Search PubMed⌕ Search

Biomedical subjects

G N Somero

Publications and source records attributed to G N Somero.

At least 19 recordsLinked to original sources
PubMed2001

Hypoxia-induced gene expression profiling in the euryoxic fish Gillichthys mirabilis.

Hypoxia is important in both biomedical and environmental contexts and necessitates rapid adaptive changes in metabolic organization. Mammals, as air breathers, have a limited capacity to withstand sustained exposure to hypoxia. By contrast, some aquatic animals, such as certain fishes, are routinely exposed and resistant to severe environmental hypoxia. Understanding the changes in gene expression in fishes exposed to hypoxic stress could reveal novel mechanisms of tolerance that may shed new light on hypoxia and ischemia in higher vertebrates. Using cDNA microarrays, we have studied gene expression in a hypoxia-tolerant burrow-dwelling goby fish, Gillichthys mirabilis. We show that a coherent picture of a complex transcriptional response can be generated for a nonmodel organism for which sequence data were unavailable. We demonstrate that: (i) although certain shifts in gene expression mirror changes in mammals, novel genes are differentially expressed in fish; and (ii) tissue-specific patterns of expression reflect the different metabolic roles of tissues during hypoxia.

Amino Acids↗
PubMed2001

Intrinsic versus extrinsic stabilization of enzymes: the interaction of solutes and temperature on A4-lactate dehydrogenase orthologs from warm-adapted and cold-adapted marine fishes.

We examined the effects of temperature and stabilizing solutes on A4-lactate dehydrogenase (A4-LDH) from warm- and cold-adapted fishes, to determine how extrinsic stabilizers affect orthologs with different intrinsic stabilities. Conformational changes during substrate binding are rate-limiting for A4-LDH, thus stabilization due to intrinsic or extrinsic factors leads to decreased activity. A4-LDH from a warm-temperate goby (Gillichthys mirabilis), which has lower values for kcat and the Michaelis constant for pyruvate ( K m PYR), was intrinsically more stable than the orthologs of the cold-adapted Antarctic notothenioids Parachaenichthys charcoti and Chionodraco rastrospinosus, as shown by a higher apparent transition ('melting') temperature (Tm(APP)). We used four solutes, glycerol, sucrose, trimethylamine-N-oxide and poly(ethylene glycol) 8000, which stabilize proteins through different modes of preferential exclusion, to study temperature-solute interactions of the three orthologs. Changes in Tm(APP) were similar for all orthologs in each solute tested, but the catalytic rate of G. mirabilis A4-LDH was decreased most by solutes and increased most by temperature. In contrast, the K m PYR values of the Antarctic orthologs were more affected than that of the goby by both solutes and temperature. We conclude that (a) preferential exclusion of solutes functions within the native state of A4-LDH to favor conformational microstates with minimal surface area; (b) the varied effects of the different solutes on the kinetic properties are due to the interaction between this nonspecific stabilization and the differing intrinsic stabilities of the orthologs; (c) the catalytic rates of A4-LDH orthologs are equally affected by stabilizing solutes, if measurements are made at physiologically appropriate temperatures; and (d) global stability and localized flexibility of these A4-LDH orthologs may evolve independently.

Animals↗
PubMed2001

A comparative analysis of the evolutionary patterning and mechanistic bases of lactate dehydrogenase thermal stability in porcelain crabs, genus Petrolisthes.

The kinetic properties of orthologous homologs (orthologs) of enzymes are typically correlated with environmental temperatures in species adapted to different thermal regimes, but correlations between adaptation temperature and enzyme thermal stability are less clear. Although the thermal stability of a protein is related chiefly to its primary structure (including post-translational modification), thermal stability can also be altered by extrinsic factors present in the intracellular milieu. Here, we present a comparative analysis of the thermal stability of lactate dehydrogenase (LDH) orthologs from 22 congeneric species of porcelain crab (genera Petrolisthes and Allopetrolisthes) from a broad range of thermal habitats. Interspecific diversity of LDH stability is high: temperatures required for a 50 % loss of activity in 10 min ranged from 65 to 75.5 degrees C, corresponding to half-lives of less than 1 min to more than 3 h at 70 degrees C. Although stability is positively correlated with maximal habitat temperature in some sister taxa, phylogenetic comparative analysis incorporating all 22 species does not indicate that the interspecific diversity of LDH stability represents an adaptive response to current thermal habitats. Examination of the mechanistic bases of LDH stabilization indicates that differences in stability are related both to properties of the LDH molecule itself (intrinsic stability) and to the effects of extrinsic protein(s). Intrinsic differences were shown by the unfolding of structure during heating, as measured by circular dichroism spectroscopy. Stabilizing effects of extrinsic proteins are implied by the results of cellular fractionation experiments that removed low-molecular-mass solutes and proteins from the muscle homogenates. We conclude that the overall structural stability and functional properties of proteins can evolve independently and that in vivo protein-protein interactions can provide another means to regulate protein stability selectively.

Animals↗
PubMed2000

Heat-shock protein expression is absent in the antarctic fish Trematomus bernacchii (family Nototheniidae).

The heat-shock response, the enhanced expression of one or more classes of molecular chaperones termed heat-shock proteins (hsps) in response to stress induced by high temperatures, is commonly viewed as a 'universal' characteristic of organisms. We examined the occurrence of the heat-shock response in a highly cold-adapted, stenothermal Antarctic teleost fish, Trematomus bernacchii, to determine whether this response has persisted in a lineage that has encountered very low and stable temperatures for at least the past 14-25 million years. The patterns of protein synthesis observed in in vivo metabolic labelling experiments that involved injection of (35)S-labelled methionine and cysteine into whole fish previously subjected to a heat stress of 10 degrees C yielded no evidence for synthesis of any size class of heat-shock protein. Parallel in vivo labelling experiments with isolated hepatocytes similarly showed significant amounts of protein synthesis, but no indication of enhanced expression of any class of hsp. The heavy metal cadmium, which is known to induce synthesis of hsps, also failed to alter the pattern of proteins synthesized in hepatocytes. Although stress-induced chaperones could not be detected under any of the experimental condition used, solid-phase antibody (western) analysis revealed that a constitutively expressed 70 kDa chaperone was present in this species, as predicted on the basis of requirements for chaperoning during protein synthesis. Amounts of the constitutively expressed 70 kDa chaperone increased in brain, but not in gill, during 22 days of acclimation to 5 degrees C. The apparent absence of a heat-shock response in this highly stenothermal species is interpreted as an indication that a physiological capacity observed in almost all other organisms has been lost as a result of the absence of positive selection during evolution at stable sub-zero temperatures. Whether the loss of the heat-shock response is due to dysfunctional genes for inducible hsps (loss of open reading frames or functional regulatory regions), unstable messenger RNAs, the absence of a functional heat-shock factor or some other lesion remains to be determined.

Acclimatization↗
PubMed1998

Hot spots in cold adaptation: localized increases in conformational flexibility in lactate dehydrogenase A4 orthologs of Antarctic notothenioid fishes.

To elucidate mechanisms of enzymatic adaptation to extreme cold, we determined kinetic properties, thermal stabilities, and deduced amino acid sequences of lactate dehydrogenase A4 (A4-LDH) from nine Antarctic (-1.86 to 1 degree C) and three South American (4 to 10 degree C) notothenioid teleosts. Higher Michaelis-Menten constants (Km) and catalytic rate constants (kcat) distinguish orthologs of Antarctic from those of South American species, but no relationship exists between adaptation temperature and the rate at which activity is lost because of heat denaturation. In all species, active site residues are conserved fully, and differences in kcat and Km are caused by substitutions elsewhere in the molecule. Within geographic groups, identical kinetic properties are generated by different substitutions. By combining our data with A4-LDH sequences for other vertebrates and information on roles played by localized conformational changes in setting kcat, we conclude that notothenioid A4-LDHs have adapted to cold temperatures by increases in flexibility in small areas of the molecule that affect the mobility of adjacent active-site structures. Using these findings, we propose a model that explains linked temperature-adaptive variation in Km and kcat. Changes in sequence that increase flexibility of regions of the enzyme involved in catalytic conformational changes may reduce energy (enthalpy) barriers to these rate-governing shifts in conformation and, thereby, increase kcat. However, at a common temperature of measurement, the higher configurational entropy of a cold-adapted enzyme may foster conformations that bind ligands poorly, leading to high Km values relative to warm-adapted orthologs.

Adaptation, Physiological↗
PubMed1997

Evolution of lactate dehydrogenase-A homologs of barracuda fishes (genus Sphyraena) from different thermal environments: differences in kinetic properties and thermal stability are due to amino acid substitutions outside the active site.

Orthologous homologs of lactate dehydrogenase-A (LDH-A) (EC 1.1.1.27; NAD+:lactate oxidoreductase) of six barracuda species (genus Sphyraena) display differences in Michaelis-Menten constants (apparent Km) for substrate (pyruvate) and cofactor (NADH) that reflect evolution at different habitat temperatures. Significant increases in Km with increasing measurement temperature occur for all homologs, yet Km at normal body temperatures is similar among species because of the inverse relationship between adaptation temperature and Km. Thermal stabilities of the homologs also differ. To determine the amino acid substitutions responsible for differences in Km and thermal stability, peptide mapping of the LDH-As of all six species was first performed. Then, the amino acid sequences of the three homologs having the most similar peptide maps, those of the north temperate species, S. argentea, the subtropical species, S. lucasana, and the south temperate species, S. idiastes, were deduced from the respective cDNA sequences. At most, there were four amino acid substitutions between any pair of species, none of which occurred in the loop or substrate binding sites of the enzymes. The sequence of LDH-A from S. lucasana differs from that of S. idiastes only at position 8. The homolog of S. argentea differs from the other two sequences at positions 8, 61, 68, and 223. We used a full-length cDNA clone of LDH-A of S. lucasana to test, by site-directed mutagenesis, the importance of these sequence changes in establishing the observed differences in kinetics and thermal stability. Differences in sequence at sites 61 and/or 68 appear to account for the differences in Km between the LDH-As of S. argentea and S. lucasana. Differences at position 8 appear to account for the difference in thermal stability between the homologs of S. argentea and S. lucasana. Evolutionary adaptation of proteins to temperature thus may be achieved by minor changes in sequence at locations outside of active sites, and these changes may independently affect kinetic properties and thermal stabilities.

Amino Acid Sequence↗
PubMed1996

Differences in protein patterns of gill epithelial cells of the fish Gillichthys mirabilis after osmotic and thermal acclimation.

Different protein patterns in gill epithelium of a euryhaline and eurythermal teleost fish (Gillichthys mirabilis, Family Gobiidae) in response to long-term (2 months) osmotic and thermal acclimation were found for the first time. Gill epithelial cells were isolated to remove extracellular proteins and quantify specialized cell types. Chloride cells were identified on the basis of size (> 10 microns) and bright appearance after [2-(p-dimethylaminostyryl)-1-methyl-pyridinium-iodine] staining. Small mitochondria-rich cells were < 5 microns in diameter and showed intermediate fluorescence. Abundance of chloride cells and small mitochondria-rich cells was significantly influenced by osmotic but not thermal acclimation (dilute seawater/25 degrees C: 1.4 +/- 0.2% chloride cells, 11.9 +/- 4.6% small mitochondria-rich cells; seawater/25 degrees C: 2.4 +/- 0.6% chloride cells, 2.2 +/- 1.3% small mitochondria-rich cells; seawater/10 degrees C: 2.9 +/- 0.3% chloride cells, 1.2 +/- 0.7% small mitochondria-rich cells). Pavement cells, identified by low fluorescence and intermediate size (5-10 microns), largely predominated under all conditions (> 85% of cells). Thus, they represented the major protein source in gill epithelium. Differences in protein patterns were detectable using two-dimensional but not one-dimensional electrophoresis. Of 602 proteins identified by charge and molecular weight properties, only two were induced by high temperature (25 degrees C) and three in response to cold acclimation (10 degrees C). Nine proteins were induced in diluted seawater-acclimated fish, whereas no seawater-induced proteins were found. We hypothesize that proteins induced under dilute seawater conditions are important for the function of pavement cells in gills of hyper-osmoregulating G. mirabilis.

Acclimatization↗
PubMed1996

Activity of lactate dehydrogenase but not its concentration of messenger RNA increases with body size in barred sand bass, Paralabrax nebulifer (Teleostei).

In white skeletal muscle of conspecific pelagic fishes, the activity of enzymes associated with anaerobic glycolysis, e.g., lactate dehydrogenase (LDH), usually scale positively with increasing body size; this pattern is opposite to that found for enzymes of aerobic metabolism, which decrease in mass-specific activity with size (1-3). The higher mass-specific capacities for anaerobic ATP generation in larger conspecifics are thought to facilitate conservation of high-speed ("burst") swimming ability in fishes of different sizes (1). To investigate the mechanisms responsible for scaling of LDH activity, total RNA, and the specific mRNA for LDH-A (the skeletal muscle isoform of the enzyme) in white muscle of paralabrax nebulifer, the barred sand bass. We also measured total protein concentration and the concentration of actin, the major protein of thin filaments, and its specific mRNA. Although LDH activity scaled significantly with body size as predicted (1-4), no other biochemical trait measured showed a significant size-dependent concentration. We conclude that the regulation of LDH activity in white muscle of this species is not governed by LDH-A mRNA concentrations, but rather by one or more other mechanisms, for example rate of translation of LDH message or a reduced rate of degradation of LDH-A in larger fish.

Animals↗
PubMed1995

Ion transport in gills of the euryhaline fish Gillichthys mirabilis is facilitated by a phosphocreatine circuit.

The function of creatine kinase (CK) isozymes in energy metabolism and the short-term regulation of active ion transport in gills of the euryhaline teleost Gillichthys mirabilis was investigated. After a transfer of fish from regular seawater [36 parts/thousand (ppt)] to hypersaline water (60 ppt), the plasma osmolality increased significantly from 361.0 +/- 5.2 to 434.2 +/- 20.6 mosmol/kgH2O within 2 h and was regulated down to 391.8 +/- 11.3 mosmol/kgH2O within 12 h. Although the ATP concentration in the gill tissue remained unchanged, the creatine concentration increased significantly from 17.3 +/- 3.2 to 37.6 +/- 5.9 nmol/mg protein within 2 h after the salinity change. CK and Na(+)-K(+)-adenosinetriphosphatase-(Na(+)-K(+)-ATPase) activities were unchanged 48 h after transfer. Independent of salinity, the activities of CK were three to seven times those of the Na(+)-K(+)-ATPase, and the creatine concentration in the gill was at least one order of magnitude higher than the ATP concentration. The occurrence of muscle-type CK (CK-M), brain-type CK, and mitochondrial CK was demonstrated. CK-M was predominant in gills (59 +/- 7.1% of total CK activity). Evidence for a direct functional coupling between CK and Na(+)-K(+)-ATPase was obtained with permeabilized gill cells, by using the CK inhibitor iodoacetamide, which abolishes the competitive channeling of ADP from the external pyruvate kinase reaction to the endogeneous CK reaction in a coupled in situ Na(+)-K(+)-ATPase assay. Our results show the significance and the central regulatory role for energy metabolism and adaptive ionoregulation of a phosphocreatine-CK circuit in situations of high and fluctuating energy demands for euryhaline fishes.

Adenosine Triphosphate↗
PubMed1992

Biochemical ecology of deep-sea animals.

Deep-sea ecosystems contain unique endemic species whose distributions show strong vertical patterning in the case of pelagic animals and sharp horizontal patterning in the case of benthic animals living in or near the deep-sea hydothermal vents. This review discusses the biochemical adaptations that enable deep-sea animals to exploit diverse deep-sea habitats and that help establish biogeographic patterning in the deep-sea. The abilities of deep-sea animals to tolerate the pressure and temperature conditions of deep-sea habitats are due to pervasive adaptations at the biochemical level: enzymes exhibit reduced perturbation of function by pressure, membranes have fluidities adapted to deep-sea pressures and temperatures, and proteins show enhanced structural stability relative to homologous proteins from cold-adapted shallow-living species. Animals from the warmest habitable regions of hydrothermal vent ecosystems have enzymes and mitochondria adapted to high pressure and relatively high temperatures. The low metabolic rates of bathypelagic fishes correlate with greatly reduced capacities for ATP turnover in locomotory muscle. Reduced light and food availability in bathypelagic regions select for low rates of energy expenditure in locomotory activity. Deep-sea animals thus reflect the importance of biochemical adaptations in establishing species distribution patterns and appropriate rates of metabolic turnover in different ecosystems.

Adaptation, Physiological↗
PubMed1992

The threshold induction temperature of the 90-kDa heat shock protein is subject to acclimatization in eurythermal goby fishes (genus Gillichthys).

Two extremely eurythermal goby fishes, Gillichthys mirabilis and Gillichthys seta, which encounter habitat temperature variations of approximately 30 degrees C, showed seasonal acclimatization of endogenous levels and of onset temperatures for enhanced synthesis of a 90-kDa-class heat shock protein (HSP90). Summer-acclimatized fishes had higher levels of HSP90 in brain tissue than winter-acclimatized specimens, as shown by Western blot analysis. For winter-acclimatized fishes, increased synthesis of HSP90 was observed when the temperature was raised from a control temperature (18 degrees C) to 28 degrees C. For summer-acclimatized fish, no significantly increased synthesis of HSP90 occurred until the experimental temperature was raised to 32 degrees C. These data suggest that the threshold temperature at which enhanced expression of HSP-encoding genes occurs is not hard-wired genetically but may be subject to acclimatization. A causal relationship between seasonal changes in steady-state levels of HSP90 and the threshold temperature for enhanced HSP90 synthesis is discussed in terms of existing models for the regulation of HSP gene expression.

Acclimatization↗
PubMed1992

Temperature- and concentration-dependence of compatibility of the organic osmolyte beta-dimethylsulfoniopropionate.

The effects of the organic osmolyte beta-dimethylsulfoniopropionate (DMSP) on the structural stability of three model proteins were examined to determine whether DMSP, like the structurally similar solute dimethyl sulfoxide (DMSO), is compatible with native protein structure at low, but not elevated, temperatures. DMSP stabilized phosphofructokinase under conditions of cold-induced denaturation. Thus, DMSP, like DMSO, may be an effective protein cryoprotectant. However, DMSP was not an effective stabilizer of protein structure under conditions of heat denaturation. Whereas low (0.2 M) concentrations of DMSP stabilized lactate dehydrogenase against inactivation at 50 degrees C, higher DMSP concentrations were ineffective. DMSP favored the denaturation of glutamate dehydrogenase at all DMSP concentrations tested. DMSP may be a compatible osmotic solute only under conditions of moderate temperature and low, yet physiological, concentrations. The mechanistic basis of DMSP's temperature- and concentration-dependent effects and the possible roles played by adaptation temperature and severity of osmotic stress in the evolutionary selection of organic osmolytes are discussed.

Dimethyl Sulfoxide↗
PubMed1992

Adaptations to high hydrostatic pressure.

The importance of adaptation to high pressure has long been implicit in the findings of studies in which 1 atm-adapted species were subjected to elevated pressures. Recent comparative studies have shown that pressure sensitivities of enzymes, structural proteins, and membrane-based systems differ markedly between shallow- and deep-living species. These studies allow operational definition of what constitutes high pressures for different biological structures and processes. These are the habitat (adaptation) pressures at which a given type of system first exhibits reduced perturbation by pressure. These threshold pressures vary among physiological systems, but are similar for a given system among different species. Dehydrogenase enzymes and adenylyl cyclases exhibit threshold perturbation pressures of only 50-100 atm; the Na(+)-K(+)-ATPase of teleost gills appears to have a pressure perturbation threshold near 200 atm, and a similar threshold was found for actin self-assembly. Even this limited sample of physiological processes indicates that the terms deep and high pressure begin to apply at depths of only 500 m or less--and processes yet to be examined in comparative analysis may yield even lower pressure thresholds. The differences in sensitivity to pressure of homologous systems in shallow- and deep-living organisms have implications at several levels of biological organization. The vertical distribution patterns of species in aquatic habitats may be established, in part, by interspecific differences in resistance to pressure. High pressures may restrict the depths to which shallow-living species can penetrate, and the obligately barophilic systems found in deep-living organisms may limit their upper distribution limits. The similarities noted among the adaptations of deep-sea species with different shallow-water ancestors reflect a high degree of convergent evolution in pressure adaptation. It will be interesting to learn if the similarities in pressure-resistance of function among diverse deep-sea species are the result of similar or identical changes at the molecular level, e.g. in protein sequence. Acclimation to pressure may be of widespread occurrence among species that undergo large changes in depth, e.g. during ontogeny. Pressure acclimation may require pressure-regulation of gene expression. Lastly, comparisons of species from the cold deep sea with those from hydrothermal vents have shown that adaptations to both temperature and pressure play critical roles in determining the distribution patterns of deep-living species.

Adaptation, Physiological↗
PubMed1989

Properties of the interaction between phosphofructokinase and actin.

The interaction of rabbit skeletal muscle phosphofructokinase (PFK) with actin is characterized in terms of the binding of PFK to actin in the presence and absence of tropomyosin and troponin, the effect of PFK on actin polymerization, and the involvement of adenylates in the binding of PFK to actin. The thin filament proteins, tropomyosin and troponin, are associated with skeletal muscle actin and reduce the binding of PFK to actin, thus influencing the probable distribution of PFK in skeletal muscle. The binding of PFK to actin is inhibited by ATP and ADP but not by fructose 6-phosphate or fructose 2,6-bisphosphate. This specific inhibition, plus evidence from fluorescence quenching and photoaffinity labeling, suggests that actin binds at the adenosine activation sites of PFK. Light scattering measurements used to monitor actin polymerization indicate that PFK dramatically increases the level of light scattering produced by the polymerization of actin, indicative of a superaggregate of PFK and actin. PFK inhibits the polymerization of actin when polymerization is induced by low concentrations of added salts. Although PFK binds to actin with high affinity, it seems to have little effect on the high shear viscosity of actin filaments.

Actins↗
PubMed1989

Pressure adaptation of Na+/K+-ATPase in gills of marine teleosts.

The effects of pressure and temperature on an integral membrane protein, Na+/K+-adenosine triphosphatase (Na+/K+-ATPase), were studied in fish gill membrane preparations from shallow- and deep-living marine teleosts. The inhibition by pressure of maximal velocity of the enzyme is nonlinear, increasing at higher pressures. Na+/K+-ATPases from deep-sea fish were less inhibited by pressure than those of shallow-living species. Habitat temperature also affected the pressure response of the enzyme. As a function of physiological pressure and temperature, the order of increasing pressure-sensitivity was cold, deep-sea less than warm, deep-sea (hydrothermal vents) less than polar = shallow and mid-depth, cold less than shallow, warm. Activation volumes in all species were conserved at 30-60 ml mol-1 at physiological pressures, which may reflect a similar membrane physical state at the actual pressure the animal experiences. Arrhenius plots [In(Na+/K+-ATPase activity) vs 1/T] were steeper for warm-water and shallow-living species than for deep-sea species. The depth at which adaptation was first observed was about 2000 m (approximately equal to 200 atm: 1 atm = 101.3 kPa). The data are consistent with a model of increased membrane fluidity resulting in reduced pressure-sensitivity of Na+/K+-ATPase from deep-sea species.

Acclimatization↗