Comparative studies on redox proteins from ammonia-oxidizing bacteria

Abstract Soluble fractions prepared from representatives of 3 genera of ammonia-oxidising bacteria all contained CO-binding c -type cytochromes and the cytochrome P-460 chromophore. Hydroxylamine oxidase from terrestrial strains of Nitrosomonas europaea was immunologically related to the analogous protein from marine strains of the same genus. Soluble cytochrome oxidase nitrite reductase activity was detected only in extracts prepared from terrestrial strains of N. europaea among the organisms examined.     

Superoxide dismutase biosynthesis by two thermophilic bacteria

Some high-molecular weight antioxidant defense system components of two thermophilic bacteria isolated from spa waters of Serbia (Yugoslavia) and identified as Bacillus stearothermophilus and Thermothrix sp. were studied. In addition to superoxide dismutase (SOD; EC 1.15.1.1), qualitative analyses demonstrated the presence of catalase (EC 1.11.1.6), peroxidases and oxidases in both bacterial strains. Cell-free extracts were subjected to nondenaturing polyacrylamide gel electrophoresis (PAGE) and SOD activity in the eluates of the corresponding bands was examined in the presence of several specific inhibitors. A slight decrease of SOD activity observed in the presence of 0.3 M potassium cyanide and its complete insensitivity to hydrogen peroxide (5 mM) and sodium azide (20 mM) action suggest that the enzyme occurring in the two thermophiles represents Mn SOD. A high SOD activity recorded in cell-free extracts strongly recommends these two bacterial strains as potential producers of this important antioxidant defense system component at industrial scale.     

Isolation and characterization of two novel ethanol-tolerant facultative-anaerobic thermophilic bacteria strains from waste compost

In a search for potential ethanologens, waste compost was screened for ethanol-tolerant thermophilic microorganisms. Two thermophilic bacterial strains, M5EXG and M10EXG, with tolerance of 5 and 10% (v/v) ethanol, respectively, were isolated. Both isolates are facultative anaerobic, non-spore forming, non-motile, catalase-positive, oxidase-negative, Gram-negative rods that are capable of utilizing a range of carbon sources including arabinose, galactose, mannose, glucose and xylose and produce low amounts of ethanol, acetate and lactate. Growth of both isolates was observed in fully defined minimal media within the temperature range 50–80°C and pH 6.0–8.0. Phylogenetic analysis of the 16S rDNA sequences revealed that both isolates clustered with members of subgroup 5 of the genus Bacillus. G+C contents and DNA–DNA relatedness of M5EXG and M10EXG revealed that they are strains belonging to Geobacillus thermoglucosidasius. However, physiological and biochemical differences were evident when isolates M5EXG and M10EXG were compared with G. thermoglucosidasius type strain (DSM 2542^T). The new thermophilic, ethanol-tolerant strains of G. thermoglucosidasius may be candidates for ethanol production at elevated temperatures.     

Starch-hydrolyzing enzymes from thermophilic archaea and bacteria

Extremophlic microorganisms have developed a variety of molecular strategies in order to survive in harsh conditions. For the utilization of natural polymeric substrates such as starch, a number of extremophiles, belonging to different taxonomic groups, produce amylolytic enzymes. This class of enzyme is important not only for the study of biocatalysis and protein stability at extreme conditions but also for the many biotechnological opportunities they offer. In this review, we report on the different molecular properties of thermostable archaeal and bacterial enzymes including alpha-amylase, alpha-glucosidase, glucoamylase, pullulanase, and cyclodextrin glycosyltransferase. Comparison of the primary sequence of the pyrococcal pullulanase with other members of the glucosyl hydrolase family revealed that significant differences are responsible for the mode of action of these enzymes.     

嗜热菌的耐热L—乳酸脱氢酶的研究

About 200 strains of extreme thermophilic bacteria were isolated from hot springs in Guandong province. A strain, HG25, was found to produce thermostable intracellular L-lactate dehydrogenase (EC. 1.1.1.27). It has the characteristic of Thermus sp. The cells were gram-negative, non-sporulating, nonmotile, aerobic rods containing yellow pigment. The optimum temperature for growth was between 65 degrees C to 75 degrees C, the maximum 85 degrees C, and minimum 40 degrees C. The generation time at the optimum was about 80 min. Starch was not hydrolyzed. Acid was not produced from glucose. The G+C content in DNA was 62-65 mol% (Tm). As the properties of strain HG25 is similar to those of Thermus aquaticus and T. thermophilus HB 8 belonging to the genus Thermus. The thermostable L-lactate dehydrogenase was partially purified by ammonium sulfate fractionation and DEAE-cellulose column chromatography. For pyruvate reduction, the optimum temperature of the enzyme was 60 degrees C and pH 8.0. After incubation in 0.1 mol/L phosphate buffer pH 7.4 at 70 degrees C for 10 min, the enzyme retained about 85% of its original activity. The half-live time (t1/2) at 85 degrees C was 10 min.     

Comparative studies of RNA polymerase subunits from various bacteria

Summary The molecular structure of RNA polymerases from Escherichia coli, Salmonella typhimurium, Salmonella anatum, Serratia marcescens, Aerobacter aerogenes, Proteus mirabilis and Bacillus subtilis were compared based on: i) inhibition of the enzyme activity by treatment with antibodies against E. coli RNA polymerase subunits; ii) analysis of antibody precipitates by sodium dodecyl sulfatepolyacrylamide gel electrophoresis; and iii) analysis of antibody precipitates by urea-isoelectrofocusing followed by sodium dodecyl sulfate-slab gel electrophoresis in the second dimension.All the bacterial RNA polymerases examined cross-react equally with anti-E. coli holopolymerase but exhibit different extents of cross-reaction with antibodies against individual subunits. Except for B. subtilis RNA polymerase, the molecular weight and isoelectric point of the enzyme subunits are close to those of E. coli polymerase. However, minor differences were found at least within the resolution of the techniques employed: S. anatum polymerase has subunit larger than E. coli subunit; P. mirabilis enzyme has subunit larger in size and more acidic in charge, and subunit smaller and more basic than corresponding E. coli subunits. The electrophoretic map of B. subtilis enzyme subunits is completely different from that of E. coli enzyme.     

嗜热菌的耐热分子机制

对嗜热菌耐热机制在其细胞表层结构、ＤＮＡ螺旋的热稳定性和嗜热菌酶耐热性等方面的研究作一综述。     

The effect of nutrients and precursors on the fatty acid composition of two thermophilic bacteria

Summary Growing the two strains B. caldolyticus and B. caldotenax on several substrates has shown that the fatty acid composition of both bacteria is not very significantly altered by the carbon source. The fatty acid pattern of B.caldolyticus was, however, drastically varied if the BHI-complex was omitted from the medium, resulting mainly in an increase of the br.-even, str.-even, str.-odd, and anteiso compounds, accompanied by a sharp decrease of the br.-odd fatty acids. Leucine, isoleucine, or valine were found to act as precursors for the corresponding fatty acids even with final concentrations as low as 0.05 mM, leading to the predominance of either iso-odd, anteiso-odd, or iso-even compounds. Simultaneously the activity of extracellular enzymes was found to vary. Along with the decrease of the n-even and iso-even fatty acids, and the increase of the iso-odd compounds as a result of increased amounts of leucine added to the medium, the growth of B.caldolyticus was found to decline.     

Thermostability of l-phenylalanine aminotransferase from thermophilic bacteria

Summary Various mesophilic and thermophilic bacteria were screened for the presence of thermostable l-phenylalanine aminotransferases. With organisms from culture collections best results were obtained with Thermus aquaticus and Bacillus caldolyticus. Cell-free extracts of these bacteria contained enzymes which did not lose activity by heat treatment at 60°C for 25 min, although they became rapidly inactivated during incubation at 70°C. Bacillus species able to grow at 70–75°C in mineral medium with phenylalanine as the sole carbon- and energy source were subsequently isolated in pure culture. At 70°C Bacillus strain IS1 grew on phenylalanine with a doubling time of 35 min and synthesized a phenylalanine aminotransferase which only slowly lost activity when incubated at 70°C and was stable at 60°C for at least 7 h.During the purification of the phenylalanine aminotransferase from Bacillus IS1 only a single peak of activity was observed consistently. This enzyme showed activity with phenylalanine and tyrosine but not with aspartate. The apparent K _m values for phenylalanine and tyrosine were 0.95 and 0.77 mM, respectively. The enzyme had an optimum pH of 6.4 and a temperature optimum of 71.5°C for the deamination of phenylalanine. Similar levels of the enzyme were synthesized during growth of Bacillus IS1 on a variety of substrates, suggesting that it functions in phenylalanine (and tyrosine) biosynthesis rather than in phenylalanine catabolism.Dedicated to Prof. Dr. H. J. Rehm on the occasion of his 60th birthday     

Growth conditions and temperature-dependent substrate specificity of two extremely thermophilic bacteria

Summary Conditions for cultivating two extremely thermophilic bacteria, isolated from the hot springs of Yellowstone National Park, are described. One of these strains, Thermus aquaticus, can be grown on either succinate or pyruvate as the best substrates at 78° C. Acetate, glucose, and sucrose can also be utilized at this temperature. The temperature optimum was found to be 70° C, but the bacterium can be adapted to grow on succinate or pyruvate at 80° C. The other strain, YT-G has its growth optimum at 80° C and the maximum temperature was found to be 84° C. At this temperature pyruvate is the only substrate which gives good results, while glucose cannot be used as a carbon source. At 70° C, however, the yields obtained with glucose as a substrate are better than those with pyruvate at 80° C.Experiments with C¹⁴-labelled glucose have shown that the inability to utilize glucose at 80° C is not due to an inactivation of the initial steps of the glycolytic pathway. Phosphorylated sugars and a compound corresponding to -glycerophosphate were found to be formed, the latter being accumulated as a side product of normal glycolysis. The enzymes leading to this product, and those which are involved in the conversion of pyruvate were found to be functioning at 80° C, while intermediate enzymes of the glycolytic pathway are assumed to be less heat resistant, thus blocking the utilization of glucose at this temperature. The ability of strain YT-G to grow on glucose is, however, promptly resumed if the temperature is lowered.Lysozyme treatment was found to lead to a complete conversion of T. aquaticus cells to spheroplast while cells of strain YT-G are only slightly altered by this procedure.     

Cellulose- and xylan-degrading thermophilic anaerobic bacteria from biocompost

Nine thermophilic cellulolytic clostridial isolates and four other noncellulolytic bacterial isolates were isolated from self-heated biocompost via preliminary enrichment culture on microcrystalline cellulose. All cellulolytic isolates grew vigorously on cellulose, with the formation of either ethanol and acetate or acetate and formate as principal fermentation products as well as lactate and glycerol as minor products. In addition, two out of nine cellulolytic strains were able to utilize xylan and pretreated wood with roughly the same efficiency as for cellulose. The major products of xylan fermentation were acetate and formate, with minor contributions of lactate and ethanol. Phylogenetic analyses of 16S rRNA and glycosyl hydrolase family 48 (GH48) gene sequences revealed that two xylan-utilizing isolates were related to a Clostridium clariflavum strain and represent a distinct novel branch within the GH48 family. Both isolates possessed high cellulase and xylanase activity induced independently by either cellulose or xylan. Enzymatic activity decayed after growth cessation, with more-rapid disappearance of cellulase activity than of xylanase activity. A mixture of xylan and cellulose was utilized simultaneously, with a significant synergistic effect observed as a reduction of lag phase in cellulose degradation.     

Structural and dynamic aspects of beta-glycosidase from mesophilic and thermophilic bacteria by multitryptophanyl emission decay studies

The tryptophanyl emission decay of beta-glycosidase from the extremophilic archaeon Sulfolobus solfataricus (Sbetagly) has been investigated by frequency domain fluorometry. The data were analyzed in terms of sum of discrete lifetimes as well as in terms of quasi- continuous lifetime distributions of different shape. At neutral pH the emission decay is characterized by two components: a long-lived component, centered at 7.4 ns, and a short one at 2.7 ns, irrespective of the decay scheme used for the interpretation of the experimental results. The effects of an irreversible inhibitor, that is, cyclophellitol, and that of a powerful denaturant such as guanidinium hydrochloride on the dynamics of Sbetagly has been investigated by observing the changes induced in the two components of the tryptophanyl emission decay. The addition of cyclophellitol to native Sbetagly reduces the contribution of the short-lived component but does not affect the long-lived one. Increasing concentrations of guanidinium hydrochloride differently affect the contributions of the two emission components. Higher concentrations were required to unfold the molecular regions containing the long-lived indolic fluorophores. These results indicate that the long-lived contribution arises from tryptophanyl residues deeply clustered in the interior of the protein matrix, whereas the short-lived one includes residues located in less rigid and more solvent accessible regions, some of which might be located in functionally important parts of protein. The knowledge of the crystallographic structure of Sbetagly allowed us to evaluate some average parameters for each tryptophanyl microenvironment in the Sbetagly such as hydrophobicity, structural flexibility, and ability of side chains to act as fluorescence quenchers. These results permitted to divide the tryptophanyl fluorescence of Sbetagly in the contribution of two emitting groups: one consisting of eight closely clustered tryptophans, that is, Trp 33, 36, 60, 84, 151 174, 425, and 433, responsible for the long-lived emission component and the other one, composed of nine tryptophans nearer to the subunit surface, that is, Trp 12, 156, 192, 287, 288, 316, 361, 376, 455, associable to the short-lived emission component. Finally, the examination of the tryptophanyl emission decay of the mesophilic beta-galactosidase from Escherichia coli (Cbetagal) and the Arrhenius analysis of its dependence on temperature indicated that the tryptophanyl environments of the mesophilic enzyme are rather homogeneous in consequence of a larger protein dynamics.     

Phylogenetic studies of two rubredoxins from sulfate reducing bacteria

Summary The sequences of two rubredoxins isolated from the sulfate reducing bacteria:Desulfovibrio vulgaris andDesulfovibrio gigas have been elucidated. They have similar sequences but many more differences occur than would be expected from two bacteria of the same genus. Of the 52 sites, only 37 are occupied by identical residues. The primary structures are compared with those of the anaerobic bacteria rubredoxins ofClostridium pasteurianum, Micrococcus aerogenes, Pseudomonas oleovorans andPeptostreptococcus elsdenii: only 12 identities are found, mostly in the two clusters that contain two iron-bound cysteines each. A phylogenetic tree based on the primary structures is presented and possible relations with plant and bacterial ferredoxins are discussed. A secondary and tertiary structure, stereochemically compatible with the sequence data, is proposed.To whom reprint requests should be addressed     

Ethanol and hydrogen production by two thermophilic, anaerobic bacteria isolated from Icelandic geothermal areas

Microbial fermentations are potential producers of sustainable energy carriers. In this study, ethanol and hydrogen production was studied by two thermophilic bacteria (strain AK15 and AK17) isolated from geothermal springs in Iceland. Strain AK15 was affiliated with Clostridium uzonii (98.8%), while AK17 was affiliated with Thermoanaerobacterium aciditolerans (99.2%) based on the 16S rRNA gene sequence analysis. Both strains fermented a wide variety of sugar residues typically found in lignocellulosic materials, and some polysaccharides. In the batch cultivations, strain AK17 produced ethanol from glucose and xylose fermentations of up to 1.6 mol-EtOH/mol-glucose (80% of the theoretical maximum) and 1.1 mol-EtOH/mol-xylose (66%), respectively. The hydrogen yields by AK17 were up to 1.2 mol-H2/ mol-glucose (30% of the theoretical maximum) and 1.0 mol-H2/mol-xylose (30%). The strain AK15 produced hydrogen as the main fermentation product from glucose (up to 1.9 mol-H2/mol-glucose [48%]) and xylose (1.1 mol-H2/mol-xylose [33%]). The strain AK17 tolerated exogenously added ethanol up to 4% (v/v). The ethanol and hydrogen production performance from glucose by a co-culture of the strains AK15 and AK17 was studied in a continuous-flow bioreactor at 60 degrees C. Stable and continuous ethanol and hydrogen co-production was achieved with ethanol yield of 1.35 mol-EtOH/mol-glucose, and with the hydrogen production rate of 6.1 mmol/h/L (H2 yield of 0.80 mol-H2/mol-glucose). PCR-DGGE analysis revealed that the AK17 became the dominant bacterium in the bioreactor. In conclusion, strain AK17 is a promising strain for the co-production of ethanol and hydrogen with a wide substrate utilization spectrum, relatively high ethanol tolerance, and ethanol yields among the highest reported for thermoanaerobes.     

Ethanol formation from cellulose by thermophilic bacteria

Summary A wild coculture of obligately thermophilic bacteria, including only a single cellulolytic species Clostridium, ferments 2% crystalline cellulose and produces 4.6–5.1 g·l^–1 of ethanol at 55°–60° C; that is, 0.96–1.1 moles of ethanol from 1 mole of glucose equivalent of cellulose degraded. However, the ethanol yield decreases with increasing cellulose concentration. Ethanolacetic acid ratio varies around 1 and cannot be influenced by substrate concentration. However, this ratio can be influenced by changing pH and temperature. For the ethanol production from cellulose, neutral and weekly alkaline media with a pH of 7.0–8.0 and a temperature of 55° C are optimal. Experiments in which the coculture was subjected to high ethanol concentrations showed that higher concentrations of added ethanol (up to 20 g·l^–1) suppress cellulose degradation by 50% and inhibit the actual production of ethanol.     

Alcohol dehydrogenases from thermophilic and hyperthermophilic archaea and bacteria

Many studies have been undertaken to characterise alcohol dehydrogenases (ADHs) from thermophiles and hyperthermophiles, mainly to better understand their activities and thermostability. To date, there are 20 thermophilic archaeal and 17 thermophilic bacterial strains known to have ADHs or similar enzymes, including the hypothetical proteins. Some of these thermophiles are found to have multiple ADHs, sometimes of different types. A rigid delineation of amino acid sequences amongst currently elucidated thermophilic ADHs and similar proteins is phylogenetically apparent. All are NAD(P)-dependent, with one exception that utilises the cofactor F(420) instead. Within the NAD(P)-dependent group, the thermophilic ADHs are orderly clustered as zinc-dependent ADHs, short-chain ADHs, and iron-containing/activated ADHs. Distance matrix calculations reveal that thermophilic ADHs within one type are homologous, with those derived from a single genus often showing high similarities. Elucidation of the enzyme activity and stability, coupled with structure analysis, provides excellent information to explain the relationship between them, and thermophilic ADHs diversity.