Amino acid substitutions in malate dehydrogenases of piezophilic bacteria isolated from intestinal contents of deep-sea fishes retrieved from the abyssal zone

Environmental Adaptation of Dihydrofolate Reductase from Deep-Sea Bacteria

In order to elucidate the molecular adaptation mechanisms of enzymes to the high hydrostatic pressure of the deep sea, we cloned, purified, and characterized more than ten dihydrofolate reductases (DHFRs) from bacteria living in deep-sea and ambient atmospheric pressure environments. The nucleotide and amino acid sequences of these DHFRs indicate the deep-sea bacteria are adapted to their environments after the differentiation of their genus from ancestors inhabiting atmospheric pressure environments. In particular, the backbone structure of the deep-sea DHFR from Moritella profunda (mpDHFR) almost overlapped with the normal homolog from Escherichia coli (ecDHFR). Thus, those of other DHFRs would also overlap on the basis of their sequence similarities. However, the structural stability of both DHFRs was quite different: compared to ecDHFR, mpDHFR was more thermally stable but less stable against urea and pressure unfolding. The smaller volume changes due to unfolding suggest that the native structure of mpDHFR has a smaller cavity and/or enhanced hydration compared to ecDHFR. High hydrostatic pressure reduced the enzymatic activity of many DHFRs, but three deep-sea DHFRs and the D27E mutant of ecDHFR exhibited pressure-dependent activation. The inverted activation volumes from positive to negative values indicate the modification of their structural dynamics, conversion of the rate-determining step of the enzymatic reaction, and different contributions of the cavity and hydration to the transition-state structure. Since the cavity and hydration depend on amino acid side chains, DHFRs would adapt to the deep-sea environment by regulating the cavity and hydration by substituting their amino acid side chains without altering their backbone structure. The results of this study clearly indicate that the cavity and hydration play important roles in the adaptation of enzymes to the deep-sea environment.

Thermodynamic and functional characteristics of deep-sea enzymes revealed by pressure effects

Hydrostatic pressure analysis is an ideal approach for studying protein dynamics and hydration. The development of full ocean depth submersibles and high pressure biological techniques allows us to investigate enzymes from deep-sea organisms at the molecular level. The aim of this review was to overview the thermodynamic and functional characteristics of deep-sea enzymes as revealed by pressure axis analysis after giving a brief introduction to the thermodynamic principles underlying the effects of pressure on the structural stability and function of enzymes.

Introduction to high-pressure bioscience and biotechnology

The manipulation of biological materials using elevated pressure is providing an ever-growing number of opportunities in both the applied and basic sciences. Manipulation of pressure is a useful parameter for enhancing food quality and shelf life; inactivating microbes, viruses, prions, and deleterious enzymes; affecting recombinant protein production; controlling DNA hybridization; and improving vaccine preparation. In biophysics and biochemistry, pressure is used as a tool to study intermediates in protein folding, enzyme kinetics, macromolecular interactions, amyloid fibrous protein aggregation, lipid structural changes, and to discern the role of solvation and void volumes in these processes. Biologists, including many microbiologists, examine the utility and basis of pressure inactivation of cells and cellular processes, and conversely seek to discover how deep-sea life has evolved a preference for high-pressure environments. This introduction and the papers that follow provide information on the nature and promise of the highly interdisciplinary field of high-pressure bioscience and biotechnology (HPBB).