| 1. |
- Abou-Hachem, Maher, et al.
(author)
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Probing stability of the modular thermostable xylanase Xyn10A
- 2003
-
In: Extremophiles. - : Springer Science and Business Media LLC. - 1433-4909 .- 1431-0651. ; 7:6, s. 483-491
-
Journal article (peer-reviewed)abstract
- The thermophilic bacterium Rhodothermus marinus produces a modular xylanase (Xyn10A) consisting of two N-terminal carbohydrate-binding modules (CBMs), followed by a domain of unknown function, and a catalytic module flanked by a fifth domain. Both Xyn10A CBMs bind calcium ions, and this study explores the effect of these ions on the stability of the full-length enzyme. Xyn10A and truncated forms thereof were produced and their thermostabilities were evaluated under different calcium loads. Studies performed using differential scanning calorimetry showed that the unfolding temperature of the Xyn10A was significantly dependent on the presence of Ca2+, and that the third domain of the enzyme binds at least one Ca2+. Thermal inactivation studies confirmed the role of tightly bound Ca2+ in stabilizing the enzyme, but showed that the presence of a large excess of this ion results in reduced kinetic stability. The truncated forms of Xyn10A were less stable than the full-length enzyme, indicative of module/domain thermostabilizing interactions. Finally, possible roles of the two domains of unknown function are discussed in the light of this study. This is the first report on the thermostabilizing role of calcium on a modular family 10 xylanase that displays multiple calcium binding in three of its five domains/modules.
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| 2. |
- Baker-Austin, Craig, et al.
(author)
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Biofilm development in the extremely acidophilic archaeon 'Ferroplasma acidarmanus' Fer1
- 2010
-
In: Extremophiles. - : Springer. - 1431-0651 .- 1433-4909. ; 14:6, s. 485-491
-
Journal article (peer-reviewed)abstract
- 'Ferroplasma acidarmanus' Fer1 is an ironoxidizing extreme acidophile isolated from the Iron Mountain mine, California, USA This archaeon is predominantly found in biofilm-associated structures in the environment, and produces two distinct biofilm morphologies Bioinformatic analysis of the acidarmanus' Fer1 genome Identified genes annotated as involved in attachment and biofilm formation No putative quorum sensing signaling genes were identified and no N-acyl homoserine lactone-like compounds were found in acidarmanus' Fer1 biofilm supernatant Scanning confocal microscopy analysis of biofilm development on the surface of pyrite demonstrated the temporal and spatial development of biofilm growth Furthermore, two-dimensional polyacrylamide gel electrophoresis was used to examine differential protein expression patterns between biofilm and planktonic populations Ten up-regulated proteins were identified that included six enzymes associated with anaerobic growth, suggesting that the dominating phenotype in the mature biofilm was associated with anaerobic modes of growth This report increases our knowledge of the genetic and proteomic basis of biofilm formation in an extreme acidophilic archaeon.
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| 3. |
- Baker-Austin, Craig, et al.
(author)
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Extreme arsenic resistance by the acidophilic archaeon 'Ferroplasma acidarmanus' Fer1.
- 2007
-
In: Extremophiles. - : Springer Science and Business Media LLC. - 1431-0651 .- 1433-4909. ; 11:3, s. 425-34
-
Journal article (peer-reviewed)abstract
- 'Ferroplasma acidarmanus' Fer1 is an arsenic-hypertolerant acidophilic archaeon isolated from the Iron Mountain mine, California; a site characterized by heavy metals contamination. The presence of up to 10 g arsenate per litre [As(V); 133 mM] did not significantly reduce growth yields, whereas between 5 and 10 g arsenite per litre [As(III); 67-133 mM] significantly reduced the yield. Previous bioinformatic analysis indicates that 'F. acidarmanus' Fer1 has only two predicted genes involved in arsenic resistance and lacks a recognizable gene for an arsenate reductase. Biochemical analysis suggests that 'F. acidarmanus' Fer1 does not reduce arsenate indicating that 'F. acidarmanus' Fer1 has an alternative resistance mechanism to arsenate other than reduction to arsenite and efflux. Primer extension analysis of the putative ars transcriptional regulator (arsR) and efflux pump (arsB) demonstrated that these genes are co-transcribed, and expressed in response to arsenite, but not arsenate. Two-dimensional polyacrylamide gel electrophoresis analysis of 'F. acidarmanus' Fer1 cells exposed to arsenite revealed enhanced expression of proteins associated with protein refolding, including the thermosome Group II HSP60 family chaperonin and HSP70 DnaK type heat shock proteins. This report represents the first molecular and proteomic study of arsenic resistance in an acidophilic archaeon.
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| 4. |
- Barragan, Carlos Eduardo, et al.
(author)
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RNA transcript response by an Acidithiobacillus spp. mixed culture reveals adaptations to growth on arsenopyrite
- 2021
-
In: Extremophiles. - : Springer. - 1431-0651 .- 1433-4909. ; 25, s. 143-158
-
Journal article (peer-reviewed)abstract
- Biooxidation of gold-bearing refractory mineral ores such as arsenopyrite (FeAsS) in stirred tanks produces solutions containing highly toxic arsenic concentrations. In this study, ferrous iron and inorganic sulfur-oxidizing Acidithiobacillus strain IBUN Ppt12 most similar to Acidithiobacillus ferrianus and inorganic sulfur compound oxidizing Acidithiobacillus sp. IBUNS3 were grown in co-culture during biooxidation of refractory FeAsS. Total RNA was extracted and sequenced from the planktonic cells to reveal genes with different transcript counts involved in the response to FeAsS containing medium. The co-culture's response to arsenic release during biooxidation included the ars operon genes that were independently regulated according to the arsenopyrite concentration. Additionally, increased mRNA transcript counts were identified for transmembrane ion transport proteins, stress response mechanisms, accumulation of inorganic polyphosphates, urea catabolic processes, and tryptophan biosynthesis. Acidithiobacillus spp. RNA transcripts also included those encoding the Rus and PetI proteins involved in ferrous iron oxidation and gene clusters annotated as encoding inorganic sulfur compound metabolism enzymes. Finally, mRNA counts of genes related to DNA methylation, management of oxidative stress, chemotaxis, and motility during biooxidation were decreased compared to cells growing without mineral. The results provide insights into the adaptation of Acidithiobacillus spp. to growth during biooxidation of arsenic-bearing sulfides.
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| 5. |
- Birgisson, Hakon, et al.
(author)
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Cold adapted yeasts as producers of cold active polygalacturonases
- 2003
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In: Extremophiles. - : Springer Science and Business Media LLC. - 1433-4909 .- 1431-0651. ; 7:3, s. 185-193
-
Journal article (peer-reviewed)abstract
- Eight cold-adapted, polygalacturonase-producing yeasts belonging to four species were isolated from frozen environmental samples in Iceland. They were identified as Cystofilobasidium lari-marini, Cystofilobasidium capitatum, Cryptococcus macerans and Cryptococcus aquaticus species by sequence analysis of rDNA regions. Growth behavior of the isolates was investigated. All strains could grow at 2°C. Addition of glucose to pectin-containing culture medium had a repressive effect on enzyme production except for C. aquaticus, which showed increased polygalacturonase activity. Optimal temperature for enzyme production for the Cystofilobasidium strains was 14°C, while that for the Cryptococcus strains was lower. Among the isolates, C. lari-marini S3B produced highest levels of enzyme activity at pH 3.2. Preliminary characterization of the polygalacturonases in the culture supernatant showed the enzyme from Cystofilobasidium strains to be optimally active at 40°C and pH 5, and that from the Cryptococcus strains at 50°C and pH 4. The polygalacturonase from C. macerans started to lose activity after 1 h of incubation at 40°C, while that from the other strains had already lost activity at 30°C. All the strains except C. aquaticus produced isoenzymes of polyglacturonase. In addition to polygalacturonase, the Cystofilobasidium strains produced pectin lyase, C. aquaticus pectin esterase, and C. macerans pectin lyase, pectate lyase and pectin esterase.
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| 6. |
- Callac, Nolwenn, et al.
(author)
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Biogeochemical insights into microbe-mineral-fluid interactions in hydrothermal chimneys using enrichment culture
- 2015
-
In: Extremophiles. - : Springer Science and Business Media LLC. - 1431-0651 .- 1433-4909. ; 19:3, s. 597-617
-
Journal article (peer-reviewed)abstract
- Active hydrothermal chimneys host diverse microbial communities exhibiting various metabolisms including those involved in various biogeochemical cycles. To investigate microbe-mineral-fluid interactions in hydrothermal chimney and the driver of microbial diversity, a cultural approach using a gas-lift bioreactor was chosen. An enrichment culture was performed using crushed active chimney sample as inoculum and diluted hydrothermal fluid from the same vent as culture medium. Daily sampling provided time-series access to active microbial diversity and medium composition. Active archaeal and bacterial communities consisted mainly of sulfur, sulfate and iron reducers and hydrogen oxidizers with the detection of Thermococcus, Archaeoglobus, Geoglobus, Sulfurimonas and Thermotoga sequences. The simultaneous presence of active Geoglobus sp. and Archaeoglobus sp. argues against competition for available carbon sources and electron donors between sulfate and iron reducers at high temperature. This approach allowed the cultivation of microbial populations that were under-represented in the initial environmental sample. The microbial communities are heterogeneously distributed within the gas-lift bioreactor; it is unlikely that bulk mineralogy or fluid chemistry is the drivers of microbial community structure. Instead, we propose that micro-environmental niche characteristics, created by the interaction between the mineral grains and the fluid chemistry, are the main drivers of microbial diversity in natural systems.
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| 7. |
- Castán, Pablo, et al.
(author)
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The periplasmic space in Thermus thermophilus : evidence from a regulation-defective S-layer mutant overexpressing an alkaline phosphatase
- 2002
-
In: Extremophiles. - : Springer Science and Business Media LLC. - 1431-0651 .- 1433-4909. ; 6:3, s. 225-232
-
Journal article (peer-reviewed)abstract
- The presence of a periplasmic space within the cell envelope of Thermus thermophilus was analyzed in a mutant (HB8(Delta)UTR1) defective in the regulation of its S-layer (surface crystalline layer). This mutant forms round multicellular bodies (MBs) surrounded by a common envelope as the culture approaches the stationary phase. Confocal microscopy revealed that the origin of the MBs is the progressive detachment of the external layers coupled with the accumulation of NH(2)-containing material between the external envelopes and the peptidoglycan. A specific pattern of proteins was found as soluble components of the intercellular space of the MBs by a single fractionation procedure, suggesting that they are periplasmic-like components. To demonstrate this, we cloned a gene ( phoA) from T. thermophilus HB8 encoding a signal peptide-wearing alkaline phosphatase (AP), and engineered it to be overexpressed in the mutant from a shuttle vector. Most of the AP activity (>80%) was found as a soluble component of the MBs' intercellular fraction. All these data indicate that Thermus thermophilus actually has a periplasmic space which is functionally similar to that of Proteobacteria. The potential application of the HB8(Delta)UTR1 mutant for the overexpression of periplasmic thermophilic proteins is discussed.
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| 8. |
- Cava, Felipe, et al.
(author)
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Thermus thermophilus as biological model
- 2009
-
In: Extremophiles. - : Springer Science and Business Media LLC. - 1431-0651 .- 1433-4909. ; 13:2, s. 213-31
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Journal article (peer-reviewed)abstract
- Thermus spp is one of the most wide spread genuses of thermophilic bacteria, with isolates found in natural as well as in man-made thermal environments. The high growth rates, cell yields of the cultures, and the constitutive expression of an impressively efficient natural competence apparatus, amongst other properties, make some strains of the genus excellent laboratory models to study the molecular basis of thermophilia. These properties, together with the fact that enzymes and protein complexes from extremophiles are easier to crystallize have led to the development of an ongoing structural biology program dedicated to T. thermophilus HB8, making this organism probably the best so far known from a protein structure point view. Furthermore, the availability of plasmids and up to four thermostable antibiotic selection markers allows its use in physiological studies as a model for ancient bacteria. Regarding biotechnological applications this genus continues to be a source of thermophilic enzymes of great biotechnological interest and, more recently, a tool for the over-expression of thermophilic enzymes or for the selection of thermostable mutants from mesophilic proteins by directed evolution. In this article, we review the properties of this organism as biological model and its biotechnological applications.
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| 9. |
- Chawachart, Niwat, et al.
(author)
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Thermal behaviour and tolerance to ionic liquid [emim] OAc in GH10 xylanase from Thermoascus aurantiacus SL16W
- 2014
-
In: Extremophiles. - : Springer Japan. - 1431-0651 .- 1433-4909. ; 18:6, s. 1023-1034
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Journal article (peer-reviewed)abstract
- GH10 xylanase from Thermoascus aurantiacus strain SL16W (TasXyn10A) showed high stability and activity up to 70–75 C. The enzyme’s half-lives were 101 h, 65 h, 63 min and 6 min at 60, 70, 75 and 80 C, respectively. The melting point (Tm), as measured by DSC, was 78.5 C, which is in line with a strong activity decrease at 75–80 C. The biomass-dissolving ionic liquid 1-ethyl-3-methylimidazolium acetate ([emim]OAc) in 30 % concentration had a small effect on the stability of TasXyn10A; Tm decreased by only 5 C. It was also observed that [emim]OAc inhibited much less GH10 xylanase (TasXyn10A) than the studied GH11 xylanases. The Km of TasXyn10A increased 3.5-fold in 15 % [emim]OAc with xylan as the substrate, whereas the approximate level of Vmax was not altered. The inhibition of enzyme activity by [emim]OAc was lesser at higher substrate concentrations. Therefore, high solid concentrations in industrial conditions may mitigate the inhibition of enzyme activity by ionic liquids. Molecular docking experiments indicated that the [emim] cation has major binding sites near the catalytic residues but in lower amounts in GH10 than in GH11 xylanases. Therefore, [emim] cation likely competes with the substrate when binding to the active site. The docking results indicated why the effect is lower in GH10.
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| 10. |
- Christel, Stephan, et al.
(author)
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Acidithiobacillus ferrivorans SS3 presents little RNA transcript response related to cold stress during growth at 8 A degrees C suggesting it is a eurypsychrophile
- 2016
-
In: Extremophiles. - : Springer Science and Business Media LLC. - 1431-0651 .- 1433-4909. ; 20:6, s. 903-913
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Journal article (peer-reviewed)abstract
- Acidithiobacillus ferrivorans is an acidophilic bacterium that represents a substantial proportion of the microbial community in a low temperature mining waste stream. Due to its ability to grow at temperatures below 15 A degrees C, it has previously been classified as 'psychrotolerant'. Low temperature-adapted microorganisms have strategies to grow at cold temperatures such as the production of cold acclimation proteins, DEAD/DEAH box helicases, and compatible solutes plus increasing their cellular membrane fluidity. However, little is known about At. ferrivorans adaptation strategies employed during culture at its temperature extremes. In this study, we report the transcriptomic response of At. ferrivorans SS3 to culture at 8 A degrees C compared to 20 A degrees C. Analysis revealed 373 differentially expressed genes of which, the majority were of unknown function. Only few changes in transcript counts of genes previously described to be cold adaptation genes were detected. Instead, cells cultured at cold (8 A degrees C) altered the expression of a wide range of genes ascribed to functions in transcription, translation, and energy production. It is, therefore, suggested that a temperature of 8 A degrees C imposed little cold stress on At. ferrivorans, underlining its adaptation to growth in the cold as well as suggesting it should be classified as a 'eurypsychrophile'.
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| 11. |
- Csitári, Bianka, et al.
(author)
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Anion-type modulates the effect of salt stress on saline lake bacteria
- 2022
-
In: Extremophiles. - : Springer Nature. - 1431-0651 .- 1433-4909. ; 26
-
Journal article (peer-reviewed)abstract
- Beside sodium chloride, inland saline aquatic systems often contain other anions than chloride such as hydrogen carbonate and sulfate. Our understanding of the biological effects of salt composition diversity is limited; therefore, the aim of this study was to examine the effect of different anions on the growth of halophilic bacteria. Accordingly, the salt composition and concentration preference of 172 strains isolated from saline and soda lakes that differed in ionic composition was tested using media containing either carbonate, chloride or sulfate as anion in concentration values ranging from 0 to 0.40 mol/L. Differences in salt-type preference among bacterial strains were observed in relationship to the salt composition of the natural habitat they were isolated from indicating specific salt-type adaptation. Sodium carbonate represented the strongest selective force, while majority of strains was well-adapted to growth even at high concentrations of sodium sulfate. Salt preference was to some extent associated with taxonomy, although variations even within the same bacterial species were also identified. Our results suggest that the extent of the effect of dissolved salts in saline lakes is not limited to their concentration but the type of anion also substantially impacts the growth and survival of individual microorganisms.
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| 12. |
- Dopson, Mark, et al.
(author)
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ATP generation during reduced inorganic sulfur compound oxidation by Acidithiobacillus caldus is exclusively due to electron transport phosphorylation.
- 2002
-
In: Extremophiles. - : Springer Science and Business Media LLC. - 1431-0651 .- 1433-4909. ; 6:2, s. 123-129
-
Journal article (peer-reviewed)abstract
- The synthesis of adenosine 5-triphosphate (ATP) (increase in phosphorylation potential) during the oxidation of reduced inorganic sulfur compounds was studied in the moderately thermophilic acidophileAcidithiobacillus caldus (strain KU) (formerly Thiohacillus caldus). The phosphorylation potential increased during the oxidation of all reduced inorganic sulfur compounds tested compared with resting cells. The generation of ATP in whole cells was inhibited by the F0F1 ATPase inhibitor oligomycin, electron transport chain inhibitors, valinomycin and potassium ions. There was no increase in the phosphorylation potential, nor synthesis of ATP. in the absence of electron transport. An apparent lack of substrate-level phosphorylation was indicated by the lack of adenosine 5-phosphosulfate reductase in tetrathionate-grown At. caldus. Studies were also performed on the synthesis of ATP by membrane vesicles of At. caldus when presented with an artificial proton gradient. Complete inhibition of ATP synthesis in these vesicles occurred when they were loaded with N,N-dicyclohexylcarbodiimide (DCCD), but not when they were loaded with oligomycin, vanadate or electron transport chain inhibitors. The data presented here suggest that during the oxidation of reduced inorganic sulfur compounds by At. caldus, all ATP is synthesized by oxidative phosphorylation via a membrane-bound F0F1 ATPase driven by a proton gradient.
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| 13. |
- Dopson, Mark, et al.
(author)
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Chromosomally encoded arsenical resistance of the moderately thermophilic acidophile Acidithiobacillus caldus.
- 2001
-
In: Extremophiles. - : Springer Science and Business Media LLC. - 1431-0651 .- 1433-4909. ; 5:4, s. 247-255
-
Journal article (peer-reviewed)abstract
- Arsenical resistance is important to bioleaching microorganisms because these organisms release arsenic from minerals such as arsenopyrite during bioleaching. The acidophile Acidithiobacillus caldus KU was found to be resistant to the arsenical ions arsenate, arsenite, and antimony via an inducible, chromosomally encoded resistance mechanism. Because no apparent alteration of the toxic ions was observed, Acidithiobacillus (At.) caldus was tested to determine if it was resistant as a result of decreased accumulation of toxic ions. Reduced accumulation of arsenate and arsenite by induced At. caldus cells supported this hypothesis. It was also found that, with the addition of an energy source, induced At. caldus could transport arsenate and arsenite out of the cell against a concentration gradient. The lack of efflux in the absence of an added energy source and in the presence of inhibitors suggested that efflux was energy dependent. Induced At. caldus also expressed arsenate reductase activity, indicating that At. caldus has an arsenical resistance mechanism that is analogous to previously described systems from other Bacteria. Southern hybridization analysis showed that At. caldus and other gram-negative acidophiles carry an Escherichia coli arsB homologue on the chromosome.
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| 14. |
- Dopson, Mark, et al.
(author)
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Towards determining details of anaerobic growth coupled to ferric iron reduction by the acidophilic archaeon 'Ferroplasma acidarmanus' Fer1.
- 2007
-
In: Extremophiles. - : Springer Science and Business Media LLC. - 1431-0651 .- 1433-4909. ; 11:1, s. 159-68
-
Journal article (peer-reviewed)abstract
- Elucidation of the different growth states of Ferroplasma species is crucial in understanding the cycling of iron in acid leaching sites. Therefore, a proteomic and biochemical study of anaerobic growth in 'Ferroplasma acidarmanus' Fer1 has been carried out. Anaerobic growth in Ferroplasma spp. occurred by coupling oxidation of organic carbon with the reduction of Fe(3+); but sulfate, nitrate, sulfite, thiosulfate, and arsenate were not utilized as electron acceptors. Rates of Fe(3+) reduction were similar to other acidophilic chemoorganotrophs. Analysis of the 'F. acidarmanus' Fer1 proteome by 2-dimensional polyacrylamide gel electrophoresis revealed ten key proteins linked with central metabolic pathways > or =4 fold up-regulated during anaerobic growth. These included proteins putatively identified as associated with the reductive tricarboxylic acid pathway used for anaerobic energy production, and others including a putative flavoprotein involved in electron transport. Inhibition of anaerobic growth and Fe(3+) reduction by inhibitors suggests the involvement of electron transport in Fe(3+)reduction. This study has increased the knowledge of anaerobic growth in this biotechnologically and environmentally important acidophilic archaeon.
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| 15. |
- Ettema, Thijs J. G., et al.
(author)
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The non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase (GAPN) of Sulfolobus solfataricus : a key-enzyme of the semi-phosphorylative branch of the Entner-Doudoroff pathway
- 2008
-
In: Extremophiles. - : Springer Science and Business Media LLC. - 1431-0651 .- 1433-4909. ; 12:1, s. 75-88
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Journal article (peer-reviewed)abstract
- Archaea utilize a branched modification of the classical Entner-Doudoroff (ED) pathway for sugar degradation. The semi-phosphorylative branch merges at the level of glyceraldehyde 3-phosphate (GAP) with the lower common shunt of the Emden-Meyerhof-Parnas pathway. In Sulfolobus solfataricus two different GAP converting enzymes-classical phosphorylating GAP dehydrogenase (GAPDH) and the non-phosphorylating GAPDH (GAPN)-were identified. In Sulfolobales the GAPN encoding gene is found adjacent to the ED gene cluster suggesting a function in the regulation of the semi-phosphorylative ED branch. The biochemical characterization of the recombinant GAPN of S. solfataricus revealed that-like the well-characterized GAPN from Thermoproteus tenax-the enzyme of S. solfataricus exhibits allosteric properties. However, both enzymes show some unexpected differences in co-substrate specificity as well as regulatory fine-tuning, which seem to reflect an adaptation to the different lifestyles of both organisms. Phylogenetic analyses and database searches in Archaea indicated a preferred distribution of GAPN (and/or GAP oxidoreductase) in hyperthermophilic Archaea supporting the previously suggested role of GAPN in metabolic thermoadaptation. This work suggests an important role of GAPN in the regulation of carbon degradation via modifications of the EMP and the branched ED pathway in hyperthermophilic Archaea.
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| 16. |
- Frankenberg, R J, et al.
(author)
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Effect of temperature and pressure on the proteolytic specificity of the recombinant 20S proteasome from Methanococcus jannaschii
- 2003
-
In: Extremophiles. - : Springer Science and Business Media LLC. - 1433-4909 .- 1431-0651. ; 7:5, s. 353-360
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Journal article (peer-reviewed)abstract
- The hydrolytic specificity of the recombinant 20S proteasom from the deep-sea thermophile Methanococcus jannaschii was evaluated toward oxidized insulin B-chain across a range of temperatures (35degrees, 55degrees. 75degrees, and 90degreesC) and hydrostatic pressures (1, 250, 500, and 1,000 atm). Of the four temperatures considered, the same maximum overall hydrolysis rate was observed at both 55degrees and 75degreesC, which are much lower than the T-opt of 116degreesC previously observed for a small amide substrate (Michels and Clark 1997). At 35degreesC the rates of cleavage were highest at the carboxyl side of glutamine and leucine, whereas at the three higher temperatures, the most rapid cleavages occurred after leucine and glutamic acid residues. The distribution of proteolytic fragments and the cleavage sequence also varied between the lowest and higher temperatures. Application of hydrostatic pressure did not increase proteasome activity, as observed previously for the amide substrate (Michels and Clark 1997). but instead significantly reduced the overall conversion of the polypeptide substrate. Overall cleavage patterns observed for the recombinant M. jannaschii proteasome were similar to those reported previously for Thermoplasma acidophilum (Akopian et al. 1997) and human proteasomes (Dick et al. 1991). indicating that proteasome specificity has been conserved despite significant environmental diversity.
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| 17. |
- Fusco, Salvatore, 1985
(author)
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A standardized protocol for the UV induction of Sulfolobus spindle‑shaped virus 1
- 2015
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In: Extremophiles. - 1433-4909 .- 1431-0651. ; 19, s. 539-546
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Journal article (peer-reviewed)abstract
- The Fuselloviridae prototype member Sulfolobusspindle-shaped virus 1 is a model of UV-inducibleviruses infecting Crenarchaeota. Previous works on SSV1UV induction were bases on empirically determined parametersthat have not yet been standardized. Thus, in manypeer reviewed literature, it is not clear how the fluence andirradiance have been determined. Here, we describe a protocolfor the UV induction of SSV1 replication, which isbased on the combination of the following instrumentallymonitored parameters: (1) the fluence; (2) the irradiance;(3) the exposure time, and (4) the exposure distance. Withthe aim of finding a good balance between the viral replicationinduction and the host cells viability, UV-irradiatedcultures were monitored for their ability to recover in theaftermath of the UV exposure. This UV irradiation procedurehas been set up using the well-characterized Sulfolobussolfataricus P2 strain as model system to study host–virus interaction.
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| 18. |
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| 19. |
- Karlström, Mikael, et al.
(author)
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Thermodynamic and kinetic stability of a large multi-domain enzyme from the hyperthermophile Aeropyrum pernix
- 2010
-
In: Extremophiles. - : Springer Science and Business Media LLC. - 1431-0651 .- 1433-4909. ; 14:2, s. 213-223
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Journal article (peer-reviewed)abstract
- The multi-domain enzyme isocitrate dehydrogenase from the hyperthermophile Aeropyrum pernix was studied by denaturant-induced unfolding. At pH 7.5, changes in circular dichroism ellipticity and intrinsic fluorescence showed a complex unfolding transition, whereas at pH 3.0, an apparently two-state and highly reversible unfolding occurred. Analytical ultracentrifugation revealed the dissociation from dimer to monomer at pH 3.0. The thermodynamic and kinetic stability were studied at pH 3.0 to explore the role of inter-domain interactions independently of inter-subunit interplay on the wild type and R211M, a mutant where a seven-membered inter-domain ionic network has been disrupted. The unfolding and folding transitions occurred at slightly different denaturant concentrations even after prolonged equilibration time. The difference between the folding and the unfolding profiles was decreased in the mutant R211M. The apparent Gibbs free energy decreased approximately 2 kcal/mol and the unfolding rate increased 4.3-fold in the mutant protein, corresponding to a decrease in activation free energy of unfolding of 0.86 kcal/mol. These results suggest that the inter-domain ionic network might be responsible for additional stabilization through a significant kinetic barrier in the unfolding pathway that could also explain the larger difference observed between the folding and unfolding transitions of the wild type.
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| 20. |
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| 21. |
- Kostesha, Natalie, et al.
(author)
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Probing the redox metabolism in the strictly anaerobic, extremely thermophilic, hydrogen-producing Caldicellulosiruptor saccharolyticus using amperometry
- 2011
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In: Extremophiles. - : Springer Science and Business Media LLC. - 1433-4909 .- 1431-0651. ; 15:1, s. 77-87
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Journal article (peer-reviewed)abstract
- Changes in the redox metabolism in the anaerobic, extremely thermophilic, hydrogen-forming bacterium Caldicellulosiruptor saccharolyticus were probed for the first time in vivo using mediated amperometry with ferricyanide as a thermotolerant external mediator. Clear differences in the intracellular electron flow were observed when cells were supplied with different carbon sources. A higher electrochemical response was detected when cells were supplied with xylose than with sucrose or glucose. Moreover, using the mediated electrochemical method, it was possible to detect differences in the electron flow between cells harvested in the exponential and stationary growth phases. The electron flow of C. saccharolyticus was dependent on the NADH- and reduced ferredoxin generation flux and the competitive behavior of cytosolic and membrane-associated oxidoreductases. Sodium oxamate was used to inhibit the NADH-dependent lactate dehydrogenase, upon which more NADH was directed to membrane-associated enzymes for ferricyanide reduction, leading to a higher electrochemical signal. The method is noninvasive and the results presented here demonstrate that this method can be used to accurately detect changes in the intracellular electron flow and to probe redox enzyme properties of a strictly anaerobic thermophile in vivo.
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| 22. |
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| 23. |
- Ljungqvist, Emil E., et al.
(author)
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Insights into the rapid metabolism of Geobacillus sp. LC300 : unraveling metabolic requirements and optimal growth conditions
- 2024
-
In: Extremophiles. - : Springer Nature. - 1431-0651 .- 1433-4909. ; 28:1
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Journal article (peer-reviewed)abstract
- This study investigated the metabolism of Geobacillus sp. LC300, a promising biorefinery host organism with high substrate utilization rates. A new defined medium was designed and tested that allows for exponential growth to elevated cell densities suitable for quantitative physiological studies. Screening of the metabolic requirements of G. sp. LC300 revealed prototrophy for all essential amino acids and most vitamins and only showed auxotrophy for vitamin B12 and biotin. The effect of temperature and pH on growth rate was investigated, adjusting the optimal growth temperature to several degrees lower than previously reported. Lastly, studies on carbon source utilization revealed a capability for fast growth on several common carbon sources, including monosaccharides, oligosaccharides, and polysaccharides, and the highest ever reported growth rate in defined medium on glucose (2.20 h(-1)) or glycerol (1.95 h(-1)). These findings provide a foundation for further exploration of G. sp. LC300's physiology and metabolic regulation, and its potential use in bioproduction processes.
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| 24. |
- Mamo, Gashaw, et al.
(author)
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Fusion of carbohydrate binding modules from Thermotoga neapolitana with a family 10 xylanase from Bacillus halodurans S7
- 2007
-
In: Extremophiles. - : Springer Science and Business Media LLC. - 1433-4909 .- 1431-0651. ; 11:1, s. 169-177
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Journal article (peer-reviewed)abstract
- Xylanase A of Thermotoga neapolitana contains binding domains both at the N- and C-terminal ends of the catalytic domain. In the N-terminal position it contains two carbohydrate-binding modules (CBM) which belong to family 22. These CBMs bind xylan but not to cellulose. The gene encoding the mature peptide of these CBMs was fused with an alkaline active GH10 xylanase from Bacillus halodurans S7 and expressed in Escherichia coli. The (His)(6) tagged hybrid protein was purified by immobilized metal affinity chromatography and characterized. Xylan binding by the chimeric protein was influenced by NaCl concentration and pH of the binding medium. Binding increased with increasing salt concentration up to 200 mM. Higher extent of binding was observed under acidic conditions. The fusion of the CBM structures enhanced the hydrolytic efficiency of the xylanase against insoluble xylan, but decreased the stability of the enzyme. The optimum temperature and pH for the activity of the xylanase did not change.
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| 25. |
- Mangold, Stefanie, 1981-, et al.
(author)
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Extreme zinc tolerance in acidophilic microorganisms from the bacterial and archaeal domains
- 2013
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In: Extremophiles. - : Springer Science and Business Media LLC. - 1431-0651 .- 1433-4909. ; 17:1, s. 75-85
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Journal article (peer-reviewed)abstract
- Zinc can occur in extremely high concentrations in acidic, heavy metal polluted environments habited by acidophilic prokaryotes. Although these organisms are able to thrive in such severely ntaminated ecosystems their resistance mechanisms have not been well studied. Bioinformatic alysis of a range of acidophilic bacterial and archaeal genomes identified homologues of several own zinc homeostasis systems. These included primary and secondary transporters, such as the imary heavy metal exporter ZntA and Nramp super-family secondary importer MntH. Three idophilic model microorganisms, the archaeon 'Ferroplasma acidarmanus', the Gram negative cterium Acidithiobacillus caldus, and the Gram positive bacterium Acidimicrobium ferrooxidans, were lected for detailed analyses. Zinc speciation modeling of the growth media demonstrated that a large action of the free metal ion is complexed, potentially affecting its toxicity. Indeed, many of the tative zinc homeos! asis genes were constitutively expressed and with the exception of 'F. acidarmanus' ZntA, they were t up-regulated in the presence of excess zinc. Proteomic analysis revealed that zinc played a role in idative stress in At. caldus and Am. ferrooxidans. Furthermore, 'F. acidarmanus' kept a constant level intracellular zinc over all conditions tested whereas the intracellular levels increased with increasing nc exposure in the remaining organisms.
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| 26. |
- Mangold, Stefanie, et al.
(author)
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Response of Acidithiobacillus caldus toward suboptimal pH conditions
- 2013
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In: Extremophiles. - : Springer Science and Business Media LLC. - 1431-0651 .- 1433-4909. ; 17:4, s. 689-696
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Journal article (peer-reviewed)abstract
- Maintenance of a circumneutral intracellular pH is important for any organism. Acidophilic microorganisms thrive at low pH while maintaining their intracellular pH around 6.5. However, the mechanisms contributing to acidophile pH homeostasis are not well characterized. The authors investigated the proteomic response and cytoplasmic membrane fatty acid profiles of Acidithiobacillus caldus toward three pH values: 1.1, 2.5, and 4.0. Major rearrangements were observed but lower pH elicited larger changes. Differentially expressed transcription factors suggested tight transcriptional control of pH induced genes. Enzymes involved in sulfur metabolism were up-regulated at pH 1.1 suggesting either that: (1) cells required more energy for maintenance or (2) increased metabolic activity was a specific acid stress response to export intracellular protons via 1A degrees electron transport proton pumps. Furthermore, glutamate decarboxylase, an important enzyme in Escherichia coli acid resistance, was uniquely expressed at pH 1.1. Other proteins previously shown to be involved in neutrophilic acid response, such as spermidine synthase, PspA, and toluene tolerance protein, were differentially expressed in At. caldus but require further investigation to show a direct link to pH homeostasis. Their roles in acidophilic organisms are discussed. Active modulation of fatty acid profiles was detected and suggested a more rigid membrane at low pH.
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| 27. |
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| 28. |
- Nordberg Karlsson, Eva, et al.
(author)
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Citrate synthase from Thermus aquaticus: a thermostable bacterial enzyme with a five-membered inter-subunit ionic network.
- 2003
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In: Extremophiles. - : Springer Science and Business Media LLC. - 1433-4909 .- 1431-0651. ; 7:1, s. 9-16
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Journal article (peer-reviewed)abstract
- A bacterial thermostable citrate synthase has been analyzed to investigate the structural basis of its thermostability, and to compare such features with those previously identified in archaeal citrate synthases. The gene encoding the citrate synthase from Thermus aquaticus was identified from a gene library by screening with a PCR fragment amplified from genomic DNA using a primer based on the determined N-terminal amino acid sequence and a citrate synthase consensus primer. Apart from high sequence similarities with citrate synthase sequences within the Thermus/Deinococcus group, the analyzed enzyme has highest similarities with the enzyme from the hyperthermophilic Archaeon Pyrococcus furiosus. The recombinant enzyme is a dimer with high specific activity. Compared to its thermoactivity (Topt at 80°C), the thermal stability of the enzyme is high, as judged from its Tm (101°C), and from irreversible thermal inactivation assays. Molecular modeling of the structure revealed an inter-subunit ion-pair network, comparable in size to the network found in the citrate synthase from P. furiosus; these networks are discussed in relation to the high thermal stability of these bacterial and archaeal enzymes.
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| 29. |
- Nordberg Karlsson, Eva, et al.
(author)
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Rhodothermus marinus: a thermophilic bacterium producing dimeric and hexameric citrate synthase isoenzymes.
- 2002
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In: Extremophiles. - : Springer Science and Business Media LLC. - 1433-4909 .- 1431-0651. ; 6:1, s. 51-56
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Journal article (peer-reviewed)abstract
- Two separate citrate synthases from the extremely thermophilic bacterium Rhodothermus marinus have been identified and purified. One of the enzymes is a hexameric protein and is the first thermostable, hexameric citrate synthase to be isolated. The other is a dimeric enzyme, which is also thermostable but possesses both citrate synthase and 2-methyl citrate synthase activities. 2-Methyl citrate synthase uses propionyl-coenzyme A as one of its substrates and in Escherichia coli, for example, it has been implicated in the metabolism of propionate. However, no growth of R. marinus was observed using minimal medium with propionate as the sole carbon source, and both hexameric and dimeric enzymes were produced irrespective of whether propionate was included in the growth medium. The data are discussed with respect to the evolutionary relationships between the known hexameric and dimeric citrate synthases and 2-methyl citrate synthase.
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| 30. |
- Pedersen, Karsten, 1952, et al.
(author)
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Distribution, diversity and activity of microorganisms in the hyper-alkaline spring waters of Maqarin in Jordan
- 2004
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In: Extremophiles. - : Springer Science and Business Media LLC. - 1431-0651 .- 1433-4909. ; 8:2, s. 151-164
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Journal article (peer-reviewed)abstract
- The hyper-alkaline, high-Ca2+ springs of Maqarin, Jordan, were investigated as an analogue for various microbial processes at the extremely high pH generated by cement and concrete in some underground radioactive waste repositories. Leaching of metamorphic, cementitious phases in Maqarin has produced current, hyper-alkaline groundwater with a maximum pH of 12.9. Six consecutive expeditions were undertaken to the area during 19942000. The total number of microorganisms in the alkaline waters was 103105 cells/ml. Analysis of the 16S-ribosomal ribonucleic acid (rRNA) diversity revealed microorganisms mainly belonging to the Proteobacteria. Obvious similarities between the obtained sequences and sequences from other alkaline sites could not be found. Numerous combinations of culture media compositions were inoculated with spring, seepage and groundwaters and incubated under aerobic and anaerobic conditions with various carbon sources. Assimilation studies were performed using identical radio-labeled carbon sources. Glucose seemed to be the preferred carbon source for assimilation, followed by acetate, lactate, and leucine. The results demonstrate that microorganisms from the hyper-alkaline springs of Maqarin could grow and be metabolically active under aerobic and anaerobic hyper-alkaline conditions. However, the growth and activity found were not vigorous; instead, slow growth, low numbers, and a generally low metabolic activity were found. This suggests that microbial activity will be low during the hyper-alkaline phase of cementitious repositories
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| 31. |
- Ron, Emanuel Y C, et al.
(author)
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Cultivation technology development of Rhodothermus marinus DSM 16675
- 2019
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In: Extremophiles : life under extreme conditions. - : Springer Science and Business Media LLC. - 1433-4909. ; 23:6, s. 735-745
-
Journal article (peer-reviewed)abstract
- This work presents an evaluation of batch, fed-batch, and sequential batch cultivation techniques for production of R. marinus DSM 16675 and its exopolysaccharides (EPSs) and carotenoids in a bioreactor, using lysogeny broth (LB) and marine broth (MB), respectively, in both cases supplemented with 10 g/L maltose. Batch cultivation using LB supplemented with maltose (LBmalt) resulted in higher cell density (OD620 = 6.6) than use of MBmalt (OD620 = 1.7). Sequential batch cultivation increased the cell density threefold (OD620 = 20) in LBmalt and eightfold (OD620 = 14) in MBmalt. In both single and sequential batches, the production of carotenoids and EPSs using LBmalt was detected in the exponential phase and stationary phase, respectively, while in MBmalt formation of both products was detectable in both the exponential and stationary phases of the culture. Heteropolymeric EPSs were produced with an overall volumetric productivity (QE) of 0.67 (mg/L h) in MBmalt and the polymer contained xylose. In LB, QE was lower (0.1 mg/L h) and xylose could not be detected in the composition of the produced EPSs. In conclusion, this study showed the importance of a process design and medium source for production of R. marinus DSM 16675 and its metabolites.
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| 32. |
- Sjöling, Sara, et al.
(author)
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High 16S rDNA bacterial diversity in glacial meltwater lake sediment, Bratina Island, Antarctica
- 2003
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In: Extremophiles. - Japan : Springer Japan KK. - 1431-0651 .- 1433-4909. ; 7:4, s. 275-282
-
Journal article (peer-reviewed)abstract
- The microbial diversity in maritime meltwater pond sediments from Bratina Island, Ross Sea, Antarctica was investigated by 16S rDNA-dependent molecular phylogeny. Investigations of the vertical distribution, phylogenetic composition, and spatial variability of Bacteria and Archaea in the sediment were carried out. Results revealed the presence of a highly diverse bacterial population and a significantly depth-related composition. Assessment of 173 partial 16S rDNA clones analyzed by amplified rDNA restriction analysis (ARDRA) using tetrameric restriction enzymes (HinP1I 5'GdelCGC3'and Msp I. 5'CdelCGG3', BioLabs) revealed 153 different bacterial OTUs (operational taxonomic units). However, only seven archaeal OTUs were detected, indicating low archaeal diversity. Based on ARDRA results, 30 bacterial clones were selected for sequencing and the sequenced clones fell into seven major lineages of the domain Bacteria; the alpha, gamma, and delta subdivisions of Proteobacteria, the Cytophaga-Flavobacterium-Bacteroides, the Spirochaetaceae, and the Actinobacteria. All of the archaeal clones sequenced belonged to the group Crenarchaeota and phylogenetic analysis revealed close relationships with members of the deep-branching Group 1 Marine Archaea.
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| 33. |
- Srimathi, Soundararajan, et al.
(author)
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Intrinsic halotolerance of the psychrophilic alpha-amylase from Pseudoalteromonas haloplanktis
- 2007
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In: Extremophiles. - : Springer Science and Business Media LLC. - 1433-4909 .- 1431-0651. ; 11:3, s. 505-515
-
Journal article (peer-reviewed)abstract
- The halotolerance of a cold adapted alpha-amylase from the psychrophilic bacterium Pseudoalteromonas haloplanktis (AHA) was investigated. AHA exhibited hydrolytic activity over a broad range of NaCl concentrations (0.01-4.5 M). AHA showed 28% increased activity in 0.5-2.0 M NaCl compared to that in 0.01 M NaCl. In contrast, the corresponding mesophilic (Bacillus amyloliquefaciens) and thermostable (B. licheniformis) alpha-amylases showed a 39 and 46% decrease in activity respectively. Even at 4.5 M NaCl, 80% of the initial activity was detected for AHA, whereas the mesophilic and thermostable enzymes were inactive. Besides an unaltered fluorescence emission and secondary structure, a 10 degrees C positive shift in the temperature optimum, a stabilization factor of > 5 for thermal inactivation and a Delta T-m of 8.3 degrees C for the secondary structure melting were estimated in 2.7 M NaCl. The higher activation energy, half-life time and T-m indicated reduced conformational dynamics and increased rigidity in the presence of higher NaCl concentrations. A comparison with the sequences of other halophilic alpha-amylases revealed that AHA also contains higher proportion of small hydrophobic residues and acidic residues resulting in a higher negative surface potential. Thus, with some compromise in cold activity, psychrophilic adaptation has also manifested halotolerance to AHA that is comparable to the halophilic enzymes.
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| 34. |
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| 35. |
- Säwström, Christin, et al.
(author)
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Bacteriophage in polar inland waters.
- 2008
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In: Extremophiles. - : Springer Science and Business Media LLC. - 1431-0651 .- 1433-4909. ; 12:2, s. 167-175
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Journal article (peer-reviewed)abstract
- Bacteriophages are found wherever microbial life is present and play a significant role in aquatic ecosystems. They mediate microbial abundance, production, respiration, diversity, genetic transfer, nutrient cycling and particle size distribution. Most studies of bacteriophage ecology have been undertaken at temperate latitudes. Data on bacteriophages in polar inland waters are scant but the indications are that they play an active and dynamic role in these microbially dominated polar ecosystems. This review summarises what is presently known about polar inland bacteriophages, ranging from subglacial Antarctic lakes to glacial ecosystems in the Arctic. The review examines interactions between bacteriophages and their hosts and the abiotic and biotic variables that influence these interactions in polar inland waters. In addition, we consider the proportion of the bacteria in Arctic and Antarctic lake and glacial waters that are lysogenic and visibly infected with viruses. We assess the relevance of bacteriophages in the microbial loop in the extreme environments of Antarctic and Arctic inland waters with an emphasis on carbon cycling.
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| 36. |
- Åhrman, Emma, et al.
(author)
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Small heat shock proteins prevent aggregation of citrate synthase and bind to the N-terminal region which is absent in thermostable forms of citrate synthase
- 2007
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In: Extremophiles. - : Springer Science and Business Media LLC. - 1433-4909 .- 1431-0651. ; 11:5, s. 659-666
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Journal article (peer-reviewed)abstract
- Citrate synthase (CS) is often used in chaperone assays since this thermosensitive enzyme aggregates at moderately increased temperatures. Small heat shock proteins (sHsps) are molecular chaperones specialized in preventing the aggregation of other proteins, termed substrate proteins, under conditions of transient heat stress. To investigate the mechanism whereby sHsps bind to and stabilize a substrate protein, we here used peptide array screening covering the sequence of porcine CS (P00889). Strong binding of sHsps was detected to a peptide corresponding to the most N-terminal alpha-helix in CS (amino acids Leu(13) to Gln(27)). The N-terminal alpha-helices in the CS dimer intertwine with the C-terminus in the other subunit and together form a stem-like structure which is protruding from the CS dimer. This stem-like structure is absent in thermostable forms of CS from thermophilic archaebacteria like Pyrococcus furiosus and Sulfolobus solfatacarium. These data therefore suggest that thermostabilization of thermosensitive CS by sHsps is achieved by stabilization of the C- and N-terminae in the protruding thermosensitive softspot, which is absent in thermostable forms of the CS dimer.
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