Pressure Adaptations in Deep-Sea Moritella Dihydrofolate Reductases: Compressibility versus Stability.

Ryan W Penhallurick,Toshiko Ichiye

doi:10.3390/biology10111211

Abstract

Simple SummaryDeep-sea organisms must have proteins that function under high hydrostatic pressure to survive. Adaptations used in proteins from “pressure-loving” piezophiles may include greater compressibility or greater stability against pressure-induced destabilization. However, while greater compressibility can be accomplished by greater void volume, larger cavities in a protein have been associated with greater destabilization and even unfolding as pressure is increased. Here, computer simulations of dihydrofolate reductase from a moderate piezophile and a hyperpiezophile were performed to understand the balance between adaptations for greater compressibility and those against pressure destabilization and unfolding. The results indicate that while compressibility appears to be important for deep-sea microbes, adaptation for the greatest depths may be to prevent water penetration into the interior.Proteins from “pressure-loving” piezophiles appear to adapt by greater compressibility via larger total cavity volume. However, larger cavities in proteins have been associated with lower unfolding pressures. Here, dihydrofolate reductase (DHFR) from a moderate piezophile Moritella profunda (Mp) isolated at ~2.9 km in depth and from a hyperpiezophile Moritella yayanosii (My) isolated at ~11 km in depth were compared using molecular dynamics simulations. Although previous simulations indicate that MpDHFR is more compressible than a mesophile DHFR, here the average properties and a quasiharmonic analysis indicate that MpDHFR and MyDHFR have similar compressibilities. A cavity analysis also indicates that the three unique mutations in MyDHFR are near cavities, although the cavities are generally similar in size in both. However, while a cleft overlaps an internal cavity, thus forming a pathway from the surface to the interior in MpDHFR, the unique residue Tyr103 found in MyDHFR forms a hydrogen bond with Leu78, and the sidechain separates the cleft from the cavity. Thus, while Moritella DHFR may generally be well suited to high-pressure environments because of their greater compressibility, adaptation for greater depths may be to prevent water entry into the interior cavities.

Highlights

IntroductionThe discovery of life thriving under extreme conditions of temperature, pressure, and composition has led to intriguing questions about the limits at which life can survive
The discovery of life thriving under extreme conditions of temperature, pressure, and composition has led to intriguing questions about the limits at which life can survive.Mechanisms used by “extremophiles” to adapt their biological macromolecules to these extremes could assist in our understanding of these limits of life
Discussion between MpDHFR and MyDHFR. While both MpDHFR and MyDHFR are both exPressure to compressibilities a decreased total volume of the system, which occur bywith decreaspected to haveleads larger compared to EcDHFR, this iscan consistent the ing the total cavity volume or increasing the hydration of cavities

Summary

Introduction

The discovery of life thriving under extreme conditions of temperature, pressure, and composition has led to intriguing questions about the limits at which life can survive. Mechanisms used by “extremophiles” to adapt their biological macromolecules to these extremes could assist in our understanding of these limits of life. Studies of extremophiles have largely focused on temperature adaptation. The corresponding states hypothesis that enzyme activity is high near the growth conditions (i.e., growth temperature TG and growth pressure PG ) of the microbe [2] and that maximal activity is achieved by balancing the stability and flexibility of the protein [3] is mainly based on studies of homologous enzymes of temperature-adapted microbes. Less is understood about adaptations to high hydrostatic pressure largely due to limited access to extreme oceanic depths until recently. Since about 88% of the ocean has biologically high pressures, comprising the largest portion of the biosphere [4,5], and “piezophiles”

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