Activity, stability and structural studies of lactate dehydrogenases adapted to extreme thermal environments

Lactate dehydrogenase (LDH) catalyzes the conversion of pyruvate to lactate with concomitant oxidation of NADH during the last step in anaerobic glycolysis. In the present study, we present a comparative biochemical and structural analysis of various LDHs adapted to function over a large temperature range. The enzymes were from Champsocephalus gunnari (an Antarctic fish), Deinococcus radiodurans (a mesophilic bacterium) and Thermus thermophilus (a hyperthermophilic bacterium). The thermodynamic activation parameters of these LDHs indicated that temperature adaptation from hot to cold conditions was due to a decrease in the activation enthalpy and an increase in activation entropy. The crystal structures of these LDHs have been solved. Pairwise comparisons at the structural level, between hyperthermophilic versus mesophilic LDHs and mesophilic versus psychrophilic LDHs, have revealed that temperature adaptation is due to a few amino acid substitutions that are localized in critical regions of the enzyme. These substitutions, each having accumulating effects, play a role in either the conformational stability or the local flexibility or in both. Going from hot- to cold-adapted LDHs, the various substitutions have decreased the number of ion pairs, reduced the size of ionic networks, created unfavorable interactions involving charged residues and induced strong local disorder. The analysis of the LDHs adapted to extreme temperatures shed light on how evolutionary processes shift the subtle balance between overall stability and flexibility of an enzyme.     

Structural basis of the substrate subsite and the highly thermal stability of xylanase 10B from Thermotoga maritima MSB8

The crystal structure of xylanase 10B from Thermotoga maritima MSB8 (TmxB), a hyperthermostable xylanase, has been solved in its native form and in complex with xylobiose or xylotriose at 1.8 A resolution. In order to gain insight into the substrate subsite and the molecular features for thermal stability, we compared TmxB with family 10 xylanase structures from nine microorganisms. As expected, TmxB folds into a (beta/alpha)8-barrel structure, which is common among the glycoside hydrolase family 10. The enzyme active site and the environment surrounding the xylooligosaccharide of TmxB are highly similar to those of family 10 xylanases. However, only two xylose moieties were found in its binding pocket from the TmxB-xylotriose complex structure. This finding suggests that TmxB could be a potential biocatalyst for the large-scale production of xylobiose. The result of structural analyses also indicated that TmxB possesses some additional features that account for its thermostability. In particular, clusters of aromatic residues together with a lack of exposed hydrophobic residues are characteristic of the TmxB structure. TmxB has also a significant number of ion pairs on the protein surface that are not found in other thermophilic family 10 xylanases.     

Purification,Characterization, and Gene Analysis of Cellulase (Cel8A) from Lysobacter sp. IB-9374

An enzyme that has both β-1,4-glucanase and chitosanase activities was found in the culture medium of the soil bacterium Lysobacter sp. IB-9374, a high lysyl endopeptidase-producing strain. The enzyme was purified to homogeneity from the culture filtrate using five purification steps and designated Cel8A. The purified Cel8A had a molecular mass of 41 kDa, as estimated by sodium dodecyl sulfate–polyacrylamide gel electrophoresis. A pH optimum of 5.0 was found for the β-1,4-glucanase activity, and pH optima of 5.0 and 7.0 were found for the chitosanase activity. Nucleotide sequencing of the Cel8A gene yielded a deduced amino acid sequence that comprises a 33-amino acid, N-terminal signal peptide and a mature enzyme consisting of a 381-residue polypeptide with a predicted molecular mass of 41,241 Da. The amino acid sequence of the Cel8A, which contains the catalytic module of glycosyl hydrolase family 8, is homologous to β-1,3-1,4-D-glucanase from Bacillus circulans WL-12 and endoglucanase N-257 from B. circulans KSM-N257.     

Physiological flexibility: the key to success and survival for Antarctic fairy shrimps in highly fluctuating extreme environments

1. The anostracan fairy shrimp Branchinecta gaini inhabits one of the most hostile environments on earth, living in pools and lakes in Antarctica. Between January 2002 and January 2003 temperatures in two pools where B. gaini are extremely abundant on Adelaide Island ranged from ?18.6 to ?15.7 °C in winter, to 19.4 to 17.1 °C in summer, whilst air temperatures ranged from ?34 to 6.3 °C. 2. Branchinecta gaini survives winter as cysts, but endures large summer temperature fluctuations as adults. Cysts froze between ?24.4 and ?25.7 °C. In experiments adults survived 0–10 °C with no mortality for 1 week, 25 °C for nearly 48 h with 50% mortality, and at 32 °C complete mortality occurred in <1 h. 3. Oxygen consumption (M?O₂) in B. gaini approximately doubled for every 10 °C temperature rise (Q₁₀ = 2.04) up to 20 °C where it reached a peak. Females had, on average 19% higher M?O₂ than males. Females also had greater metabolic scopes, (maximum–minimum M?O₂ across temperatures was ×3.6 for females, ×3.1 for males). 4. Ventilation frequency increased linearly with temperature, and did not decline at 25 °C, indicating animals were ‘trying’ progressively harder to supply oxygen to tissues, and oxygen deficiency was the probable cause of death. Females had a higher ventilation frequency than males (8.6–17.1% higher) and they also exhibited greater scope to raise ventilation frequency (×2.4 for females versus ×1.5 for males). 5. Great metabolic flexibility allows B. gaini to exploit extreme, highly fluctuating environments, and larger ventilatory and respiratory scopes allow females to survive higher temperatures than males. Because of this flexibility their prospects for coping with physical environmental change are high.     

Activity and thermal stability of acid phosphatase in homogenates of Amoeba proteus, acclimated to various temperatures

Activity and thermoresistance of acid phosphatase were determined in supernatant of Amoeba proteus homogenates using 1-naphthyl phosphate (pH 4.0) and p-nitrophenyl phosphate (pH 5.5). Although tartrate-resistant and tartrate-sensitive acid phosphatases hydrolyse both substrates, the former mainly hydrolyses p-nitrophenyl phosphate and the latter 1-naphthyl phosphate. A decrease in the activity of the total and tartrate-sensitive acid phosphatases, when using 1-naphthyl phosphate, and of the total and tartrate-resistant acid phosphatases, when using p-nitrophenyl phosphate, was found in amoebae acclimated to 10 degrees C (10 degrees-amoebae) compared to those acclimated to 25 degrees C (25 degrees-amoebae). Using 1-naphthyl phosphate, the thermoresistance of the total acid phosphatase was lower in 10 degrees-amoebae than in 25 degrees-amoebae, but the thermostability of tartrate-resistant enzyme was the same in both groups of amoebae. Using p-nitrophenyl phosphate, the thermoresistance of the total and tartrate-resistant acid phosphatases was lower (the latter only slightly) in 10 degrees-amoebae than in 25 degrees-amoebae. It is suggested that at least with the use of 1-naphthyl phosphate a decrease in thermostability of the total acid phosphatase may be due to a decrease in thermoresistance of tartrate-sensitive enzyme. The results obtained confirm the author's previous data on the activity and thermostability of electrophoretic forms of acid phosphatase using 2-naphthyl phosphate in 10- and 25 degrees-amoebae (Sopina, 2001). It is the first case of discovering a correlation between changes in primary cell thermoresistance of amoebae cultured at different temperatures and changes in the activity and thermostability of acid phosphatase in their homogenates, with the number of electrophoretic forms of this enzyme and their mobility being permanent.     

Leaf size variations in a dominant desert shrub,Reaumuria soongarica,adapted to heterogeneous environments

The climate in arid Central Asia (ACA) has changed rapidly in recent decades, but the ecological consequences of this are far from clear. To predict the impacts of climate change on ecosystem functioning, greater attention should be given to the relationships between leaf functional traits and environmental heterogeneity. As a dominant constructive shrub widely distributed in ACA, Reaumuria soongarica provided us with an ideal model to understand how leaf functional traits of desert ecosystems responded to the heterogeneous environments of ACA. Here, to determine the influences of genetic and ecological factors, we characterized species‐wide variations in leaf traits among 30 wild populations of R. soongarica and 16 populations grown in a common garden. We found that the leaf length, width, and leaf length to width ratio (L/W) of the northern lineage were significantly larger than those of other genetic lineages, and principal component analysis based on the in situ environmental factors distinguished the northern lineage from the other lineages studied. With increasing latitude, leaf length, width, and L/W in the wild populations increased significantly. Leaf length and L/W were negatively correlated with altitude, and first increased and then decreased with increasing mean annual temperature (MAT) and mean annual precipitation (MAP). Stepwise regression analyses further indicated that leaf length variation was mainly affected by latitude. However, leaf width was uncorrelated with altitude, MAT, or MAP. The common garden trial showed that leaf width variation among the eastern populations was caused by both local adaptation and phenotypic plasticity. Our findings suggest that R. soongarica preferentially changes leaf length to adjust leaf size to cope with environmental change. We also reveal phenotypic evidence for ecological speciation of R. soongarica. These results will help us better understand and predict the consequences of climate change for desert ecosystem functioning.     

Regulation of sodium in the shore crabCarcinus maenas,adapted to environments of constant and changing salinities

The activity of Na-K-ATPase was determined in the posterior gills of the shore crabCarcinus maenas during a period following transfer from 35 to 10 ‰ salinity and vice versa at 15 °C. After transfer from high to low salinity, Na-K-ATPase activity increased from 3.2 to 7.0 μmoles P_i mg protein^?1 h^?1 within a period of 2 to 3 weeks. Transfer of crabs from low to high salinity resulted in reduction of activity from 7.4 to 4.5 μmoles P_i mg protein^?1 h^?1 within about the same period. The relatively slow response following salinity change indicates that the amounts of Na-K-ATPase in the gills may play a role in hyperionic Na regulation in relatively constant brackish-water environments. Instant responses to salinity result from activation and inhibition of Na-K-ATPase activity by Na. Gill Na-K-ATPase is activated by the Na concentration of the incubation medium to attain a steep maximum at about 75 mM Na, which corresponds to the lowest environmental Na levels tolerated byC. maenas equivalent to a salinity of ca 6 ‰. Activity greatly decreased towards higher Na levels, equivalent to the salinity of normal sea water, at which hyperregulation no longer occurs. Selective addition of either Na or Cl to brackish water of 9 ‰ S resulted in effective hyperregulation of the non-increased ion, and passive distribution between medium and blood of the increased ion. These data indicate that under appropriate conditions the normally coupled transport of Na and Cl may be uncoupled and take place independently of each other.     

Amino Acid Regions of Family 45 Endoglucanases Involved in Cotton Defibrillation and in Resistance to Anionic Surfactants and Oxidizing Agents

In the detergent industry, fungal endoglucanases are used to release microfibrils from the surfaces of dyed cellulosic fabrics to enhance color brightness. Family 45 endoglucanase (glycoside hydrolase family 45, GH45) EGL3 from Humicola grisea is more resistant to anionic surfactants and oxidizing agents than family 45 endoglucanase RCE1 from Rhizopus oryzae, while in the present study, a catalytic domain of RCE1 had higher defibrillation activity on dyed cotton fabrics than did that of EGL3. To identify the amino acid regions involved in these properties, we compared the characteristics of RCE1, EGL3, and three chimeric endoglucanases, in which each of the three regions of the catalytic domain of EGL3 was replaced by the corresponding region of the catalytic domain of RCE1. Amino acids in the N-terminal region were involved in resistance to anionic surfactants and oxidizing agents. Furthermore, amino acids in the region adjacent to the N-terminal region were involved in releasing microfibrils and in binding to dyed cotton fabrics, indicating that the binding of the amino acids in this region might be important in the release of microfibrils from dyed cotton fabrics.     

Larval damselflies in extreme environments: behavioral and physiological response to hypoxic stress

The extensive papyrus (Cyperus papyrus) swamps of East and Central Africa form a habitat of great ecological importance due to their extent, the extreme and chronic hypoxia of the interior swamp, and the unique assemblages of water-breathing insects that characterize these communities, including zygopteran (damselfly) larvae. The major goal of this study was to quantify physiological and behavioral responses of gilled and gill-less damselfly larvae of a papyrus swamp specialist, Proischnura subfurcatum, to low-oxygen conditions. Gill autotomization was common in P. subfurcatum of the Rwembaita Swamp in Kibale National Park, Uganda, with one to three gills missing from 56% of the specimens surveyed. We examined behavioral (ventilation activity and vertical migration) and physiological (metabolic rate) response to hypoxia in gilled and gill-less P. subfurcatum. Behavioral response to progressive hypoxia indicated that gill-less individuals rely more on use of wing sheaths (lifting and spreading) than gilled P. subfurcatum larvae. However, both morphs migrated to the surface to gain contact with atmospheric air under extreme hypoxia. On average, the rate of oxygen consumption of gill-less individuals was 51% lower than that of gilled individuals. This observed metabolic depression in gill-less P. subfurcatum may be attributed to the loss of major respiratory appendages. However, the apparent ability of both gilled and gill-less individuals to maintain their metabolic rates to a similar critical tension suggests other mechanisms may compensate for loss of gills, though not enough to mediate metabolic depression.     

Structural and biochemical studies of GH family 12 cellulases: improved thermal stability, and ligand complexes

In this review we will describe how we have gathered structural and biochemical information from several homologous cellulases from one class of glycoside hydrolases (GH family 12), and used this information within the framework of a protein-engineering program for the design of new variants of these enzymes. These variants have been characterized to identify some of the positions and the types of mutations in the enzymes that are responsible for some of the biochemical differences in thermal stability and activity between the homologous enzymes. In this process we have solved the three-dimensional structure of four of these homologous GH 12 cellulases: Three fungal enzymes, Humicola grisea Cel12A, Hypocrea jecorina Cel12A and Hypocrea schweinitzii Cel12A, and one bacterial, Streptomyces sp. 11AG8 Cel12A. We have also determined the three-dimensional structures of the two most stable H. jecorina Cel12A variants. In addition, four ligand-complex structures of the wild-type H. grisea Cel12A enzyme have been solved and have made it possible to characterize some of the interactions between substrate and enzyme. The structural and biochemical studies of these related GH 12 enzymes, and their variants, have provided insight on how specific residues contribute to protein thermal stability and enzyme activity. This knowledge can serve as a structural toolbox for the design of Cel12A enzymes with specific properties and features suited to existing or new applications.     

Surface hydrophobic groups, stability, and flip-flopping in lattice proteins

Two-dimensional lattice protein models were studied in two approximations of the conformational equilibrium to elucidate the role of surface hydrophobic groups in their stabilities. We demonstrate that stability of any compactly folded sequence is determined by its ability to "flip-flop" (refold) into alternative compact structures. The degree of stability required for folded sequences determines the average numbers of surface hydrophobic groups in stable lattice structures which are in good agreement with ratios of core to surface hydrophobic groups in real proteins. However, the average destabilization of the native structure per surface hydrophobic group is small (0-0.25 kcal/mol), often disagrees with the free energies derived from the ratios of core to surface hydrophobic groups in the same structures, and has a combinatorial entropic nature independent of the strength of structure stabilizing interactions. This suggests that the free energies derived from the core to surface ratios of hydrophobic groups in real proteins have little to do with folding thermodynamics. On average, sequences with highly stable native structures are the least hydrophobic. The results suggest that in designing novel stable proteins hydrophobic groups on the surface should be avoided to reduce the possibility of flip-flopping. The average stability of highly designable structures is never higher than that of some low designability structures, contrary to the accepted view. In the equilibrium approximation with alternative compact and partially unfolded structures, the requirement of high stability selects a unique 5 x 5 structure formed by only a few sequences, suggesting much stronger sequence selectivity than commonly thought.     

The structural analysis and the role of calcium binding site for thermal stability in mannanase

Mannanase is an important enzyme involved in the degradation of mannan, production of bioactive oligosaccharides, and biobleaching of kraft pulp. Mannanase must be thermostable for use in industrial applications. In a previous study, we found that the thermal stability of mannanase from Streptomyces thermolilacinus (StMan) and Thermobifida fusca (TfMan) is enhanced by calcium. Here, we investigated the relationship between the three-dimensional structure and primary sequence to identify the putative calcium-binding site. The results of site-directed mutagenesis experiments indicated that Asp-285, Glu-286, and Asp-287 of StMan (StDEDAAAdC) and Asp-264, Glu-265, and Asp-266 of TfMan (TfDEDAAAdC) were the key residues for calcium binding affinity. Isothermal titration calorimetry revealed that the catalytic domain of StMan and TfMan (StMandC and TfMandC, respectively) bound calcium with a K_a of 3.02 × 10⁴ M⁻¹ and 1.52 × 10⁴ M⁻¹, respectively, both with stoichiometry consistent with one calcium-binding site per molecule of enzyme. Non-calcium-binding mutants (StDEDAAAdC and TfDEDAAAdC) did not show any calorimetric change. From the primary structure alignment of several mannanases, the calcium-binding site was found to be highly conserved in GH5 bacterial mannanases. This is the first study indicating enhanced thermal stability of GH5 bacterial mannanases by calcium binding.     

Genetic variation in photosynthetic capacity, carbon isotope discrimination and mesophyll conductance in provenances of Castanea sativa adapted to different environments

1. Provenances of Castanea sativa from populations adapted to different climatic areas of Turkey were grown in a field trial in Italy. Carbon isotope discrimination (Δ) in leaf dry matter and in leaf soluble sugar, were measured, along with photosynthesis, stomatal conductance and mesophyll conductance, to study the variability of primary productivity and its ecological significance in European Chestnut.
2. Genetic variations were found in RuBP carboxylase, chlorophyll, leaf soluble protein and leaf thickness.
3. Carbon isotope discrimination (Δ) in leaf dry matter was greater in drought-adapted than in wet-adapted provenances. A similar variation of Δ was observed in leaf soluble carbohydrates either under watered or drought conditions. Possible environmental effects of variables such as vapour pressure difference, on the relationship between transpiration efficiency and carbon isotope discrimination are discussed, on the basis of short-term and long-term results.
4. Generally low values of Δ encountered among provenances were explained not only by low values of intercellular CO₂ partial pressure but also by consistently low values of mesophyll conductance leading to reduced chloroplastic CO₂ partial pressure. A decrease in mesophyll conductance was induced by water shortage. Co-ordination was found between stomatal and mesophyll conductance, with the drought-adapted provenances showing much higher mesophyll conductance than the wet-adapted provenances. Variations in mesophyll conductance were related to differences in leaf protein content.
5. Possible ecophysiological adaptive mechanisms are discussed taking into account stomatal sensitivity, modulation of photosynthetic capacity and water-use efficiency under drought conditions.     

Natural transformation in Gram-negative bacteria thriving in extreme environments: from genes and genomes to proteins,structures and regulation

Extremophiles - Extremophilic prokaryotes live under harsh environmental conditions which require far-reaching cellular adaptations. The acquisition of novel genetic information via natural...     

Microbiome of juvenile corals in the outer reef slope and lagoon of the South China Sea: insight into coral acclimatization to extreme thermal environments

Environmental conditions between the outer reef slope (ORS) and lagoon in tropical atolls are significantly different, but the variations of juvenile coral-microbiomes in the two environments and their relationship with coral thermal acclimatization are poorly understood. We explored this issue based on local water conditions and the microbiome of juvenile corals in the ORS and lagoon in the central South China Sea. Coral-symbiotic Symbiodiniaceae showed significant differences among coral species; Pocillopora verrucosa and Pachyseris rugosa in the ORS, and Acropora formosa in the lagoon were dominated by Durusdinium, but other corals were dominated by Cladocopium. Although A. formosa in the ORS were dominated by Cladocopium (C3u), they were dominated by Durusdinium (D1/D1a) and Cladocopium (C50) in the lagoon. Other coral species were both dominated by Cladocopium in the lagoon and ORS. The relative abundance of bacteria in the Deinococcus–Thermus was generally higher in the lagoon corals than in the ORS corals. Our study indicates that P. verrucosa, P. rugosa and Porites lutea may have high thermal tolerance based on the relatively high abundance of heat-tolerant Durusdinium and Thermus scotoductus. Likewise, A. formosa in the lagoon may acclimatize to the thermal environment based on a high relative abundance of heat-tolerant Durusdinium.     

Relationship between stability and flexibility in the most flexible region of Photinus pyralis luciferase

Firefly luciferase is a protein with a large N-terminal and a small C-terminal domain. B-factor analysis shows that its C-terminal is much more flexible than its N-terminal. Studies on hyperthermophile proteins have been shown that the increased thermal stability of hyperthermophile proteins is due to their enhanced conformational rigidity and the relationship between flexibility, stability and function in most of proteins is on debate. Two mutations (D474K and D476N) in the most flexible region of firefly luciferase were designed. Thermostability analysis shows that D476N mutation doesn't have any significant effect but D474K mutation destabilized protein. On the other hand, flexibility analysis using dynamic quenching and limited proteolysis demonstrates that D474K mutation became much more flexible than wild type although D476N doesn't have any significant difference. Intrinsic and ANS fluorescence studies demonstrate that D476N mutation is brought about by structural changes without significant effect on thermostability and flexibility. Molecular modeling reveals that disruption of a salt bridge between D⁴⁷⁴ and K⁴⁴⁵ accompanying with some H-bond deletion may be involved in destabilization of D474K mutant.     

Biodiversity in extreme aquatic environments: Lakes, ponds and streams of the Ross Sea sector, Antarctica

The Ross Sea Sector (RSS) of Antarcticallies between the lines of longitude 150°E and 150°W and contains diverse landscapes with a variety of lakes, ponds and streams. Neither insects nor crustacean species have been recorded in these ecosystems but most contain planktonic and/or benthic communities that are composed exclusively of microscopic organisms. Microbial brodiversity is low with a small number of species (e.g. filamentous cyanobacteria of the family Oscillatoriaceae) occurring under a broad range of environmental conditions throughout the region. There is no evidence to date of microbial endemism in the RSS; however, there is a need to apply molecular and cellular techniques to compare biodiversity and genetic characteristics with assemblages elsewhere in Antarctica and with comparable communities in the north polar zone. A series of hypotheses are advanced to help guide further work. These derive from the conclusion that environmental extremes plus biogeographical isolation control the biodiversity of RSS communities, and that biological interactions (competition, grazing, predation, parasitism) are weak and play a minor role by comparison with temperate latitude ecosystems.     

Ecotypes of planktonic actinobacteria with identical 16S rRNA genes adapted to thermal niches in temperate, subtropical, and tropical freshwater habitats

Seven strains with identical 16S rRNA genes affiliated with the Luna2 cluster (Actinobacteria) were isolated from six freshwater habitats located in temperate (Austria and Australia), subtropical (People's Republic of China), and tropical (Uganda) climatic zones. The isolates had sequence differences at zero to five positions in a 2,310-nucleotide fragment of the ribosomal operon, including part of the intergenic spacer upstream of the 16S rRNA gene, the complete 16S rRNA gene, the complete 16S-23S internal transcribed spacer (ITS1), and a short part of the 23S rRNA gene. Most of the few sequence differences found were located in the internal transcribed spacer sequences. Two isolates obtained from habitats in Asia and Europe, as well as two isolates obtained from different habitats in the People's Republic of China, had identical sequences for the entire fragment sequenced. In spite of minimal sequence differences in the part of the ribosomal operon investigated, the strains exhibited significant differences in their temperature response curves (with one exception), as well as pronounced differences in their temperature optima (25.0 to 35.6 degrees C). The observed differences in temperature adaptation were generally in accordance with the thermal conditions in the habitats where the strains were isolated. Strains obtained from temperate zone habitats had the lowest temperature optima, strains from subtropical habitats had intermediate temperature optima, and a strain from a tropical habitat had the highest temperature optimum. Based on the observed temperature responses, we concluded that the strains investigated are well adapted to the thermal conditions in their home habitats. Consequently, these closely related strains represent different ecotypes adapted to different thermal niches.