Adaptation of Extremophilic Proteins with Temperature and Pressure: Evidence from Initiation Factor 6

Mesophilic Pyrophosphatase Function at High Temperature: A Molecular Dynamics Simulation Study

The mesophilic inorganic pyrophosphatase from Escherichia coli (EcPPase) retains function at 353 K, the physiological temperature of hyperthermophilic Thermococcus thioreducens, whereas the homolog protein (TtPPase) from this hyperthermophilic organism cannot function at room temperature. To explain this asymmetric behavior, we examined structural and dynamical properties of the two proteins using molecular dynamics simulations. The global flexibility of TtPPase is significantly higher than its mesophilic homolog at all tested temperature/pressure conditions. However, at 353 K, EcPPase reduces its solvent-exposed surface area and increases subunit compaction while maintaining flexibility in its catalytic pocket. In contrast, TtPPase lacks this adaptability and has increased rigidity and reduced protein/water interactions in its catalytic pocket at room temperature, providing a plausible explanation for its inactivity near room temperature.

Insights into high-pressure acclimation: comparative transcriptome analysis of sea cucumber Apostichopus japonicus at different hydrostatic pressure exposures

Background

Global climate change is predicted to force the bathymetric migrations of shallow-water marine invertebrates. Hydrostatic pressure is proposed to be one of the major environmental factors limiting the vertical distribution of extant marine invertebrates. However, the high-pressure acclimation mechanisms are not yet fully understood.

Results

In this study, the shallow-water sea cucumber Apostichopus japonicus was incubated at 15 and 25 MPa at 15 °C for 24 h, and subjected to comparative transcriptome analysis. Nine samples were sequenced and assembled into 553,507 unigenes with a N50 length of 1204 bp. Three groups of differentially expressed genes (DEGs) were identified according to their gene expression patterns, including 38 linearly related DEGs whose expression patterns were linearly correlated with hydrostatic pressure, 244 pressure-sensitive DEGs which were up-regulated at both 15 and 25 MPa, and 257 high-pressure-induced DEGs which were up-regulated at 25 MPa but not up-regulated at 15 MPa.

Conclusions

Our results indicated that the genes and biological processes involving high-pressure acclimation are similar to those related to deep-sea adaptation. In addition to representative biological processes involving deep-sea adaptation (such as antioxidation, immune response, genetic information processing, and DNA repair), two biological processes, namely, ubiquitination and endocytosis, which can collaborate with each other and regulate the elimination of misfolded proteins, also responded to high-pressure exposure in our study. The up-regulation of these two processes suggested that high hydrostatic pressure would lead to the increase of misfolded protein synthesis, and this may result in the death of shallow-water sea cucumber under high-pressure exposure.

Dynamics of proteins in solution

The dynamics of proteins in solution includes a variety of processes, such as backbone and side-chain fluctuations, interdomain motions, as well as global rotational and translational (i.e. center of mass) diffusion. Since protein dynamics is related to protein function and essential transport processes, a detailed mechanistic understanding and monitoring of protein dynamics in solution is highly desirable. The hierarchical character of protein dynamics requires experimental tools addressing a broad range of time- and length scales. We discuss how different techniques contribute to a comprehensive picture of protein dynamics, and focus in particular on results from neutron spectroscopy. We outline the underlying principles and review available instrumentation as well as related analysis frameworks.

Fractional electron transfer kinetics and a quantum breaking of ergodicity

The dissipative curve-crossing problem provides a paradigm for electron-transfer (ET) processes in condensed media. It establishes the simplest conceptual test bed to study the influence of the medium's dynamics on ET kinetics both on the ensemble level, and on the level of single particles. Single electron description is particularly important for nanoscaled systems like proteins, or molecular wires. Especially insightful is this framework in the semiclassical limit, where the environment can be treated classically, and an exact analytical treatment becomes feasible. Slow medium's dynamics is capable of enslaving ET and bringing it on the ensemble level from a quantum regime of nonadiabatic tunneling to the classical adiabatic regime, where electrons follow the nuclei rearrangements. This classical adiabatic textbook picture contradicts, however, in a very spectacular fashion to the statistics of single electron transitions, even in the Debye, memoryless media, also named Ohmic in the parlance of the famed spin-boson model. On the single particle level, ET always remains quantum, and this was named a quantum breaking of ergodicity in the adiabatic ET regime. What happens in the case of subdiffusive, fractional, or sub-Ohmic medium's dynamics, which is featured by power-law decaying dynamical memory effects typical, e.g., for protein macromolecules, and other viscoelastic media? Such a memory is vividly manifested by anomalous Cole-Cole dielectric response in such media. We address this question based both on accurate numerics and analytical theory. The ensemble theory remarkably agrees with the numerical dynamics of electronic populations, revealing a power-law relaxation tail even in a profoundly nonadiabatic electron transfer regime. In other words, ET in such media should typically display fractional kinetics. However, a profound difference with the numerically accurate results occurs for the distribution of residence times in the electronic states, both on the ensemble level and the level of single trajectories. Ergodicity is broken dynamically even in a more spectacular way than in the memoryless case. Our results question the applicability of all the existing and widely accepted ensemble theories of electron transfer in fractional, sub-Ohmic environments, on the level of single molecules, and provide a real challenge to face, both for theorists and experimentalists.

Comparative transcriptome analysis of Eogammarus possjeticus at different hydrostatic pressure and temperature exposures

Hydrostatic pressure is an important environmental factor affecting the vertical distribution of marine organisms. Laboratory-based studies have shown that many extant shallow-water marine benthic invertebrates can tolerate hydrostatic pressure outside their known natural distributions. However, only a few studies have focused on the molecular mechanisms of pressure acclimatisation. In the present work, we examined the pressure tolerance of the shallow-water amphipod Eogammarus possjeticus at various temperatures (5, 10, 15, and 20 °C) and hydrostatic pressures (0.1–30 MPa) for 16 h. Six of these experimental groups were used for transcriptome analysis. We found that 100% of E. possjeticus survived under 20 MPa at all temperature conditions for 16 h. Sequence assembly resulted in 138, 304 unigenes. Results of differential expression analysis revealed that 94 well-annotated genes were up-regulated under high pressure. All these findings indicated that the pressure tolerance of E. possjeticus was related to temperature. Several biological processes including energy metabolism, antioxidation, immunity, lipid metabolism, membrane-related process, genetic information processing, and DNA repair are probably involved in the acclimatisation in deep-sea environments.

Misprediction of Structural Disorder in Halophiles

Whereas the concept of intrinsic disorder derives from biophysical observations of the lack of structure of proteins or protein regions under native conditions, many of our respective concepts rest on proteome-scale bioinformatics predictions. It is established that most predictors work reliably on proteins commonly encountered, but it is often neglected that we know very little about their performance on proteins of microorganisms that thrive in environments of extreme temperature, pH, or salt concentration, which may cause adaptive sequence composition bias. To address this issue, we predicted structural disorder for the complete proteomes of different extremophile groups by popular prediction methods and compared them to those of the reference mesophilic group. While significant deviations from mesophiles could be explained by a lack or gain of disordered regions in hyperthermophiles and radiotolerants, respectively, we found systematic overprediction in the case of halophiles. Additionally, examples were collected from the Protein Data Bank (PDB) to demonstrate misprediction and to help understand the underlying biophysical principles, i.e., halophilic proteins maintain a highly acidic and hydrophilic surface to avoid aggregation in high salt conditions. Although sparseness of data on disordered proteins from extremophiles precludes the development of dedicated general predictors, we do formulate recommendations for how to address their disorder with current bioinformatics tools.

Deciphering the rationale behind specific codon usage pattern in extremophiles

Protein stability is affected at different hierarchies – gene, RNA, amino acid sequence and structure. Gene is the first level which contributes via varying codon compositions. Codon selectivity of an organism differs with normal and extremophilic milieu. The present work attempts at detailing the codon usage pattern of six extremophilic classes and their harmony. Homologous gene datasets of thermophile-mesophile, psychrophile-mesophile, thermophile-psychrophile, acidophile-alkaliphile, halophile-nonhalophile and barophile-nonbarophile were analysed for filtering statistically significant attributes. Relative abundance analysis, 1–9 scale ranking, nucleotide compositions, attribute weighting and machine learning algorithms were employed to arrive at findings. AGG in thermophiles and barophiles, CAA in mesophiles and psychrophiles, TGG in acidophiles, GAG in alkaliphiles and GAC in halophiles had highest preference. Preference of GC-rich and G/C-ending codons were observed in halophiles and barophiles whereas, a decreasing trend was reflected in psychrophiles and alkaliphiles. GC-rich codons were found to decrease and G/C-ending codons increased in thermophiles whereas, acidophiles showed equal contents of GC-rich and G/C-ending codons. Codon usage patterns exhibited harmony among different extremophiles and has been detailed. However, the codon attribute preferences and their selectivity of extremophiles varied in comparison to non-extremophiles. The finding can be instrumental in codon optimization application for heterologous expression of extremophilic proteins.

Viscoelastic subdiffusion in a random Gaussian environment

Viscoelastic subdiffusion governed by a fractional Langevin equation is studied numerically in a random Gaussian environment modeled by stationary Gaussian potentials with decaying spatial correlations. This anomalous diffusion is archetypal for living cells, where cytoplasm is known to be viscoelastic and a spatial disorder also naturally emerges. We obtain some first important insights into it within a model one-dimensional study. Two basic types of potential correlations are studied: short-range exponentially decaying and algebraically slow decaying with an infinite correlation length, both for a moderate (several k_BT, in the units of thermal energy), and strong (5-10k_BT) disorder. For a moderate disorder, it is shown that on the ensemble level viscoelastic subdiffusion can easily overcome the medium's disorder. Asymptotically, it is not distinguishable from the disorder-free subdiffusion. However, a strong scatter in single-trajectory averages is nevertheless seen even for a moderate disorder. It features a weak ergodicity breaking, which occurs on a very long yet transient time scale. Furthermore, for a strong disorder, a very long transient regime of logarithmic, Sinai-type diffusion emerges. It can last longer and be faster in the absolute terms for weakly decaying correlations as compared with the short-range correlations. Residence time distributions in a finite spatial domain are of a generalized log-normal type and are reminiscent also of a stretched exponential distribution. They can be easily confused for power-law distributions in view of the observed weak ergodicity breaking. This suggests a revision of some experimental data and their interpretation.

Effects of pressure on the dynamics of an oligomeric protein from deep-sea hyperthermophile

Inorganic pyrophosphatase (IPPase) from Thermococcus thioreducens is a large oligomeric protein derived from a hyperthermophilic microorganism that is found near hydrothermal vents deep under the sea, where the pressure is up to 100 MPa (1 kbar). It has attracted great interest in biophysical research because of its high activity under extreme conditions in the seabed. In this study, we use the quasielastic neutron scattering (QENS) technique to investigate the effects of pressure on the conformational flexibility and relaxation dynamics of IPPase over a wide temperature range. The β-relaxation dynamics of proteins was studied in the time ranges from 2 to 25 ps, and from 100 ps to 2 ns, using two spectrometers. Our results indicate that, under a pressure of 100 MPa, close to that of the native environment deep under the sea, IPPase displays much faster relaxation dynamics than a mesophilic model protein, hen egg white lysozyme (HEWL), at all measured temperatures, opposite to what we observed previously under ambient pressure. This contradictory observation provides evidence that the protein energy landscape is distorted by high pressure, which is significantly different for hyperthermophilic (IPPase) and mesophilic (HEWL) proteins. We further derive from our observations a schematic denaturation phase diagram together with energy landscapes for the two very different proteins, which can be used as a general picture to understand the dynamical properties of thermophilic proteins under pressure.