Primary structure of glyceraldehyde-3-phosphate dehydrogenase deduced from the nucleotide sequence of the thermophilic archaebacterium Methanothermus fervidus

The gene for the glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from the thermophilic methanogenic archaebacterium Methanothermus fervidus (growth optimum at 84 degrees C) was cloned in Escherichia coli and the nucleotide sequence was determined. A striking preference for adenine and thymidine bases was found in the gene, which is in agreement with the low G + C content of the M. fervidus DNA. The deduced amino acid sequence indicates an Mr of 37,500 for the protein subunit. Alignment with the amino acid sequences of GAPDHs from other organisms shows that the archaebacterial GAPDH is homologous to the respective eubacterial and eukaryotic enzymes, but the similarity between the archaebacterial enzyme and the eubacterial or eukaryotic GAPDHs is much less than that between the latter two.     

Ethanol production with Saccharomyces cerevisiae under aerobic conditions at different potassium concentrations

The specific ethanol productivity with Saccharomyces cerevisiae grown aerobicly in a chemostat was found to be highly dependent on the ratio of intracellular to extracellular potassium concentration through variations in the energy consumption used for maintenance of the concentration gradient of potassium across the cell membrane. The specific ethanol productivity progressively rose from 0 to 20 mmol h(-1) g(-1) cell dry matter at a growth rate of 0.17 h(-1) when the ratio of intracellular to extracellular potassium concentration was increased from 10 to 80. The ethanol production under potassium limited growth conditions was caused neither by a reduction in the specific respiratory activity nor by variations in the potassium content in cell dry matter. Results which strongly that ethanol production under potassium limited growth conditions is brought about by changes in the ratio of pyruvate oxidase to pyruvate decarboxylase activity through changes in the intracellular pyruvate concentration are presented.     

Glyceraldehyde-3-phosphate dehydrogenase from the hyperthermophilic archaebacterium Pyrococcus woesei: characterization of the enzyme, cloning and sequencing of the gene, and expression in Escherichia coli.

The glyceraldehyde-3-phosphate dehydrogenase from the hyperthermophilic archaebacterium Pyrococcus woesei (optimal growth temperature, 100 to 103 degrees C) was purified to homogeneity. This enzyme was strictly phosphate dependent, utilized either NAD+ or NADP+, and was insensitive to pentalenolactone like the enzyme from the methanogenic archaebacterium Methanothermus fervidus. The enzyme exhibited a considerable thermostability, with a 44-min half-life at 100 degrees C. The amino acid sequence of the glyceraldehyde-3-phosphate dehydrogenase from P. woesei was deduced from the nucleotide sequence of the coding gene. Compared with the enzyme homologs from mesophilic archaebacteria (Methanobacterium bryantii, Methanobacterium formicicum) and an extremely thermophilic archaebacterium (Methanothermus fervidus), the primary structure of the P. woesei enzyme exhibited a strikingly high proportion of aromatic amino acid residues and a low proportion of sulfur-containing residues. The coding gene of P. woesei was expressed at a high level in Escherichia coli, thus providing an ideal basis for detailed structural and functional studies of that enzyme.     

Organic Solutes in Hyperthermophilic Archaea

We examined the accumulation of organic solutes under optimum growth conditions in 12 species of thermophilic and hyperthermophilic Archaea belonging to the Crenarchaeota and Euryarchaeota. Pyrobaculum aerophilum, Thermoproteus tenax, Thermoplasma acidophilum, and members of the order Sulfolobales accumulated trehalose. Pyrococcus furiosus accumulated di-myo-inositol-1,1(prm1)(3,3(prm1))-phosphate and (beta)-mannosylglycerate, Methanothermus fervidus accumulated cyclic-2,3-bisphosphoglycerate and (beta)-mannosylglycerate, while the only solute detected in Pyrodictium occultum was di-myo-inositol-1,1(prm1)(3,3(prm1))-phosphate. Methanopyrus kandleri accumulated large concentrations of cyclic-2,3-bisphosphoglycerate. On the other hand, Archaeoglobus fulgidus accumulated three phosphorylated solutes; prominent among them was a compound identified as di-glycerol-phosphate. This solute increased in concentration as the salinity of the medium and the growth temperature were raised, suggesting that this compound serves as a general stress solute. Di-myo-inositol-1,1(prm1)(3,3(prm1))-phosphate accumulated at supraoptimal temperature only. The relationship between the accumulation of unusual solutes and high temperatures is also discussed.     

Expression of the glyceraldehyde-3-phosphate dehydrogenase gene from the extremely thermophilic archaebacterium Methanothermus fervidus in E. coli. Enzyme purification, crystallization, and preliminary crystal data

The gene of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from the extremely thermophilic archaebacterium Methanothermus fervidus (growth optimum 82 degrees C) was cloned in vector pJF118EH and expressed in E. coli cells. As shown by molecular mass determination, protein sequencing, heat stability, and substrate saturation kinetics, the enzyme synthesized in E. coli is identical to the original enzyme from M. fervidus. The high thermostability of the E. coli-produced M. fervidus GAPDH allows rapid purification to homogeneity. From this enzyme protein crystals were grown which proved to be suitable for X-ray analysis. The crystals are of tetragonal space group P4(1)22 and contain a dimer per asymmetric unit.     

Effect of fluoride and other metabolic inhibitors on intracellular sodium and potassium concentrations in L cells

Fluoride, iodoacetate, oxamate, 2,4-dinitrophenol, cycloheximide, and ouabain were studied to determine if any of these inhibitors affected the intracellular concentration of sodium and potassium in an L cell strain of mouse fibroblasts and to determine if the changes observed in these parameters could be correlated with growth rate. The results indicated that (1) the intracellular concentration of sodium and potassium could not be correlated with growth rate, (2) fluoride, iodoacetate, oxamate, 2,4-dinitrophenol, and cycloheximide at concentrations having an equal effect on growth had a similar effect on the intracellular sodium and potassium concentration These changes were not as great as those seen with ouabain, which at a concentration which did not inhibit growth, had an equal or greater effect on the intracellular sodium and potassium concentration.     

Histone HMf from the hyperthermophilic archaeon Methanothermus fervidus binds to DNA in vitro using physiological conditions

Abstract The concentration of HMf (histone Methanothermus fervidus ) in vivo has been shown to be between 1 and 2 × 10⁴ molecules per genome. At this mass ratio the amount of HMf bound to pUC19 DNA in vitro was found to be dependent on the topology of the plasmid DNA. M. fervidus grows optimally between 80 and 85°C and contains approx. 1 M K⁺ plus 300 mM 2'3'(cyclic) diphosphoglycerate. (Hensel, R. and König, H. 1988. FEMS Microbiol. Lett. 49, 75–79). HMf binding to DNA in vitro under these conditions has been demonstrated.     

Issues in the culture of the extremely thermophilic methanogen, Methanothermus fervidus

Basic issues in the culture of the extremely thermophilic archaeon, Methanothermus fervidus, have been investigated, including culture medium formulation, substrate yield and product yield coefficient, growth rate and stoichiometry, and H(2) uptake kinetics. The pH optimum for growth of this organism was estimated at 6.9. Growth medium buffered with PIPES instead of bicarbonate supported both increased growth rate and maximum biomass concentration. Substitution of titanium(III) citrate for the reducing agent sodium sulfide improved culture performance as well. However, independent adjustment of iron and nickel concentrations from 11 to 111 muM, respectively, and carbon dioxide partial pressure from 5 to 20 psia did not impact the culture of M. fervidus significantly. An elemental balance approach was utilized to aid in design of a defined medium to support growth to a target maximum biomass concentration of at least 1.0 g dry wt/L. The growth of this organism was limited by H(2) availability in this reformulated culture medium. The maximum growth rate and biomass concentration achieved in anaerobic vials with the defined medium was 0.16 h(-1) and 0.74 g dry wt/L, respectively. This maximum biomass concentration was a 72% improvement over that obtained with a literature-based defined medium. The Monod parameter, K(s), with H(2) as limiting substrate, was estimated at 1.1 +/- 0.4 psia (55 +/- 20 muM in the broth), based on a H(2) consumption study. Representative values for the substrate yield, Y(X/CO(2) ), and product yield coefficient, Y(CH(4)/) (X), were determined experimentally to be 1.78 +/- 0.04 g dry wt/mol CO(2), and 0.52 +/- 0.01 mol CH(4)/g dry wt, respectively. A bench-scale fermentation system suitable for the culture of extremely thermophilic anaerobes was designed and constructed and proved effective for the culture of M. fervidus. (c) 1993 Wiley & Sons, Inc.     

Dehydrogenase and electrochemical activity of <Emphasis Type="Italic">Escherichia coli</Emphasis> extracts

The dehydrogenase activity of Escherichia coli BB cell extracts was studied at different growth stages in the presence of different substrates and triphenyl tetrazolium chloride as an electron acceptor. It was shown that the highest degree of reduction of triphenyl tetrazolium chloride was observed during exponential growth of the bacteria when potassium isocitrate was used as a substrate. It was found that extracts of the bacteria during the exponential phase of growth on an inert glassy carbon electrode in a three-electrode liquid electrochemical cell manifested electrochemical activity in the presence of potassium citrate and methylene blue or potassium hexacyanoferrate(III) as redox mediators.     

Purification and characterization of D-glyceraldehyde-3-phosphate dehydrogenase from the thermophilic archaebacterium Methanothermus fervidus

The D-glyceraldehyde-3-phosphate dehydrogenase from the extremely thermophilic archaebacterium Methanothermus fervidus was purified and crystallized. The enzyme is a homomeric tetramer (molecular mass of subunits 45 kDa). Partial sequence analysis shows homology to the enzymes from eubacteria and from the cytoplasm of eukaryotes. Unlike these enzymes, the D-glyceraldehyde-3-phosphate dehydrogenase from Methanothermus fervidus reacts with both NAD+ and NADP+ and is not inhibited by pentalenolactone. The enzyme is intrinsically stable up to 75 degrees C. It is stabilized by the coenzyme NADP+ and at high ionic strength up to about 90 degrees C. Breaks in the Arrhenius and Van't Hoff plots indicate conformational changes of the enzyme at around 52 degrees C.     

Engineering thermostability in archaebacterial glyceraldehyde-3-phosphate dehydrogenase. Hints for the important role of interdomain contacts in stabilizing protein conformation

Construction of hybrid enzymes between the glyceraldehyde-3-phosphate dehydrogenases from the mesophilic Methanobacterium bryantii and the thermophilic Methanothermus fervidus by recombinant DNA techniques revealed that a short C-terminal fragment of the Mt. fervidus enzyme contributes largely to its thermostability. This C-terminal region appears to be homologous to the alpha 3-helix of eubacterial and eukaryotic glyceraldehyde-3-phosphate dehydrogenases which is involved in the contacts between the two domains of the enzyme subunit. Site-directed mutagenesis experiments indicate that hydrophobic interactions play an important role in these contacts.     

Inhibition of growth of Rhizobium japonicum by cyclic GMP.

Exogenous cyclic guanosine-3',5'-monophosphate (cGMP) inhibited the growth of Rhizobium japonicum at less than 100 microM. Other nucleotides, including cyclic AMP, cyclic IMP, and cyclic CMP, had no inhibitory effect even at higher concentrations nor was the inhibition by cGMP reversed by cyclic AMP. The inhibitory effect was independent of the carbon and nitrogen source(s) used. cGMP did not inhibit the growth of any other species of bacterium tested, including several fast-growing Rhizobium species. The kinetics of growth inhibition are multiphasic, with no apparent effect for several hours after addition, followed by a period of total inhibition. Subsequently, growth resumed at a slower rate. Resumption of growth was not due to destruction of the nucleotide. Studies of the intracellular cGMP concentration did not reveal significant changes in cells grown under aerobic or microaerobic conditions. No effect of cGMP on the derepression of respiratory nitrate reductase was observed.     

Adenosine 3′:5′-cyclic monophosphate concentrations and phosphodiesterase activities during axenic growth and differentiation of cells of the cellular slime mould Dictyostelium discoideum

During growth of myxamoebae of Dictyostelium discoideum (strain Ax-2) in axenic medium, the myxamoebae secrete cyclic AMP. As the cells leave the exponential phase of growth and enter the stationary phase, there is an approximate doubling of the intracellular cyclic AMP content, but the amount of extracellular cyclic AMP remains proportional, at all times, to the number of myxamoebae present. During development of axenically grown myxamoebae, there is first a rise in the intracellular concentration of cyclic AMP, followed by a rise in the amount of extracellular cyclic AMP, which reaches a peak at the time of aggregation and then declines. There is a second peak in the amount of extracellular cyclic AMP found at the time of fruiting-body formation, but this second peak is not associated with a rise in the intracellular cyclic AMP concentration. Controls thus exist over the synthesis and secretion of cyclic AMP. Evidence is presented for the belief that the activity of the adenylate cyclase enzyme controls the amount of cyclic AMP synthesized rather than the activity or amount of cyclic AMP phosphodiesterase present. Similar changes occur in extracellular cyclic AMP and phosphodiesterase concentrations during incubation of myxamoebae in buffered suspensions to those occuring during the first few hours of development of such cells on solid media, but the timing of these changes is different.     

Nucleotide sequence of the glyceraldehyde-3-phosphate dehydrogenase gene from the mesophilic methanogenic archaebacteria Methanobacterium bryantii and Methanobacterium formicicum. Comparison with the respective gene structure of the closely related extreme thermophile Methanothermus fervidus

The genes for glyceraldehyde-3-phosphate dehydrogenase (gap genes) from the mesophilic methanogenic archaebacteria Methanobacterium formicicum and Methanobacterium bryantii were cloned and sequenced. The deduced amino acid sequences show 95% identity to each other and about 70% identity to the glyceraldehyde-3-phosphate dehydrogenase from the thermophilic methanogenic archaebacterium Methanothermus fervidus. Although the sequence similarity between the archaebacterial glyceraldehyde-3-phosphate dehydrogenase and the homologous enzyme of eubacteria and eukaryotes is low, an equivalent secondary-structural arrangement can be deduced from the profiles of the physical parameters hydropathy, chain flexibility and amphipathy. In order to find possible thermophile-specific structural features of the enzyme from M. fervidus, a comparative primary-sequence analysis was performed. Amino acid exchanges leading, to a stabilization of the main-chain conformation, could be found throughout the sequence of the thermophile enzyme. Striking features of the thermophile sequence are the preference for isoleucine, especially in beta-sheets, and a low arginine/lysine ratio of 0.54.     

Regulation of phosphoglycerate dehydrogenase levels and effect on serine synthesis in Escherichia coli K-12.

The level of phosphoglycerate dehydrogenase, the first enzyme in the biosynthetic pathway to serine and glycine, has been studied in Escherichia coli grown under different conditions. The enzyme level was not reduced by growth in a medium which contained the end products of the pathway, nor was it elevated when the growth rates was limited by the supply of serine. Elevation of phosphoglycerate dehydrogenase did not occur when charging of tRNA ser was inhibited by serine hydroxamate. However, phosphoglycerate dehydrogenase levels were subject to regulation. Elevated levels of enzyme activity were observed in merodiploids containing multiple copies of the serA gene, and lowered enzyme levels were found in cells grown on carbon sources other than glucose or when certain amino acids were present in the growth medium. The combined effect of these nutritional changes (carbon source and amino acids) reduced the level of phosphoglycerate dehydrogenase to 10 to 12% of that found in wild-type cells and to about 5% of the level in the merodiploids. By using antibody prepared against purified phosphoglycerate dehydrogenase we established that the decrease in enzyme activity reflected decreased amounts of enzyme protein. Constant intracellular concentrations of 3-phosphoglycerate and serine were found in cells with marked differences in phosphoglycerate dehydrogenase activity, indicating that end product inhibition of phosphoglycerate dehydrogenase activity, rather than the amount of the biosynthetic enzymes, is the major factor in regulating the intracellular concentration of serine.     

The effect of potassium on growth of Carex species from swamp habitats varying from oligotrophic to eutrophic and comparison of physiological reactions of Carex species to P stress and K stress

In a growth experiment at potassium levels varying between 0.001 m M and 3.0 m M potassium, relative growth rate (RGR) and other growth parameters were determined in Carex species: C. rostrata Stokes, C. limosa L., C. lasiocarpa Ehrh., C. diandra Schrank and C. acutiformis Ehrh., listed in order of increasing nutrient availability of their habitats. Carex species of nutrient poor sites did grow faster at low potassium concentration than species from nutrient rich habitats. The RGR of C. limosa was not affected by the K concentration, even at the lowest potassium concentration (0.001) m M ) used. At high potassium availability Carex species from nutrient-rich sites responded with greatly increased RGR, whereas the Carex from nutrient-poor sites absorbed potassium in excess of immediate growth requirements: luxury consumption. A comparison is made of the physiology of the Carex species as affected by stress and abundance of phosphate and potassium.     

Thermolability of Malic Dehydrogenase from the Obligate Psychrophile Vibrio marinus

Langridge, Patricia (Oregon State University, Corvallis), and Richard Y. Morita. Thermolability of malic dehydrogenase from the obligate psychrophile Vibrio marinus. J. Bacteriol. 92:418-423. 1966.-The thermolability of malic dehydrogenase in whole cells of Vibrio marinus MP-1 grown at 15 C was compared with that of cell-free extracts and partially purified fractions. The intracellular enzyme was found to be stable between 0 C, and the organism's optimal growth temperature, 15 C. In cell-free extracts, considerable lability was noted even at 0 C, and this lability did not increase further until the enzyme was exposed to temperatures above the organism's maximal growth temperature (20 C). Twenty-fold purified enzyme was stable between 15 and 20 C, but both above and below this there was considerable inactivation. A 5-min exposure of both cold- and heat-inactivated enzyme to 15 C allowed reactivation, although to a different extent. Ammonium sulfate was found both to stimulate enzyme activity and to reactivate temperature-inactivated enzyme.     

Dependence of intracellular alkali-ion concentrations of 3T3 and SV 40-3T3 cells on growth density.

Intracellular contents of potassium and of sodium are determined for 3T3 and SV 40-3T3 cells in dependence of growth density. In parallel, total cell volume and volume of intracellular water is determined for these cells suspended in physiological buffer. Intracellular potassium concentration thus evaluated for suspended 3T3 cells exhibits a sharp decrease at cellular growth densities which lead to density dependent inhibition of cell proliferation. In the case of SV 40-3T3 cells, this drop of potassium concentration with increasing cellular growth density is not observed, which correlates well with the absence of cell density dependent inhibition of cell growth in the transformed cell line. These results support the notion that processes of stimulation of quiescent 3T3 cells or of cell density dependent inhibition of their proliferation are mediated by processes including changes of potassium transport characteristics leading to increase or decrease respectively of their intracellular potassium concentration. Furthermore, these and other results suggest, that a difference between normal and transformed cells most relevant to their different proliferation behaviour might reside in different transport characteristics for potassium of the plasma membranes of these cells.     

Phospholipid etherlipid and phospholipid fatty acid fingerprints in selected euryarchaeotal monocultures for taxonomic profiling

Phospholipid etherlipid (PLEL) derived isoprenoids and phospholipid fatty acids (PLFA) were determined in eight Euryarchaeotal monocultures for taxonomic profiling. For the first time significant amounts of fatty acids in the PLFA of Euryarchaeota were determined. The PLFA proportion varied between 11.3 and 35.5% of the total phospholipid side chains except in Methanothermus fervidus where PLFA accounted for 89.0% of the total phospholipid side chains. Fractionation of fatty acids prior to gas chromatography mass spectrometry analysis revealed that non-ester-linked fatty acids dominated which accounted for 85.5-95.2% of total PLFA in all investigated archaeal strains. PLEL concentration and composition was estimated in accordance with previous studies with two exceptions. In the polar (phospho)lipid fraction of Methanopyrus kandleri side chains possibly derived from hydroxyarchaeol as well as acyclic and cyclic caldarchaeol were identified. In phospholipid extracts of Methanothermus fervidus the 'H-formed' caldarchaeol could not be detected. Overall, PLEL derived isoprenoids as well as PLFA enabled taxonomic differentiation of the selected microorganisms into phylogenetically related groups.     

Osmotic repression of anaerobic metabolic systems in Escherichia coli.

The influence of the osmolarity of the growth medium on anaerobic fermentation and nitrate respiratory pathways was analyzed. The levels of several enzymes, including formate dehydrogenase, hydrogenase, and nitrate reductase, plus a nickel uptake system were examined, as was the expression of the corresponding structural and regulatory genes. While some functions appear to be only moderately affected by an increase in osmolarity, others were found to vary considerably. An increase in the osmolarity of the medium inhibits both fermentation and anaerobic respiratory pathways, though in a more dramatic fashion for the former. fnr expression is affected by osmolarity, but the repression of anaerobic gene expression was shown to be independent of FNR regulatory protein, at least for hyd-17 and fdhF. This repression could be mediated by the intracellular concentration of potassium and is reversed by glycine betaine.