Proteolysis at pressure and HPLC peptide mapping of M4-lactate dehydrogenase homologs from marine fishes living at different depths.

1. The effects at 10 degrees C of moderate hydrostatic pressure (136 atm) on trypsinolysis of muscle-type (M4) lactate dehydrogenase homologs (LDH, EC 1.1.1.27, L-lactate:NAD+ oxidoreductase) from shallow- and deep-occurring marine fishes were examined by mapping the partial digests by reverse phase HPLC. 2. Comparison of peptide maps of digests generated at 1 and 136 atm revealed that increased pressure did not expose new cleavage sites in homologs of any of the species; no new peptides were generated. 3. Increased pressure did alter the relative amounts of peptides produced. The net effect of increased pressure was to increase the amount of peptides generated in the shallow-occurring species. For deep-living species pressure did not alter the net amount of peptides produced compared to the 15 min atmospheric pressure samples, although the relative amounts of some of the peptides changed. Incubation at 136 atm for 30 min decreased the net amount of peptides produced. 4. It is suggested that the effects of pressure on trypsinolysis may result from slight conformational changes in the substrate proteins.     

Pressure inactivation of tetrameric lactate dehydrogenase homologues of confamilial deep-living fishes

Summary The susceptibility to inactivation by hydrostatic pressure of the tetrameric (Fig. 1) muscletype (M₄) lactate dehydrogenase homologues (LDH, EC 1.1.1.27;l-lactate: NAD⁺ oxidoreductase) from six confamilial macrourid fishes was compared at 4 °C. These marine teleost fishes occur over depths of 260 to 4815 m. The pressures necessary to half-inactivate the LDH homologues are related to the pressures which the enzymes are exposed to in vivo (Table 1); higher hydrostatic pressures are required to inactivate the LDH homologues of the deeper-occurring macrourids. The resistance of the LDH homologues to inactivation by pressure is affected by protein concentration (Fig. 3). After an hour of incubation at pressure, the percent remaining activity approaches an asymptotic value (Fig. 2). The inactivation of the macrourid LDH homologues by pressure was not fully reversible. Assuming that inactivation by pressure was due to dissociation of the native tetramer to monomers, apparent equilibrium constants (K _eq) were calculated. Volume changes (V) were calculated over the range of pressures for which plots inK _eq versus pressure were linear (Fig. 4). The V of dissociation values of the macrourid homologues range from –219 to –439 ml mol^–1 (Table 1). Although the hydrostatic pressures required to inactivate the LDH homologues of the macrourid fishes are greater than those which the enzymes are exposed to in vivo, the pressure-stability of these enzymes may reflect the resistance of these enzymes to pressure-enhanced proteolysis in vivo.     

High-pressure, high-temperature bioreactor for comparing effects of hyperbaric and hydrostatic pressure on bacterial growth.

We describe a high-pressure reactor system suitable for simultaneous hyperbaric and hydrostatic pressurization of bacterial cultures at elevated temperatures. For the deep-sea thermophile ES4, the growth rate at 500 atm (1 atm = 101.29 kPa) and 95 degrees C under hydrostatic pressure was ca. three times the growth rate under hyperbaric pressure and ca. 40% higher than the growth rate at 35 atm.     

Trimethylamine oxide counteracts effects of hydrostatic pressure on proteins of deep-sea teleosts

In shallow marine teleost fishes, the osmolyte trimethylamine oxide (TMAO) is typically found at <70 mmol/kg wet weight. Recently we found deep-sea teleosts have up to 288 mmol/kg, increasing in the order shallow < bathyal < abyssal. We hypothesized that this protein stabilizer counteracts inhibition of proteins by hydrostatic pressure, and showed that, for lactate dehydrogenases (LDH), 250 mM TMAO fully offset an increase in NADH K(m) at physiological pressure, and partly reversed pressure-enhanced losses of activity at supranormal pressures. In this study, we examined other effects of pressure and TMAO on proteins of teleosts that live from 2000-5000 m (200-500 atmospheres [atm]). First, for LDH from a grenadier (Coryphaenoides leptolepis) at 500 atm for 8 hr, there was a significant 15% loss in activity (P < 0.05 relative to 1 atm control) that was reduced with 250 mM TMAO to an insignificant loss. Second, for pyruvate kinase from a morid cod (Antimora microlepis) at 200 atm, there was 73% increase in ADP K(m) without TMAO (P < 0.01 relative to K(m) at 1 atm) but only a 29% increase with 300 mM TMAO. Third, for G-actin from a grenadier (C. armatus) at 500 atm for 16 hr, there was a significant reduction of F-actin polymerization (P < 0.01 compared to polymerization at 1 atm) that was fully counteracted by 250 mM TMAO, but was unchanged in 250 mM glycine. These findings support the hypothesis. J. Exp. Zool. 289:172-176, 2001.     

High-pressure, high-temperature bioreactor for comparing effects of hyperbaric and hydrostatic pressure on bacterial growth.

We describe a high-pressure reactor system suitable for simultaneous hyperbaric and hydrostatic pressurization of bacterial cultures at elevated temperatures. For the deep-sea thermophile ES4, the growth rate at 500 atm (1 atm = 101.29 kPa) and 95 degrees C under hydrostatic pressure was ca. three times the growth rate under hyperbaric pressure and ca. 40% higher than the growth rate at 35 atm.     

Hydrostatic pressure alters the time course of GTP

The effects of hydrostatic pressure on the receptor-stimulated exchange of guanosine triphosphate (GTP) for guanosine diphosphate (GDP) on the a subunit of G proteins were studied in two congeneric marine teleost fishes that differ in their depths of distribution. The poorly hydrolyzable GTP analog [35S]guanosine 5'-[gamma-thio]triphosphate ([35S]GTP[S]) was used to monitor the modulation of signal transduction by the A1 adenosine receptor agonist N6-R-(phenylisopropyl)adenosine (R-PIA) in brain membranes of the scorpaenids Sebastolobus alascanus and S. altivelis. The maximal binding (Bmax) and dissociation constant (K(d)) values, determined from equilibrium binding isotherms at atmospheric pressure (5 degrees C), were similar in the two species. The Bmax values for these species are much lower than literature values for mammalian brain tissue (25 degrees C); however, the K(d) values of the teleost and mammalian G proteins are similar. The EC50 values for the A1 adenosine receptor agonist R-PIA were similar in the two species. Hydrostatic pressure of 204 atm altered the binding of [35S]GTP[S]; basal [35S]GTP[S] binding decreased 25%. The A1 adenosine receptor agonist R-PIA and the muscarinic cholinergic receptor agonist carbamyl choline stimulated [35S]GTP[S] binding at 1 and 204 atm. At atmospheric pressure the half-time (t1/2) of [35S]GTP[S] binding differed between the two species. The GTP[S] on rate (k(on)) is larger in the shallower-living S. alascanus. Increased hydrostatic pressure altered the time course, decreasing the t1/2 in both species. The pressures that elicit this change in the time course differ between the species. However, interpolating over the range of in situ pressures the species experience, the values are similar in the two species. The guanyl nucleotide binding properties of the G protein a subunits appear to be conserved at the environmental temperatures and pressures the species experience.     

Different Pressure Resistance of Lactate Dehydrogenases from Hagfish is Dependent on Habitat Depth and Caused by Tetrameric Structure Dissociation

The effects of high hydrostatic pressure on lactate dehydrogenase (LDH) activities from two species of hagfish were examined. LDH from Eptatretus okinoseanus, a deep-sea species, retained 67% of the original activity even at 100 MPa. LDH activity from Eptatretus burgeri, a shallow-sea species, was completely lost at 50 MPa but recovered to the original value at 0.1 MPa. The tetrameric structure of LDH-A₄ from E. okinoseanus did not change at 50 MPa. In contrast, almost all LDH tetramers from E. burgeri dissociated to dimers and monomers at 50 MPa but reverted to tetramers at 0.1 MPa. These results show that the dissociation of tetramers caused the inactivation of E. burgeri LDH. The difference depends on the number 6 and 10 amino acids. The mechanism of the slight, gradual inactivation of E. okinoseanus LDH at high pressure differs and is probably due to the metamorphosis of its inner structures.     

Pressure-adaptive differences in NAD-dependent dehydrogenases of congeneric marine fishes living at different depths

Summary The pressure sensitivities of the apparent Michaelis constant of coenzyme were compared at 5°C for three NAD-dependent dehydrogenases purified from the white muscle of two congeneric fishes living at different depths.Sebastolobus altivelis adults are common between 550 and 1,300 m;S. alascanus adults between 180 and 440 m. Two isozymes of cytoplasmic malate dehydrogenase (MDH, EC 1.1.1.37, NAD⁺:l-malate oxidoreductase) and glyceraldehyde 3-phosphate dehydrogenase (GAPDH, EC 1.2.1.12, NAD⁺:d-glyceraldehyde 3-phosphate oxidoreductase [phosphorylating]) were compared. For these enzymes, the homologues fromS. alascanus were markedly sensitive to moderate hydrostatic pressures (Fig. 1). TheK _m(NADH) ofS. alascanus MDH-1 and theK _m(NAD⁺) ofS. alascanus GAPDG double between 1 and 68 atm and continue to increase at a slower rate up to 476 atm, the highest pressure tested. For MDH-2 ofS. alascanus, theK _m(NADH) triples between 1 and 68 atm and increases at a slower rate to 340 atm; between 340 and 476 atm, theK _m decreases slightly from the value at 340 atm. TheK _m of coenzyme values are pressure-independent for the MDH-1 and GAPDH homologues ofS. altivelis up to 476 atm (Fig. 1). TheK _m(NADH) of theS. altivelis MDH-2 is sensitive to pressure, but much less so than the homologue ofS. alascanus (Fig. 1). TheK _m increases 63% between 1 and 68 atm and remains constant at this higher value at higher pressures up to 476 atm. The relative increases inK _m values for theS. alascanus enzymes between 1 and 68 atm are large (Table 1). Higher pressures are not as effective in perturbing theK _m of coenzyme values. Perturbation ofK _m of coenzyme by moderate hydrostatic pressures (50–100 atm) may seriously impair the function of dehydrogenases ofS. alascanus at pressures experienced by the deeper-living congener in its habitat. The reduction of the pressure-sensitivity of theK _m of coenzyme in NAD-dependent dehydrogenases may be an important and ubiquitous feature of adaptation to the deep sea.     

Pressure-adaptive differences in the binding and catalytic properties of muscle-type (M4) lactate dehydrogenases of shallow- and deep-living marine fishes

Summary The pressure sensitivities of substrate (pyruvate) and cofactor (NADH) binding and catalytic rate of purified muscle-type (M₄) lactate dehydrogenases (LDH, EC 1.1.1.27; NAD⁺: lactate oxidoreductase) from shallow- and deep-living teleost fishes were compared. The LDH's of the shallow species are significantly more pressure-sensitive than the LDH's of the deep-living fishes. The apparent Michaelis constant (K _m)¹ of pyruvate of the deep-living species' LDH's is pressure-insensitive over the entire pressure range used in these studies, 1 to 476 atmospheres (Fig. 1). For the LDH's of the shallow species, theK _m of pyruvate increases significantly between 1 and 68 atmospheres, and then remains stable up to 476 atmospheres. TheK _m of NADH displays a much higher pressure sensitivity. For the LDH's of the deep species, theK _m of NADH increases slightly (approximately 32%) between 1 and 68 atmospheres, and then remains stable up to 476 atmospheres (Fig. 1). TheK _m of the shallow species' LDH's rises sharply (approximately 113%) between 1 and 68 atmospheres, and then continues to increase at a slower rate up to 476 atmospheres. This marked inhibition of cofactor binding by pressure for the shallow species' LDH's may be of sufficient magnitude to seriously impair the function of these LDH's at pressures typical of those encountered by the deeper-living species.Pressure effects on optimal velocity, measured under high (optimal) concentrations of pyruvate and NADH, were generally lower for the LDH's of the deep species (Table 1).These results indicate that M₄-LDH's of shallow water fishes are not pre-adapted for function at deepsea pressures, and that the reduction of pressure sensitivities ofK _m's and catalysis may be a ubiquitous feature of adaptation to life at depth. The virtually identical pressure responses of M₄-LDH's from deepliving teleosts belonging to four different families represents a striking example of convergent evolution at the molecular level.     

Enzyme sequence and its relationship to hyperbaric stability of artificial and natural fish lactate dehydrogenases

The cDNAs of lactate dehydrogenase b (LDH-b) from both deep-sea and shallow living fish species, Corphaenoides armatus and Gadus morhua respectively, have been isolated, sequenced and their encoded products overproduced as recombinant enzymes in E. coli. The proteins were characterised in terms of their kinetic and physical properties and their ability to withstand high pressures. Although the two proteins are very similar in terms of their primary structure, only 21 differences at the amino acid level exist between them, the enzyme from the deep-sea species has a significantly increased tolerance to pressure and a higher thermostability. It was possible to investigate whether the changes in the N-terminal or C-terminal regions played a greater role in barophilic adaptation by the construction of two chimeric enzymes by use of a common restriction site within the cDNAs. One of these hybrids was found to have even greater pressure stability than the recombinant enzyme from the deep-living fish species. It was possible to conclude that the major adaptive changes to pressure tolerance must be located in the N-terminal region of the protein. The types of changes that are found and their spatial location within the protein structure are discussed. An analysis of the kinetic parameters of the enzymes suggests that there is clearly a trade off between K(m) and k(cat) values, which likely reflects the necessity of the deep-sea enzyme to operate at low temperatures.     

Deep-sea fishes in Canada’s Atlantic: population declines and predicted recovery times

Because of their slow growth rates, late maturity, low fecundity and long potential lifespans, deep-sea fishes are vulnerable to and theoretically slow to recover from overexploitation and bycatch. As industrial fishing moved into the deep sea, population declines were predicted and five species were shown to meet The World Conservation Union (IUCN) criteria for endangered species in Atlantic Canadian waters and two other deep-living species were listed as threatened by the Committee on the Status of Endangered Wildlife in Canada. We used data from scientific surveys to determine population trends in a 17-year time series for an additional 32 deep-sea fishes from the same geographic region. Eight species exhibited significant population declines, five increased, two were data deficient, and 17 showed no significant trends. Thus approximately 38% of the deep-sea bottom-living fishes in that well-investigated region could be at-risk, but definitive assignment to an IUCN category for most species is hampered by a lack of basic biological information, especially species specific generation times. Lack of biological information also limits efforts to determine possible recovery times, especially with respect to calculating intrinsic rates of population growth (r). For two Atlantic grenadiers (where r could be estimated using life-history parameters and standard life table techniques), the time to recovery with no fishing mortality could range from over a decade to over a century. This broad range results from the general uncertainty on life-history characteristics of these deep-sea species. Given the documented declines, the lack of basic data on life-history parameters, and the conservative assumption that recovery rates are likely to be prolonged, we argue that it is imperative to conduct additional studies pertaining to life history characteristics of deep-sea fishes and implement conservation measures in the deep sea immediately.     

Diversification of brain and sense organ morphology in Antarctic dragonfishes (Perciformes: Notothenioidei: Bathydraconidae)

In the subzero shelf waters of Antarctica, fishes of the perciform suborder Notothenioidei dominate the fish fauna and constitute an adaptive radiation and a species flock. The 16 species of dragonfishes of the family Bathydraconidae live from surface waters to nearly 3,000 m and have the greatest overall depth range among notothenioid families. We examined the anatomy and histology of the brain, retina, and cephalic lateral line system of nine bathydraconid species representing 8 of the 11 known genera. We evaluate these data against a cladogram identifying three clades in the family. We provide a detailed drawing of the brain and cranial nerves of Gymnodraco acuticeps and Akarotaxis nudiceps. Bathydraconid brain morphology falls into two categories. Brains of most species are similar to those of generalized perciforms and some basal notothenioids (Class I). However, brains of deep-living bathydraconids (members of the tribe Bathydraconini minus Prionodraco) have a reduced telencephalon and tectum that renders the neural axis visible - the stalked brain morphology (Class II). All bathydraconids have duplex (rod and cone) retinae but there is considerable interspecific variation in the ratio of cones:rods and in the number of cells in the internal nuclear layer. Retinal histology reflects habitat depth but is not tightly coupled to phylogeny. Although the deep-living species of Bathydraconini have rod-dominated retinae, the retinae of some sister species are photopic. An expanded cephalic lateral line system is also characteristic of all members of the Bathydraconini as exemplified by Akarotaxis. This morphology includes large lateral line pores, wide membranous canals, hypertrophied canal neuromasts, and large anterodorsal lateral line nerves, eminentia granulares, and crista cerebellares. The saccular otoliths are also enlarged in members of this tribe. Neural diversification among bathydraconids on the Antarctic shelf has not involved the evolution of sensory specialists. Brain and sense organ morphologies do not approach the specialized condition seen in primary deep-sea fishes or even that of some secondary deep-sea fishes including sympatric non-notothenioids such as liparids (snailfishes) and muraenolepidids (eel cods). The brains and sense organs of bathydraconids, including the deep-living species, reflect their heritage as perciform shorefishes.     

Stabilization of human serum alkaline phosphatase to histidine-induced heat inactivation by tryptic digestion.

1. Serum alkaline phosphatase [EC 3.1.3.1] was strongly inactivated by histidine during incubation at pH 8.0 and 45degrees; however, tryptic digestion of the serum strongly protected the enzyme against inactivation by histidine. In the absence of histidine, however, neither heat inactivation of the phosphatase nor the effect of trypsin [EC 3.4.21.4] was observed. Factors affecting the alkaline phosphatase inactivation were studied further. 2. The effect of trypsin on the histidine-induced heat inactivation differed considerably according to the tissue source of the enzyme, which suggests a possible method for distinguishing alkaline phosphatase isoenzymes.     

Rupture of the cell envelope by decompression of the deep-sea methanogen Methanococcus jannaschii

The effect of decompression on the structure of Methanococcus jannaschii, an extremely thermophilic deep-sea methanogen, was studied in a novel high-pressure, high-temperature bioreactor. The cell envelope of M. jannaschii appeared to rupture upon rapid decompression (ca. 1 s) from 260 atm of hyperbaric pressure. When decompression from 260 atm was performed over 5 min, the proportion of ruptured cells decreased significantly. In contrast to the effect produced by decompression from hyperbaric pressure, decompression from a hydrostatic pressure of 260 atm did not induce cell lysis.     

Rupture of the Cell Envelope by Decompression of the Deep-Sea Methanogen Methanococcus jannaschii

The effect of decompression on the structure of Methanococcus jannaschii, an extremely thermophilic deep-sea methanogen, was studied in a novel high-pressure, high-temperature bioreactor. The cell envelope of M. jannaschii appeared to rupture upon rapid decompression (ca. 1 s) from 260 atm of hyperbaric pressure. When decompression from 260 atm was performed over 5 min, the proportion of ruptured cells decreased significantly. In contrast to the effect produced by decompression from hyperbaric pressure, decompression from a hydrostatic pressure of 260 atm did not induce cell lysis.     

Conversion, by limited proteolysis, of an archaebacterial citrate synthase into essentially a citryl-CoA hydrolase.

1. Limited proteolysis of citrate synthase from Sulfolobus solfataricus by trypsin reduced the rate of the overall reaction (acetyl-CoA + oxaloacetate + H2O----citrate + CoASH) to 4% but did not affect the hydrolysis of citryl-CoA. Experimental results indicate that a connecting link between the enzyme's ligase and hydrolase activity becomes impaired specifically on treatment with trypsin. Other proteolytic enzymes like chymotrypsin and subtilisin inactivated catalytic functions of citrate synthase, ligase and hydrolase, equally well. 2. Tryptic hydrolysis occurs at the N-terminal region of citrate synthase, but a study by SDS/PAGE revealed no difference in molecular mass between native and proteolytically nicked citrate synthase. The peptide removed from the enzyme by trypsin, therefore, contains less than about 15 amino acid residues. 3. The Km values of the substrates for both native and nicked enzyme were identical, as was the state of aggregation (dimeric) of the two enzyme species. These could be separated by affinity chromatography on Blue-Sepharose and differentiated by their isoelectric points (pI = 6.68 +/- 0.08 and pI = 6.37 +/- 0.03 for native citrate synthase and the large tryptic peptide, respectively) as well as by the N-terminus which is blocked in the native enzyme only. 4. Edman degradation of the large tryptic fragment yielded the N-terminal sequence GLEDVYIKSTSLTYIDGVNGVLRY, which is 71% identical to the N-terminal region (positions 9-32) of citrate synthase from Thermoplasma acidophilum. 5. The conversion of citrate synthase into essentially a citryl-CoA hydrolase is considered the consequence of a conformational change thought to occur on tryptic removal of the N-terminal small peptide.     

Correlation between phylogenetic structure and function: examples from deep-sea Shewanella

The genus Shewanella is one of the typical deep-sea bacterial genera. Two isolated deep-sea Shewanella species, Shewanella benthica and Shewanella violacea, were found to be able to grow better under high hydrostatic pressure conditions than at atmospheric pressure. These species are not only piezophilic (barophilic), but also psychrophilic. Many psychrophilic and psychrotolerant Shewanella species have been isolated and characterized from cold environments, such as seawater in Antarctica or the North Sea. Some of these cold-adapted Shewanella were shown to be piezotolerant, meaning that growth occurs in a high-pressure habitat. In this review, we propose that two major sub-genus branches of the genus Shewanella should be recognized taxonomically, one group characterized as high-pressure cold-adapted species that produce substantial amounts of eicosapentaenoic acid, and the other group characterized as mesophilic pressure-sensitive species.     

Rapid and efficient protein digestion using trypsin-coated magnetic nanoparticles under pressure cycles

Trypsin‐coated magnetic nanoparticles (EC‐TR/NPs), prepared via a simple multilayer random crosslinking of the trypsin molecules onto magnetic nanoparticles, were highly stable and could be easily captured using a magnet after the digestion was complete. EC‐TR/NPs showed a negligible loss of trypsin activity after multiple uses and continuous shaking, whereas the conventional immobilization of covalently attached trypsin on NPs resulted in a rapid inactivation under the same conditions due to the denaturation and autolysis of trypsin. A single model protein, a five‐protein mixture, and a whole mouse brain proteome were digested at atmospheric pressure and 37°C for 12 h or in combination with pressure cycling technology at room temperature for 1 min. In all cases, EC‐TR/NPs performed equally to or better than free trypsin in terms of both the identified peptide/protein number and the digestion reproducibility. In addition, the concomitant use of EC‐TR/NPs and pressure cycling technology resulted in very rapid (∼1 min) and efficient digestions with more reproducible digestion results.     

Enzymatic profiles of 11 barophilic bacteria under in situ conditions: evidence for pressure modulation of phenotype.

Barophilic bacteria are microorganisms that grow preferentially (facultative barophiles) or exclusively (obligate barophiles) under elevated hydrostatic pressure. Barophilic bacteria have been isolated from a variety of deep-sea environments. Attempts to characterize these organisms have been hampered by a lack of appropriate methodologies. A colorimetric method for the detection of 19 constitutively expressed enzymes under in situ conditions of pressure and temperature has been devised, using a simple modification of the commercially available API ZYME enzyme assay kit. By using this method, enzyme profiles of 11 barophilic isolates, including an obligate barophile, were determined. Nine of the 10 facultatively barophilic isolates examined exhibited a change of phenotype in at least one enzyme reaction when tested at 1 atm (1 atm = 101.29 kPa), compared with results obtained under in situ pressure. The assay is simple and rapid and allows for direct determination of enzyme activity under conditions of high pressure and low temperature.     

Enzymatic profiles of 11 barophilic bacteria under in situ conditions: evidence for pressure modulation of phenotype

Barophilic bacteria are microorganisms that grow preferentially (facultative barophiles) or exclusively (obligate barophiles) under elevated hydrostatic pressure. Barophilic bacteria have been isolated from a variety of deep-sea environments. Attempts to characterize these organisms have been hampered by a lack of appropriate methodologies. A colorimetric method for the detection of 19 constitutively expressed enzymes under in situ conditions of pressure and temperature has been devised, using a simple modification of the commercially available API ZYME enzyme assay kit. By using this method, enzyme profiles of 11 barophilic isolates, including an obligate barophile, were determined. Nine of the 10 facultatively barophilic isolates examined exhibited a change of phenotype in at least one enzyme reaction when tested at 1 atm (1 atm = 101.29 kPa), compared with results obtained under in situ pressure. The assay is simple and rapid and allows for direct determination of enzyme activity under conditions of high pressure and low temperature.