Hydrostatic pressure effects on Escherichia coli: site of inhibition of protein synthesis

The genome of a hadal sea cucumber reveals novel adaptive strategies to deep-sea environments

How organisms cope with coldness and high pressure in the hadal zone remains poorly understood. Here, we sequenced and assembled the genome of hadal sea cucumber Paelopatides sp. Yap with high quality and explored its potential mechanisms for deep-sea adaptation. First, the expansion of ACOX1 for rate-limiting enzyme in the DHA synthesis pathway, increased DHA content in the phospholipid bilayer, and positive selection of EPT1 may maintain cell membrane fluidity. Second, three genes for translation initiation factors and two for ribosomal proteins underwent expansion, and three ribosomal protein genes were positively selected, which may ameliorate the protein synthesis inhibition or ribosome dissociation in the hadal zone. Third, expansion and positive selection of genes associated with stalled replication fork recovery and DNA repair suggest improvements in DNA protection. This is the first genome sequence of a hadal invertebrate. Our results provide insights into the genetic adaptations used by invertebrate in deep oceans.

Biotechnologies for Marine Oil Spill Cleanup: Indissoluble Ties with Microorganisms

The ubiquitous exploitation of petroleum hydrocarbons (HCs) has been accompanied by accidental spills and chronic pollution in marine ecosystems, including the deep ocean. Physicochemical technologies are available for oil spill cleanup, but HCs must ultimately be mineralized by microorganisms. How environmental factors drive the assembly and activity of HC-degrading microbial communities remains unknown, limiting our capacity to integrate microorganism-based cleanup strategies with current physicochemical remediation technologies. In this review, we summarize recent findings about microbial physiology, metabolism and ecology and describe how microbes can be exploited to create improved biotechnological solutions to clean up marine surface and deep waters, sediments and beaches.

Adaptive laboratory evolution of Escherichia coli K-12 MG1655 for growth at high hydrostatic pressure

Much of microbial life on Earth grows and reproduces under the elevated hydrostatic pressure conditions that exist in deep-ocean and deep-subsurface environments. In this study adaptive laboratory evolution (ALE) experiments were conducted to investigate the possible modification of the piezosensitive Escherichia coli for improved growth at high pressure. After approximately 500 generations of selection, a strain was isolated that acquired the ability to grow at pressure non-permissive for the parental strain. Remarkably, this strain displayed growth properties and changes in the proportion and regulation of unsaturated fatty acids that indicated the acquisition of multiple piezotolerant properties. These changes developed concomitantly with a change in the gene encoding the acyl carrier protein, which is required for fatty acid synthesis.

Transcriptional response reveals translation machinery as target for high pressure in Lactobacillus sanfranciscensis

The effect of sublethal hydrostatic pressure on the transcriptome of Lactobacillus sanfranciscensis was determined using a shot-gun-microarray. Among the 750 spots that passed quality analysis 42 genes were induced, while six were repressed when cells were incubated at 45 MPa for 30 min. The nature of genes and their differential expression clearly indicate cellular efforts to counteract a decrease in translational capacity. The majority of high pressure affected genes were found to encode either translation factors (EF-G, EF-TU), ribosomal proteins (S2, L6, L11), genes changing translational accuracy or molecular chaperones (GroEL, ClpL). These data agree with previously reported effects observed in in vitro studies as well as with physiological and proteomic data. This study provides in vivo evidence to identify ribosomes and impaired translation among primary targets for high pressure treatment. The observed induction of heat as well as cold shock genes (e.g. hsp60, gyrA) may be explained as a result of high pressure affected protein synthesis.

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.

Hydrostatic pressure studies of native and synthetic thick filaments: in vitro myosin aggregates at pH 7.0 with and without C-protein

Column-purified myosin at pH 7.0 will reproducibly aggregate into filaments of known average length and structure when dialyzed against a low ionic strength medium under controlled conditions. When exposed to increased hydrostatic pressure, followed by quick return to atmospheric pressure, the original filaments shorten linearly with increasing pressure; in addition, a second population of filaments is seen, presumably the result of reaggregation of myosin after release of pressure. This second population is about 0.5 microns long, bipolar, and about half the diameter of the original filaments. The number of these filaments, but not their physical characteristics, is a function of the shortening of the original filament population. Both the remnants of the original population and the new aggregates, once formed, are stable over time and at room temperature. The addition of C-protein to myosin solutions before filament preparation results in a filament population of slightly shorter length. When these filaments are exposed to increased hydrostatic pressure, they are more resistant to disaggregation than myosin filaments without C-protein. However, like the filaments prepared in the absence of C-protein, a second population of shorter, thinner filaments is visible after exposure to pressure.

Effects of isolation and high helium pressure on the nucleolus of sympathetic neurons in the rat superior cervical ganglion

In prokaryotes, unicellular eukaryotes and cell-free systems, pressure is known to exert an inhibitory effect on protein synthesis and RNA metabolism, the mechanism(s) of which remain to be investigated in detail. The purpose of the present in vitro study was to compare ultrastructural and quantitative changes of the nucleolus, which is the site of ribosome biogenesis, in sympathetic neurons of rat superior cervical ganglia (SCG) maintained for 2, 3 and 5 h in NCTC 109 medium and subjected to pressure or not. In control SCG (left) the nucleolus greatly increased in volume (+ 33%) 2 h after excision, in comparison with SCG fixed immediately. This overall enlargement was found to reflect a marked increase in all nucleolar components (from 16 to 87%). After 5 h, volumes of nucleolus, fibrillar centers and vacuolar component returned to control values, whereas dense fibrillar and granular components remained affected. Such early and transient changes are regarded as reflecting basic metabolic changes associated with increased nucleolar RNA that should be of primary concern to experiments using SCG transplanted in culture media. Compression under helium up to 180 atmospheric pressure for 1 h of right SCG maintained for 2 h in culture medium, was shown to induce, on the contrary, a marked decrease in nucleolar volume (-39%) and in volumes of all nucleolar components (from -36 to -51%). When they were kept at constant high pressure for 1 and 3 h a progressive recovery of volumes of nucleoli and nucleolar components was observed. Consequently, compression was shown to exert opposite effects to those of isolation of SCG. Present data are interpreted as an inhibitory effect of pressure on ribosome biogenesis. Such observations on a vertebrate neuron might open a new field in the search for cellular mechanisms underlying the effects of pressure on living organisms and especially on the nervous system.

Effect of hydrostatic pressure on translational fidelity

We have used the application of hydrostatic pressure to modify the misreading of polyuridylate template. Pressure was used to test ribosomes isolated from Escherichia coli strains containing mutations in the S12 ribosomal protein which lead to streptomycin-resistance and -dependence. The incorporation of phenylalanine into polypeptide, at a given pressure, was found to vary with the source of ribosomes and was found to correlate with S12-dependent changes in rates of incorporation suggesting a role of the S12 ribosomal protein in the pressure effect. Streptomycin partially alleviated the increased pressure-resistance in those cases where control rates of incorporation were found to be stimulated by the addition of streptomycin. In contrast, the misincorporation of isoleucine was substantially more sensitive to pressure application, regardless of ribosome source or the presence of streptomycin. These results suggest that the application of hydrostatic pressure affects at least two distinct ribosomal reactions important to the discrimination of these two amino acids.

The effect of high hydrostatic pressure on eukaryotic protein synthesis

The pressure response of two eukaryotic protein synthesizing systems has been characterized. The rabbit reticulocyte system has been tested, both in vivo and in vitro, using endogenous polysomes and polyuridylic acid (poly U). In addition, the poly U-directed polyphenylalanine synthesizing system obtained from wheat germ was utilized. The effect of pressure on eukaryotic protein synthesis has been found to be basically similar to that observed in prokaryotic systems, although the response of the eukaryotic protein synthesizing system is somewhat more complex signifying a greater influence of overlapping reactions. Magnesium was found to affect eukaryotic systems in much the same way as has been reported for prokaryotic systems, i.e., increasing the Mg2+ concentration in a protein synthesizing system increases the barotolerance exhibited by the system. Under conditions of high Mg2+ concentration, however, extreme (up to 160%) stimulation of protein synthesis at lower pressure levels was observed in the eukaryotic systems. Such high stimulation is not apparent in prokaryotic systems. The poly U-directed wheat germ system exhibited the most barotolerant polypeptide synthesis ever seen in our laboratory. This extreme barotolerance was only slightly decreased when the system was tested at reduced concentrations of magnesium.

Effect of S12 ribosomal mutations on peptide chain elongation in Escherichia coli: a hydrostatic pressure study

Protein synthesis in Escherichia coli mutants that differ from one another in mutations which impart streptomycin resistance was investigated by the application of hydrostatic pressure. Increased pressure resistance was only observed in mutants which exhibited reduced rates of peptide chain elongation. These findings indicate that the major effect of pressure on protein synthesis in E. coli may involve the S12 ribosomal protein.

Effects of hydrostatic pressure in the range 100-300 atmospheres on cell division and protein synthesis in synchronized Tetrahymena pyriformis: a comparison with cycloheximide and emetine

Heat-synchronized Tetrahymena pyriformis have been subjected to 5-, 15- and 30-minute pulses of hydrostatic pressure in the range 100-300 atm, without being simultaneously subjected to significant heats of compression. The pressure-induced division delays depend on (1) the level of pressure used, (2) the length of pressure pulse and (3) the time after the synchronizing treatment at which the pressure is applied. A pressure-dependent inhibition of 3H-leucine incorporation into protein was also measured. Comparison of the effects of pressure with those of pulse treatments of cycloheximide and emetine on cell division and protein synthesis revealed that the physical agent produced characteristically different responses from those of the chemical agents. Of particular interest was the fact that the division delays induced by pressures of 200 atm and above were greater than those observed after treatments with cyclohexmide and emetine which produced comparable levels of protein synthesis inhibition. Pressure also delayed cells if it was applied at a time when addition of chemical inhibitors had little effect on the first synchronous division. The results show that inhibition of protein synthesis by pressure cannot entirely account for pressure-induced effects on cell division. The possibility that pressure may also directly affect other processes, such as the assembly of proteins into structure required for division, is discussed.

Hydrostatic pressure effects upon cellular leakage and active transport by Vibrio marinus

Hydrostatic pressures greater than ca. 400 atm cause release of cellular components of Vibrio marinus MP-1 in the order protein greater than RNA greater than malate dehydrogenase greater than DNA greater than amino acids. Increased pressures also slow the rate of cycloleucine (non-metabolizable analogue of L-leucine acid L-valine) uptake but increase its efflux rate. Lineweaver-Burk plots (1/V versus 1/[S]) of cycloleucine uptake indicate that the Km increases with compression which suggests a decrease in affinity of the transport system for substrate at increased pressures.

Role of the 30S ribosomal subunit, initiation factors, and specific ion concentration in barotolerant protein synthesis in Pseudomonas bathycetes

Washed (1 M NH4Cl) ribosomes from Pseudomonas bathycetes, Pseudomonas fluorescens, and Escherichia coli were tested for their ability to synthesize protein or polypeptide at high pressure when used as such, when recombined with homologous initiation factors, and when recombined with heterologous initiation factors. The responses of natural messenger ribonucleic acid (MS-2)-directed systems to pressure were independent of the source of initiation factors and paralleled those of the washed ribosomes in polyuridylate-directed systems. In all cases, the responses to pressure were parallel to those obtained when unwashed ribosomes were utilized; therefore, we concluded that the initiation factors were interchangeable among these organisms, and that these factors did not play a critical role in determining the pressure responses of the protein-synthesizing systems. P. bathycetes ribosomal subunits were isolated under a variety of ionic conditions. These were tested for their ability to synthesize protein and polyphenylalanine at a variety of pressures when used in reconstituted P. bathycetes homologous systems and in hybrid systems with ribosomal subunits from E. coli and P. fluorescens. O. bathycetes 30S subunits, isolated in a buffer solution containing 0 mM NaCl and O mM KC] were functional at any pressure; those isolated in the presence of 150 mM NaCl and 0 mM KCl were functional at 1 atmosphere but barosensitive, and those isolated in the presence of O mM NaCl and 150 mM KCl retained the ion-mediated barotolerance characteristic of crude P. bathycetes ribosome preparations. The 50S subunit remained functional regardless of the method of isolation, and it had no effect on pressure sensitivity.

Protein synthesis at 680 atm: is it related to environmental origin, physiological type, or taxonomic group?

The ability of bacteria to synthesize protein at 680-atm pressure is not related to their environmental origin, physiological type, or taxonomic group.

Specific ion concentration as a factor in barotolerant protein synthesis in bacteria

The degree of barotolerance exhibited by Pseudomonas fluorescens and Pseudomonas bathycetes in vitro polyphenylalanine-synthesizing systems can be modified by altering the concentrations of specific ions in the reaction mixture. Hybrid-protein-synthesizing systems, utilizing all the possible S-100 supernatant fluid and ribosome combinations from Escherichia coli, P. fluorescens, and P. bathycetes, were tested for barotolerance under conditions of low (16 mM Mg2+ plus 0 mM Na+) and high (150 mM Na+ plus 60 mM Mg2+) ion concentrations. The results reveal that barotolerant synthesis is a characteristic determined by the origin of the ribosome. Systems utilizing E. coli ribosomes are barosensitive at both low and high ion concentrations, P. fluorescens ribosomes barotolerant under both conditions, and P. bathycetes ribosomes barosensitive at low and barotolerant at high ion concentrations. Therefore, certain concentrations of specific ions will increase barotolerance, but only if the ribosomes are capable of functioning at high pressures.

Heterotrophic activity of deep-sea sediment bacteria

Sediment samples, containing mixed microbial populations that were decompressed during retrieval from 7,750 and 8,130 m in the Puerto Rican Trench, were recompressed and incubated at the approximate in situ temperature (3 C) and pressure (775 or 815 atm) in the presence of 14C-labeled amino acids. Heterotrophic activity (total uptake, CO2 respiration, and cellular assimilation) and cellular-associated "pool" concentrations were measured. Compared with atmospheric controls held at 3 C, the total uptake at elevated pressure at 3 C was reduced, on an average, 55 times, CO2 respiration was reduced 45 times, and cellular assimilation was reduced 69 times. Rate of total uptake at elevated pressure was found to range from 4.0 X 10(-11) mug/cell per h for leucine to 2.61 X 10(-10) mug/cell per h for an amino acid mixture. Also, the percentage of total uptake at elevated pressures, respired as CO2, increased at the expense of cellular assimilation (ca. 22% increase). Two cellular-associated amino acid pools were detected, a large, loosely bound, outer pool and a small, tightly bound internal pool. The loosely bound outer pool was removed by a change in the pH of the incubation medium. Even though heterotrophic uptake and the outer, cellular-associated pool were markedly reduced at an elevated pressure, the percentage of total uptake calculated for the unincorporated, tightly bound, intracellular pool was 2 to 19 times that obtained for cultures held at 1 atm. The results were interpreted as indicating that bacterial metabolism and biosynthesis in the deep sea are markedly reduced, with a greater proportion of metabolic activity devoted to cellular maintenance.

Role of bacterial ribosome subunits in barotolerance

The barotolerant nature of protein synthesis in Pseudomonas fluorescens is shown to be associated with the 30S ribosomal subunit.

Stability of Escherichia coli polysomes at high hydrostatic pressure

The stability of Escherichia coli polysomes at increased hydrostatic pressure was investigated in actively growing cells, in which the initiation of transcription was blocked by rifampin. In these cells, [3-H]uridine incorporation into messenger ribonucleic acid and the subsequent degradation of the message (and therefore of polysomes) by ribonuclease could be observed. Evidence is presented that the activity of the RNases is unaffected by a pressure of 680 atm, that protein synthesis is completely inhibited at 680 atm but immediately resumes at the 1 atm rate on release of pressure, and that no degradation of messenger ribonucleic acid in polysomes occurs at 680 atm. The effects of pressure; puromycin, and chloramphenicol on polysomal degradation are discussed. These results indicate that, contrary to some previous reports, polysomes are probably stabilized by high pressures. Therefore, we consider that polysomal instability is not a factor in the inhibition of protein synthesis by high pressures.

Role of bacterial ribosomes in barotolerance

The effects of high hydrostatic pressures on protein synthesis by whole cells and cell free preparations of Escherichia coli, Pseudomonas fluorescens, and Pseudomonas bathycetes were determined. Actively growing cells of P. bathycetes and P. fluorescens were less sensitive than were E. coli cells. Protein synthesis by cell free preparations of E. coli and P. fluorescens showed the same extent of inhibition as their respective whole cell preparations, whereas cell free preparations of P. bathycetes showed a marked increase in pressure sensitivity over whole cells. Protein synthesis by hybrid protein synthesizing cell free preparations (the ribosomes from one organism and the S-100 supernatant fraction from another) demonstrated that response to high pressure is dependent on the source of the ribosome employed. A hybrid system containing E. coli ribosomes and P. fluorescens S-100 shows the same sensitivity to pressure as a homologous E. coli system, whereas a hybrid containing P. fluorescens ribosomes and E. coli S-100 shows the greater pressure tolerance characteristic of the P. fluorescens homologous system.

Deep-sea bacteria: growth and utilization of hydrocarbons at ambient and in situ pressure

Microorganisms present in Atlantic Ocean sediment samples collected at a depth of 4,940 m were found to be capable of utilizing hydrocarbons under both ambient and in situ pressures. The rate of utilization under in situ pressure (500 atm) and ambient temperature (20 C) was found to be significantly less compared with hydrocarbon utilization examined under conditions of ambient temperature (20 C) and pressure (1 atm).

Structure and function of the cell envelope of gram-negative bacteria

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Effect of helium gas at elevated pressure on iron transport and growth of Escherichia coli

Helium at an ambient pressure of 68 at m with 0.2 atm of O(2) shortened by 1 to 1.5 h the lag phase for growth of Escherichia coli in minimal medium supplemented with 2 muliters of cell-free culture filtrate (CFF) per ml or with 1 muM 2,3-dihydroxybenzoylserine (DHBS), an iron chelator. The lag phase of cultures not exposed to helium could be shortened by use of supplements, but higher concentrations were required-10 to 30 muliters of CFF per ml or 10 to 50 muM DHBS. Strain AN 193 of E. coli, which requires the DHBS precursor 2,3-dihydroxybenzoic acid (DHBA), grew well in media with 10 muM DHBA when exposed to helium at 68 atm, whereas 100 muM DHBA was required for growth in unexposed cultures. In the presence of 100 muM DHBA plus 1.0 muM ethylenediaminetetraactic acid, growth was inhibited at 1 and 68 atm. Growth was restored, however, by the addition of 0.1 muM FeSO(4) at 68 atm and 1.0 muM FeSO(4) at 1 atm, but lag times were invariably shorter in the pressurized cultures. Hydrostatic pressures of 68 atm did not reduce the lag phase in the presence of CFF, DHBS, or DHBA. Our results suggest that 68 atm of helium pressure, but not hydrostatic pressure, elicited a more rapid transport of iron into the cells.

Inhibition of cell-free protein synthesis by hydrostatic pressure

Pressure inhibition of cell-free polypeptide synthesis is manifested in the same manner as that observed in the intact cell: (i) starting at approximately 200 atm, there is a progressive inhibition with increasing pressures; (ii) there is complete inhibition at 680 atm; (iii) incorporation into polypeptide is instantaneously reversible after pressure release and proceeds at a rate parallel to an atmospheric control; and (iv) the volume change of activation (DeltaV*) is 100 cm(3)/mole. Peptide bond formation per se can occur at a pressure level which is totally inhibitory to polypeptide synthesis. The one investigated step in translation that is inhibited in an identical manner is the binding of aminoacyl-transfer ribonucleic acid (AA-tRNA) to the ribosome-messenger RNA (mRNA) complex. The volume change of activation (DeltaV*) calculated for the binding reaction is also 100 cm(3)/mole. Thus, the inability of AA-tRNA to bind to ribosomes and mRNA under pressure, possibly in conjunction with translocation, appears to be responsible for the observed inhibition of the translational mechanism.