Pressure-Induced Alterations in the Protein Pattern of the Thermophilic Archaebacterium Methanococcus thermolithotrophicus

High-Pressure Microfluidics for Ultra-Fast Microbial Phenotyping

Here, we present a novel methodology based on high-pressure microfluidics to rapidly perform temperature-based phenotyping of microbial strains from deep-sea environments. The main advantage concerns the multiple on-chip temperature conditions that can be achieved in a single experiment at pressures representative of the deep-sea, overcoming the conventional limitations of large-scale batch metal reactors to conduct fast screening investigations. We monitored the growth of the model strain Thermococcus barophilus over 40 temperature and pressure conditions, without any decompression, in only 1 week, whereas it takes weeks or months with conventional approaches. The results are later compared with data from the literature. An additional example is also shown for a hydrogenotrophic methanogen strain (Methanothermococcus thermolithotrophicus), demonstrating the robustness of the methodology. These microfluidic tools can be used in laboratories to accelerate characterizations of new isolated species, changing the widely accepted paradigm that high-pressure microbiology experiments are time-consuming.

Effects of hydrostatic pressure on growth of hyperthermophilic archaebacteria from the juan de fuca ridge

Two new strains (AL1 and AL2) of hyperthermophilic, sulfur-reducing, heterotrophic archaebacteria from high-temperature (350 degrees C) vents on the Juan de Fuca Ridge were highly barotolerant at their optimal growth temperatures (90 and 100 degrees C, respectively). A trend towards barophily at pressures greater than those encountered in situ at the sea floor was demonstrated for the more extremely thermophilic strain (AL2), implying an ability to thrive in (unexplored) habitats well below accessible vent formations.

Effects of hyperbaric pressure on a deep-sea archaebacterium in stainless steel and glass-lined vessels

The effects of hyperbaric helium pressures on the growth and metabolism of the deep-sea isolate ES4 were investigated. In a stainless steel reactor, cell growth was completely inhibited but metabolic gas production was observed. From 85 to 100 degrees C, CO(2) production proceeded two to three times faster at 500 atm (1 atm = 101.29 kPa) than at 8 atm. At 105 degrees C, no CO(2) was produced until the pressure was increased to 500 atm. Hydrogen and H(2)S were also produced biotically but were not quantifiable at pressures above 8 atm because of the high concentration of helium. In a glass-lined vessel, growth occurred but the growth rate was not accelerated by pressure. In most cases at temperatures below 100 degrees C, the growth rate was lower at elevated pressures; at 100 degrees C, the growth rates at 8, 250, and 500 atm were nearly identical. Unlike in the stainless steel vessel, CO(2) production was exponential during growth and continued for only a short time after growth. In addition, relatively little H(2) was produced in the glass-lined vessel, and there was no growth or gas production at 105 degrees C at any pressure. The behavior of ES4 as a function of temperature and pressure was thus very sensitive to the experimental conditions.

Protein synthesis in lactic acid and pathogenic bacteria during recovery from a high pressure treatment

Recovery of injured bacteria after high hydrostatic pressure (HHP) treatment is a key point in food safety. In this study, protein synthesis during the recovery of meat environment bacteria Listeria monocytogenes CTC1011, Lactobacillus sakei 23K, L. sakei CTC494, Enterococcus faecalis CTC6365 and Enterococcus faecium CTC6375 after a 400 MPa HHP treatment was analyzed by two-dimensional gel electrophoresis and peptide mass fingerprinting. After 2 h recovery from HHP treatment, the four species induced transcription factors and proteins related to protein synthesis or fate and enzymes from energy metabolism. However, several stress proteins were specifically induced in the two L. sakei strains. Proteins from the general metabolism predominated in E. faecalis and E. faecium, and stress proteins and proteases predominated in L. monocytogenes. Thus, each species induced a different number of proteins and displayed a specific response which may reflect its specific fitness status.

High pressure effects step-wise altered protein expression in Lactobacillus sanfranciscensis

In this study we investigated the cellular response to the application of high hydrostatic pressure. High pressure is increasingly used for food preservation. With high resolution 2-D electrophoresis we compared the protein patterns of atmospherically grown Lactobacillus sanfranciscensis with those pressure treated up to 200 MPa. We performed the comparative study by using overlapping immobilized pH gradients covering the pH range from 2.5 up to 12 in order to maximize the resolution for the detection of stress relevant proteins. For improved quantitative analysis, staining with SyproRuby was used in addition to silver staining. By computer aided image analysis we detected more than a dozen spots within the pH range from 3.5 to 9 that were more than two-fold increased or 50% decreased in their intensity upon high pressure treatment. Two of them (approx. values: pI 4.0 and 4.2, respectively; M(r) approximately 15 000) have almost identical matrix-assisted laser desorption/ionization-time of flight mass spectrometry spectra and were identified by liquid chromatography-tandem mass spectrometry as putative homologs/paralogs to cold shock proteins of Lactococcus lactis. Their expression is opposed (i.e. the more acidic one is repressed, while the other one is induced); this effect is maximal at 1 h, 150 MPa. It was further remarkable that by monitoring the barosensitivity of the cells within 25 MPa steps, we observed a differential pressure induction or repression of the detected proteins as well. For example one protein (approx. values: pI 4.2, M(r) approximately 15 000) shows a maximum induction after 1 h, 150 MPa while another one (pI 7.5, M(r) approximately 25 000) is maximally induced after 1 h, 50/75 MPa. This indicates a successive cell response and different signalling pathways for these responses.

Stress genes and proteins in the archaea

The field covered in this review is new; the first sequence of a gene encoding the molecular chaperone Hsp70 and the first description of a chaperonin in the archaea were reported in 1991. These findings boosted research in other areas beyond the archaea that were directly relevant to bacteria and eukaryotes, for example, stress gene regulation, the structure-function relationship of the chaperonin complex, protein-based molecular phylogeny of organisms and eukaryotic-cell organelles, molecular biology and biochemistry of life in extreme environments, and stress tolerance at the cellular and molecular levels. In the last 8 years, archaeal stress genes and proteins belonging to the families Hsp70, Hsp60 (chaperonins), Hsp40(DnaJ), and small heat-shock proteins (sHsp) have been studied. The hsp70(dnaK), hsp40(dnaJ), and grpE genes (the chaperone machine) have been sequenced in seven, four, and two species, respectively, but their expression has been examined in detail only in the mesophilic methanogen Methanosarcina mazei S-6. The proteins possess markers typical of bacterial homologs but none of the signatures distinctive of eukaryotes. In contrast, gene expression and transcription initiation signals and factors are of the eucaryal type, which suggests a hybrid archaeal-bacterial complexion for the Hsp70 system. Another remarkable feature is that several archaeal species in different phylogenetic branches do not have the gene hsp70(dnaK), an evolutionary puzzle that raises the important question of what replaces the product of this gene, Hsp70(DnaK), in protein biogenesis and refolding and for stress resistance. Although archaea are prokaryotes like bacteria, their Hsp60 (chaperonin) family is of type (group) II, similar to that of the eukaryotic cytosol; however, unlike the latter, which has several different members, the archaeal chaperonin system usually includes only two (in some species one and in others possibly three) related subunits of approximately 60 kDa. These form, in various combinations depending on the species, a large structure or chaperonin complex sometimes called the thermosome. This multimolecular assembly is similar to the bacterial chaperonin complex GroEL/S, but it is made of only the large, double-ring oligomers each with eight (or nine) subunits instead of seven as in the bacterial complex. Like Hsp70(DnaK), the archaeal chaperonin subunits are remarkable for their evolution, but for a different reason. Ubiquitous among archaea, the chaperonins show a pattern of recurrent gene duplication-hetero-oligomeric chaperonin complexes appear to have evolved several times independently. The stress response and stress tolerance in the archaea involve chaperones, chaperonins, other heat shock (stress) proteins including sHsp, thermoprotectants, the proteasome, as yet incompletely understood thermoresistant features of many molecules, and formation of multicellular structures. The latter structures include single- and mixed-species (bacterial-archaeal) types. Many questions remain unanswered, and the field offers extraordinary opportunities owing to the diversity, genetic makeup, and phylogenetic position of archaea and the variety of ecosystems they inhabit. Specific aspects that deserve investigation are elucidation of the mechanism of action of the chaperonin complex at different temperatures, identification of the partners and substitutes for the Hsp70 chaperone machine, analysis of protein folding and refolding in hyperthermophiles, and determination of the molecular mechanisms involved in stress gene regulation in archaeal species that thrive under widely different conditions (temperature, pH, osmolarity, and barometric pressure). These studies are now possible with uni- and multicellular archaeal models and are relevant to various areas of basic and applied research, including exploration and conquest of ecosystems inhospitable to humans and many mammals and plants.

Physiological Responses to Stress Conditions and Barophilic Behavior of the Hyperthermophilic Vent Archaeon Pyrococcus abyssi

The physiology of the deep-sea hyperthermophilic, anaerobic vent archaeon Pyrococcus abyssi, originating from the Fiji Basin at a depth of 2,000 m, was studied under diverse conditions. The emphasis of these studies lay in the growth and survival of this archaeon under the different conditions present in the natural habitat. Incubation under in situ pressure (20 MPa) and at 40 MPa increased the maximal and minimal growth temperatures by 4(deg)C. In situ pressure enhanced survival at a lethal high temperature (106 to 112(deg)C) relative to that at low pressure (0.3 MPa). The whole-cell protein profile, analyzed by one-dimensional sodium dodecyl sulfate gel electrophoresis, did not change in cultures grown under low or high pressure at optimal and minimal growth temperatures, but several changes were observed at the maximal growth temperature under in situ pressure. The complex lipid pattern of P. abyssi grown under in situ and 0.1- to 0.5-MPa pressures at different temperatures was analyzed by thin-layer chromatography. The phospholipids became more complex at a low growth temperature at both pressures but their profiles were not superimposable; fewer differences were observed in the core lipids. The polar lipids were composed of only one phospholipid in cells grown under in situ pressure at high temperatures. Survival in the presence of oxygen and under starvation conditions was examined. Oxygen was toxic to P. abyssi at growth range temperature, but the strain survived for several weeks at 4(deg)C. The strain was not affected by starvation in a minimal medium for at least 1 month at 4(deg)C and only minimally affected at 95(deg)C for several days. Cells were more resistant to oxygen in starvation medium. A drastic change in protein profile, depending on incubation time, was observed in cells when starved at growth temperature.

High pressure influences on gene and protein expression

Elevated hydrostatic pressure can influence gene and protein expression in both 1 atmosphere-adapted and high pressure-adapted microorganisms. Here we review experiments documenting these effects and describe their significance towards understanding the molecular bases of life in deep-sea high pressure environments.

Hydrostatic pressure promotes the acidification of vacuoles in Saccharomyces cerevisiae

Application of hydrostatic pressure caused a delay or cessation of cell growth in Saccharomyces cerevisiae. The yeast vacuole is an acidic organelle involved in cellular ion homeostasis and degradation of proteins. Hydrostatic pressure promoted the acidification of the vacuoles in the strain IFO 2347. A pressure of 40 to 60 MPa reduced the vacuolar pH, defined using 6-carboxyfluorescein, from 6.05 to 5.88, while a pressure of 20 MPa did not affect the pH. Similar results were obtained with the strain X2180. Bafilomycin A1, a specific inhibitor of vacuolar H(+)-ATPase (V-H(+)-ATPase), caused a significant alkalization of vacuoles in the strain X2180. The pHs rose to 7.34 and 6.84 at both atmospheric pressure and a pressure of 40 MPa, respectively. Meanwhile, vacuolar accumulation of the weak base quinacrine was increased by a pressure of 40 MPa, suggesting that uptake of the dye was induced by the increased pH gradient across the vacuolar membrane.

Response of bacteria and fungi to high-pressure stress as investigated by two-dimensional polyacrylamide gel electrophoresis

In an attempt to generalize previous observations (Jaenicke et al., Appl. Environ. Microbiol. 1988, 54, 2375-2380) and to find a convenient model system for studies of the pressure response, we tested the suitability of Escherichia coli and Thermotoga maritima (bacteria), and of five different eukaryotic species including the filamentous fungi Asteromyces cruciatus and Dendryphiella salina, and the marine yeasts Debaryomyces hansenii, Rhodosporidium sphaerocarpum, and Rhodotorula rubra. Using two-dimensional polyacrylamide gel electrophoresis, detailed investigations on the pressure response were carried out with E. coli and Rhodosporidium sphaerocarpum. In the former organism, major pressure response proteins could not be detected, although there are significant differences in expression of some proteins as well as some minor components that are found in all of the high pressure cell extracts but not in extracts from cultures grown at atmospheric pressure. In Rhodosporidium sphaerocarpum, no change in protein expression patterns was observed between 0.1 and 20 MPa. However, approaching the limit of viability of 50 MPa, additional protein spots became detectable at 45 MPa. This finding correlates with the observation of abnormal growth forms of the organism at this pressure (Lorenz, R. et al. manuscript in preparation).

Proteins under pressure. The influence of high hydrostatic pressure on structure, function and assembly of proteins and protein complexes

Oceans not only cover the major part of the earth's surface but also reach into depths exceeding the height of the Mt Everest. They are populated down to the deepest levels (approximately 11,800 m), which means that a significant proportion of the global biosphere is exposed to pressures of up to 120 MPa. Although this fact has been known for more than a century, the ecology of the 'abyss' is still in its infancy. Only recently, barophilic adaptation, i.e. the requirement of elevated pressure for viability, has been firmly established. In non-adapted organisms, increased pressure leads to morphological anomalies or growth inhibition, and ultimately to cell death. The detailed molecular mechanism of the underlying 'metabolic dislocation' is unresolved. Effects of pressure as a variable in microbiology, biochemistry and biotechnology allow the structure/function relationship of proteins conjugates to be analyzed. In this context, stabilization by cofactors or accessory proteins has been observed. High-pressure equipment available today allows the comprehensive characterization of the behaviour of proteins under pressure. Single-chain proteins undergo pressure-induced denaturation in the 100-MPa range, which, in the case of oligomeric proteins or protein assemblies, is preceded by dissociation at lower pressure. The effects may be ascribed to the positive reaction volumes connected with the formation of hydrophobic and ionic interactions. In addition, the possibility of conformational effects exerted by moderate, non-denaturing pressures, and related to the intrinsic compressibility of proteins, is discussed. Crystallization may serve as a model reaction of protein self-organization. Kinetic aspects of its pressure-induced inhibition can be described by a model based on the Oosawa theory of molecular association. Barosensitivity is known to be correlated with the pressure-induced inhibition of protein biosynthesis. Attempts to track down the ultimate cause in the dissociation of ribosomes have revealed remarkable stabilization of functional complexes under pseudo-physiological conditions, with the post-translational complex as the most pressure-sensitive species. Apart from the key issue of barosensitivity and barophilic adaptation, high-pressure biochemistry may provide means to develop new approaches to nonthermic industrial processes, especially in the field of food technology.

Mechanogenetic regulation of transcription

In many biological systems mechanical forces regulate gene expression: in bacteria changes in turgor pressure cause a deformation of the membrane and induce the expression of osmoregulatory genes; in plants gravity regulates cell growth ('geotropism'); in mammals stretching a muscle induces hypertrophy which is accompanied by qualitative changes in protein synthesis. Consequently, the term 'mechanogenetic control' seems to be a suitable common name for all these processes. The mechanism by which mechanical factors modulate transcriptional activity is still unknown. The purpose of this review is to bring together data from different fields in order to obtain a better understanding of the mechanogenetic control of cell growth.

Proteins under extreme physical conditions

Life on earth is ubiquitous within the limits from -5 to 110 degrees C for temperature, 0.1 to 120 MPa for hydrostatic pressure, 1.0 to 0.6 for water activity and pH 1 to 12. In general, mutative adaptation of proteins to changing environmental conditions tends to maintain 'corresponding states' regarding overall topology, flexibility and hydration. Due to the minute changes in the free energy of stabilization responsible for enhanced stability, nature provides a wide variety of different adaptative strategies. In the case of thermophilic proteins, improved packing densities are crucial. In halophilic proteins, decreased hydrophobicity and clustered surface charges serve to increase water and salt binding required for solubilization at high salt concentration. In the case of barophiles, high-pressure adaptation is expected to be less important than adaptation to low temperatures governing the deep sea. Nothing is known with respect to the mechanisms underlying psychrophilic and acidophilic/alkalophilic adaptation.

Protein content and enzyme activities in methanol- and acetate-grown Methanosarcina thermophila

The cell extract protein content of acetate- and methanol-grown Methanosarcina thermophila TM-1 was examined by two-dimensional polyacrylamide gel electrophoresis. More than 100 mutually exclusive spots were present in acetate- and methanol-grown cells. Spots corresponding to acetate kinase, phosphotransacetylase, and the five subunits of the carbon monoxide dehydrogenase complex were identified in acetate-grown cells. Activities of formylmethanofuran dehydrogenase, formylmethanofuran:tetrahydromethanopterin formyltransferase, 5,10-methenyltetrahydromethanopterin cyclohydrolase, methylene tetrahydromethanopterin:coenzyme F420 oxidoreductase, formate dehydrogenase, and carbonic anhydrase were examined in acetate- and methanol-grown Methanosarcina thermophila. Levels of formyltransferase in either acetate- or methanol-grown Methanosarcina thermophila were approximately half the levels detected in H2-CO2-grown Methanobacterium thermoautotrophicum. All other enzyme activities were significantly lower in acetate- and methanol-grown Methanosarcina thermophila.

Isolation of a gene regulated by hydrostatic pressure in a deep-sea bacterium

Barophilic bacteria inhabit the deep oceans, and the specific functional modifications and regulatory mechanisms which govern adaptation to hydrostatic pressure are beginning to be understood. For example, the rate of production of several proteins by some hydrothermal vent archaebacteria and the degree of saturation of membrane lipids in other deep-sea bacteria have been found to change as a result of cultivation at high pressure. We report here the cloning of gene, ompH, which encodes a major pressure-inducible protein of strain SS9, a gram-negative eubacterium isolated from a depth of 2.5 kilometres in the Sulu Sea. Messenger RNA encoded by ompH is expressed when cells are grown at 280 atm but not at 1 atm, indicating that transcription of the ompH gene is controlled by hydrostatic pressure. The function of the OmpH protein in adaptation to high pressure and the use of the ompH gene in studying how bacteria sense and respond to pressure is discussed.