is a negative potential, blue is a positive potential, and white indicates a relatively nonpolar potential. (b) and (d) The conserved features (in green) and unique adaptations highlighted on the surface of the models on the tRNA side and back of the molecule, respectively. The corresponding adaptations have been noted in the sequence alignment in Figure  S1 (See Figure S1 in the Supplementary Material available online at http://dx.doi.org/10.1155/2013/373275). Unique features are highlighted in different colors for the different extremes: halophilic adaptations are in pink, the thermophilic adaptations are in red, and the psychrophile adaptations are in blue. The molecular graphics were created with the USCF Chimera package [11].