Adaptations of proteins, RNA and DNA to extreme temperatures, salinity and pH.

Extremophiles are organisms that withstand harsh environmental conditions with extreme temperatures, ranges of pH, or high salt concentrations. Their enzymes are used for industrial purposes, where severe conditions prevail. Although many studies have been carried out on adaptations to temperature, pH, or salinity in isolation, no research has accessed the multiple environmental factors adaptation simultaneously. This study aimed to simultaneously resolve the mechanisms of adaptation between extreme temperature, pH, and salinity on the proteome and genome levels. Our total dataset comprised of 9306 prokaryotic organisms, where optimal growth temperatures vary from 3 to 105 °C, pH scale from 1.1 to 12, and salt concentrations as high as 34.5% NaCl. We have determined amino acid combinations that serve as a predictor of protein thermostability, salt, and pH adaptation. The principal component analysis shows that certain amino acid properties were found to be beneficial for several types of extreme adaptations. One of the examples is the negatively charged amino acids that were found to be important in both temperature and salinity adaptation. We show that some amino acid properties are beneficial for adaptation only to certain environments and are unfavorable in other types of adaptations. For example, the positively charged amino acids and hydrophobic amino acids that are useful for high-temperature adaptation are not working in the same way in high-salt adaptation. We also explore the relationship between the adaptation of proteins and nucleic acids (DNA and RNA), showing the causality or independence of observed signals on each level. On the nucleic acid level, we have found the differences in mechanistic adaptations to extreme environments between DNA and RNA.