Psychrophilic enzymes: hot topics in cold adaptation

Biomimetic construction of multi-enzyme reactor through artificial antibody-antigen-directed immobilization for cascade catalytic conversion of cellulose to gluconic acid

To achieve the biotransformation of cellulose into gluconic acid, a multi-enzyme reactor comprising cellulase, glucose oxidase, and catalase was constructed through artificial antibody-antigen-directed immobilization. Catechol was used as a template to prepare artificial antibodies, which were then used to modify the enzymes through a Schiff base reaction to form artificial antigens. The artificial antibody and antigen were subsequently assembled via affinity recognition to immobilize the enzymes. The immobilization yields for all three enzymes exceeded 85 %, with specific activities of 43.48 ± 1.54 U/mg, 0.88 ± 0.06 U/mg, and 18.47 ± 1.43 U/mg, respectively. The immobilized enzymes demonstrated excellent adaptability, storage stability, reusability, and regenerability. Through the modular assembly of artificial antigen-antibody, the multi-enzyme reactor facilitated the cascade conversion of cellulose to gluconic acid.

Bioprospecting amylase from Samiti Lake, situated in the eastern Himalayas

Enzymes, especially amylases, have been an economic boon to the industrial sector, their bioprospective and biotechnological use is an added advantage. Our primary focus of the study was to isolate the most potent amylase producer and to optimize its production parameters through One Factor At A Time (OFAT), Central Composite Rotatable Design Response Surface Methodology (CCRD RSM) and Artificial Neural Network (ANN). Based on the qualitative and quantitative analysis, SLAB1 was selected as the most potent amylase producer out of the potential isolates. Further SLAB1 was identified as Priestia flexa via 16SrRNA identification. Optimization of the production parameters showed the best carbon, nitrogen sources, temperature and pH to be fructose, peptone, 20 °C and pH 8.0 respectively. Further, the enzyme was purified using ammonium sulphate precipitation followed by dialysis. Later, DEAE Sepharose (Sigma) resin was used for ion exchange chromatography and the protein was eluted using NaCl gradients from 0.1 M - 0.6 M. Enzyme kinetics assessment of the purified amylase with the Lineweaver Burk plot showed values of maximum rate; Vmax (10.869 μmoL/min), and Michaelis-Menten constant Km to be around (14.91 mg/ml). To determine its potential application, analysis of this purified amylase in cleaning the tomato and chocolate stained cotton fabrics after comparing its compatibility with different detergents were executed. Further analysis of the washed stained fabrics via Scanning Electron Microscopy was carried out.

Enzymatic saccharification of the polysaccharides in Arthrocaulon macrostachyum biomass: Characterization and application in methylene blue removal

Wild Arthrocaulon macrostachyum biomass has been less studied for biotechnological and environmental applications. This study examines the saccharification of biomass from this coastal halophyte using multienzyme preparations from two endophytic bacteria, Bacillus sp. TKE1 (GenBank accession ON060353.1) and B. vallismortis E4 (Genome Project id: JBIMFA000000000). Under optimum conditions, the multienzyme from TKE1 demonstrated 37.8 IU mL-1 of amylase and 34.6 IU mL-1 of xylanase. While the multienzyme from the strain E4 exhibited 36.3 IU mL-1 amylase and 37.4 IU mL-1 xylanase. The preparations from TKE1 and E4 yielded 59.4 % and 37.8 % saccharification, releasing 0.66 and 0.42 mg/g of total reducing sugars, respectively. Matrix made up of saccharified biomass showed up to 98 % MB dye removal, compared to 84.9 % by the unsaccharified biomass. The pseudo-second order reaction kinetics indicated chemical adsorption. SEM images of the saccharified biomass showed significant fiber degradation, matrix loosening, and increased surface area, enhancing dye removal capacity. FTIR analysis confirmed changes in the saccharified substrate, particularly in the regions of 3074.533, 2997.38, and 2872.007 cm-1 for cellulose; 1093.639 to 829.391 cm-1 for starch, and 1720.503 cm-1 for hemicelluloses. The study concludes that biomass from halophyte can be utilized for generating value-added chemicals and environmental remediation.

Quaternary stabilization of a GH2 β-galactosidase from the psychrophile A. ikkensis, a flexible and unstable dimeric enzyme

Studies of cold-active enzymes may elucidate the basis for low-temperature activity and contribute to their wider application in energy-efficient processes. Here we investigate the cold-active GH2 β-galactosidase from the psychrophilic bacterium Alkalilactibacillus ikkensis (AiLac). AiLac has a specific activity twice as high as its closest structural homolog (the mesophilic Escherichia coli GH2 β-galactosidase) toward the lactose analog ONPG at room temperature and neutral pH, and shows biphasic behavior in Michaelis-Menten plots. AiLac is activated by Mg2+ and Na+ and is most effective at pH 7.0 and 30°C. However, early unfolding events are observed already at room temperature. Stability studies using intrinsic fluorescence, circular dichroism, and small-angle x-ray scattering (SAXS), combined with activity assays, showed AiLac to be highly sensitive to heat and urea and to be stabilized, but also inhibited, by loss of structural flexibility induced by the osmolyte trehalose. AlphaFold structure prediction combined with SAXS and flow-induced dispersion analysis support a reversible monomer-dimer model, suggesting structural adaptation to cold temperatures on a quaternary level. The low amount of dimeric buried surface area, high flexibility, and remarkably low chemical and thermal stability present an extreme example of cold adaptation promoted by high levels of solvent interactions. To investigate the relationship between evolution and oligomerization, we trained a generative deep learning model to successfully engineer functional variants that form stabilized dimers and tetramers by introducing high evolutionary fitness mutations at the interface, demonstrating an efficient way to explore the local sequence fitness landscape to modulate the equilibrium of oligomerization.

Role of electrostatics in cold adaptation: A comparative study of eury- and stenopsychrophilic triose phosphate isomerase

Psychrophilic (cold-active) organisms have developed enzymes that facilitate sufficient metabolic activity at low temperatures to sustain life. This occurs through molecular adaptations that tend to increase protein flexibility at the expense of stability. However, psychrophiles also vary in their growth conditions. Eurypsychrophiles thrive over a wide temperature range and often prefer temperatures above 20 °C, while stenopsychrophiles grow optimally below 15 °C and are more narrowly adapted to cold temperatures. To elucidate differences between these two classes of enzymes, we here compare the stability and unfolding kinetics of two orthologues of the basal household enzyme triose phosphate isomerase, one from the stenopsychrophilic Antarctic permafrost bacterium Rhodonellum psychrophilum (sTPI) and the other from the eurypsychrophilic Greenland ikaite column bacterium Rhodococcus sp. JG-3 (eTPI). Remarkably, sTPI proved significantly more thermostable and resistant to chemical denaturation than its eurypsychrophilic counterpart, eTPI, in the absence of ionic components in solution, whereas inclusion of electrostatic screening agents in the form of sodium chloride or the charged denaturant guanidinium chloride largely cancelled out this difference. Thus, electrostatics play a prominent role in stabilizing the stenopsychrophilic sTPI, and a mandatory low-temperature growth environment does not preclude the development of considerable thermotolerance for individual enzymes. We were able to increase the thermostability of sTPI using an evolutionary machine learning model, which transferred several sTPI residues into the eTPI active site. While the stabilizing effect was modest, the combination of individual mutations was additive, underscoring the potential of combining multiple beneficial mutations to achieve enhanced enzyme properties.

A case for myoglobin-macromolecular rate theory applied to pseudo peroxidase kinetics

This study explores the well-known catalytic behavior of myoglobin as a pseudo-peroxidase by applying macromolecular rate theory (MMRT) to assess its temperature-dependent enzyme kinetics. While myoglobin is primarily recognized for its oxygen-binding properties in muscle tissues, with a characterized pseudo-peroxidase ability to catalyze the degradation of hydrogen peroxide in the presence of electron donors, the claim that myoglobin is actually a true peroxidase can be explored by analyzing the heat capacity changes (ΔCp ‡) in the catalyzed reaction at different temperatures and fitting the results to the expanded Eyring equation (MMRT equation). This research uses the MMRT equation to compare myoglobin's catalytic activity (a pseudo-peroxidase) with that of lactoperoxidase (a true peroxidase) and copper ions (a non-enzymatic catalyst) across a range of temperatures at pH 5, after which the biological catalysts are compared again at pH 7. By analyzing the ΔCp ‡ of these catalysts, it was found that myoglobin exhibits a significant catalytic contribution at both pH levels, suggesting a structural/vibrational or some other relatively significant transition during the reaction. The study's findings provide a new perspective into myoglobin's enzymatic role in peroxide decomposition and highlight the utility of MMRT in quantifying the contribution of polypeptide chains in enzyme-catalyzed peroxidase reactions. Additionally, our research notes the pH-dependence of myoglobin's catalytic efficiency compared to traditional peroxidases, offering implications for understanding its broader biological roles.

Adaptation of the psychrophilic Mucor psychrophilus (Mucorales, Mucoromycota) to lower temperatures and under conditions of heat and osmotic shocks

The definitions of psychrophilia and psychrotolerance are based on the optimal temperature of growth (≤15 and 20 °C, respectively), and it is not clear whether differences exist in adaptation mechanisms. We analyzed the composition of osmolytes and membrane lipids of a true psychrophile Mucor psychrophilus during submerged cultivation at 12.5 °C and 4 °C, as well as under heat and osmotic shocks. The main osmolyte at 12.5 °C is trehalose (70 % of the total), whereas at 4 °C, comparable proportions of glycerol, glucose, and trehalose are observed. Under heat shock, the amount of trehalose increases threefold, and osmotic shock leads to an increase of the glycerol level without a reduction in the amount of trehalose. The predominant membrane lipids at both temperatures are non-bilayer phosphatidic acids (about 65 % of the sum) and phosphatidylethanolamines (20-30 %). An increase in the degree of unsaturation and a decrease in the sterols proportion are observed during growth at 4 °C, whereas at 12.5 °C, as well as under heat and osmotic shocks, the changes are insignificant. Similarity of the adaptation mechanisms of the psychrophilic and psychrotolerant fungi indicates the ambiguity of psychrophilia and psychrotolerance definitions.

Physics-based modeling in the new era of enzyme engineering

Enzyme engineering is entering a new era characterized by the integration of computational strategies. While bioinformatics and artificial intelligence methods have been extensively applied to accelerate the screening of function-enhancing mutants, physics-based modeling methods, such as molecular mechanics and quantum mechanics, are essential complements in many objectives. In this Perspective, we highlight how physics-based modeling will help the field of computational enzyme engineering reach its full potential by exploring current developments, unmet challenges and emerging opportunities for tool development.

Thermal Adaptation of Cytosolic Malate Dehydrogenase Revealed by Deep Learning and Coevolutionary Analysis

Protein evolution has shaped enzymes that maintain stability and function across diverse thermal environments. While sequence variation, thermal stability and conformational dynamics are known to influence an enzyme's thermal adaptation, how these factors collectively govern stability and function across diverse temperatures remains unresolved. Cytosolic malate dehydrogenase (cMDH), a citric acid cycle enzyme, is an ideal model for studying these mechanisms due to its temperature-sensitive flexibility and broad presence in species from diverse thermal environments. In this study, we employ techniques inspired by deep learning and statistical mechanics to uncover how sequence variation and conformational dynamics shape patterns of cMDH's thermal adaptation. By integrating coevolutionary models with variational autoencoders (VAE), we generate a latent generative landscape (LGL) of the cMDH sequence space, enabling us to explore mutational pathways and predict fitness using direct coupling analysis (DCA). Structure predictions via AlphaFold and molecular dynamics simulations further illuminate how variations in hydrophobic interactions and conformational flexibility contribute to the thermal stability of warm- and cold-adapted cMDH orthologs. Notably, we identify the ratio of hydrophobic contacts between two regions as a predictive order parameter for thermal stability features, providing a quantitative metric for understanding cMDH dynamics across temperatures. The integrative computational framework employed in this study provides mechanistic insights into protein adaptation at both sequence and structural levels, offering unique perspectives on the evolution of thermal stability and creating avenues for the rational design of proteins with optimized thermal properties.

A Low-Temperature-Active Pectate Lyase from a Marine Bacterium for Orange Juice Clarification

Cold-adapted pectin lyases are particularly useful in the extraction and clarification of freshly squeezed fruit juices at low temperatures, as they effectively reduce juice viscosity and improve light transmittance. With the increasing attention on low-temperature pectinase in industrial applications, the exploration of low-temperature pectinase with novel characteristics has become one of the key focuses of research and development. In this study, a 1026 bp gene, pel1Ba, encoding a 42.7 kDa pectin lyase, was cloned from sediment samples collected from the South China Sea and heterologously expressed in Escherichia coli. The purified Pel1Ba exhibited an optimal temperature of 40 °C and an optimal pH of 10, with a total enzyme activity of 5100 U/mL. Notably, Pel1Ba is a cold-adapted enzyme that retains 80% of its relative activity across the temperature range of 0-40 °C. When 20 U/mL purified Pel1Ba was added to orange juice, the juice volume increased by 43.00% and its clarity improved by 37.80%. Meanwhile, site-directed mutagenesis analysis revealed that the residual enzyme activities of the mutants A230I, F253I, and L292I were increased by 22.5%, 34.4%, and 25.1%, respectively, compared to the wild type. This study concludes that the cold-active pectate lyase Pel1Ba exhibits potential for applications in the food industry.

Biomimetic co-immobilization of β-glucosidase, glucose oxidase, and horseradish peroxidase to construct a multi-enzyme biosensor for determination of amygdalin

Accurate, specific, and cost-effective detection of toxic cyanogenic glycosides is crucial for ensuring biological health and food safety. In this study, a novel biosensor based on co-immobilized multi-enzyme system was constructed by artificial antibody-antigen-directed immobilization for the colorimetric detection of amygdalin through a cascade reaction catalyzed by β-glucosidase, glucose oxidase, and horseradish peroxidase. Artificial antibodies and antigens were prepared using catechol and 3,4-dihydroxybenzaldehyde, respectively, to generate mutual affinity recognition ability for enzyme immobilization. On this basis, the biosensing system showed a complete response to amygdalin within 4 min, with a linear range from 2 to 10 μM, a detection limit of 0.18 μM, and a quantification limit of 0.6 μM. In addition, this sensor had good precision, reproducibility, stability, and reusability. This study proposed a method for detecting cyanogenic glycosides, providing a successful case for the application of cascade biosensors in food safety detection.

Kraft lignin biobleaching by a dye-decolorizing peroxidase from the Antarctic Pseudomonas sp. AU10 strain

Pseudomonas sp. AU10 is an Antarctic psychrotolerant bacterium that produces a dye-decolorizing peroxidase (DyP-AU10). The recombinant enzyme (rDyP-AU10) is a heme-peroxidase that decolors dyes and modifies kraft lignin. In this work, we report the best activity parameters for lignin modification (at 45 °C and pH 4) and show that the enzyme increases the number of aldehydes, ketones, and phenolic compounds. The analyses of the HPLC profile of samples also support that rDyP-AU10 induces the chemical change of kraft lignin. The enzyme also acts as a biobleaching agent on cellulose pulps, as shown by the reduction in kappa number. We also included experiments with a commercial laccase from Trametes versicolor and performed experiments using single enzymes and, in combination. The results show that rDyP-AU10 and the commercial laccase do not have a synergic activity as a modifying system, on cellulose pulp as substrates. However, results suggest that rDyP-AU10 holds potential as a member of the portfolio of lignin-modifying enzymes.

Microbial lipases: advances in production, purification, biochemical characterization, and multifaceted applications in industry and medicine

Lipases are biocatalysts of significant industrial and medical relevance, owing to their ability to hydrolyze lipid substrates and catalyze esterification reactions under mild conditions. This review provides a comprehensive overview of microbial lipases' production, purification, and biochemical properties. It explores optimized fermentation strategies to enhance enzyme yield, including using agro-industrial residues as substrates. The challenges associated with purification techniques such as ultrafiltration, chromatography, and precipitation are discussed, alongside methods to improve enzyme stability and specificity. Additionally, the review addresses the growing importance of genetic engineering approaches for improving lipase characteristics, such as activity, stability, and specificity.Additionally, this review highlights the diverse applications of microbial lipases in industries, including food, pharmaceuticals, biofuels, and cosmetics. The enzyme's role in bioremediation, biodegradation, and the synthesis of bioactive compounds is analyzed, emphasizing its potential in sustainable and eco-friendly technologies. The biocatalytic properties of lipases make them ideal candidates for the green chemistry initiatives in these industries. In the biomedical domain, lipase has shown promise in drug delivery systems, anti-obesity treatments, and diagnostics.This review provides insights into the strategic development of microbes as microbial cell factories for the sustainable production of lipases, paving the way for future research and industrial innovations in enzyme technology.

Computer Simulations of the Temperature Dependence of Enzyme Reactions

In this review we discuss the development of methodology for calculating the temperature dependence and thermodynamic activation parameters for chemical reactions in solution and in enzymes, from computer simulations. We outline how this is done by combining the empirical valence bond method with molecular dynamics free energy simulations. In favorable cases it turns out that such simulations can even capture temperature optima for the catalytic rate. The approach turns out be very useful both for addressing questions regarding the roles of enthalpic and entropic effects in specific enzymes and also for attacking evolutionary problems regarding enzyme adaptation to different temperature regimes. In the latter case, we focus on cold-adaptation of enzymes from psychrophilic species and show how computer simulations have revealed the basic mechanisms behind such adaptation. Understanding these mechanisms also opens up the possibility of designing the temperature dependence, and we highlight a recent example of this.

Cold-active enzymes from deep marine psychrophiles: harnessing their potential in enhanced food production and sustainability

Exploring the untapped potential of deep-sea microorganisms, particularly their cold-active enzymes, or psychrozymes, offers exciting possibilities for revolutionizing various aspects of the food processing industry. This review focuses on these enzymes, derived from the largely unexplored depths of the deep ocean, where microorganisms have developed unique adaptations to extreme conditions. Psychrozymes, as bioactive molecules, hold significant promise for food industry applications. However, despite their potential, the understanding and industrial utilization of psychrozymes remains limited. This review provides an in-depth analysis of how psychrozymes can: improve processing efficiency, enhance sensory qualities, extend product shelf life, and reduce energy consumption across the food production chain. We explore the cryodefense strategies and cold-adaptation mechanisms that support these enzymes, shedding light on the most extensively studied psychrozymes and assessing their journey from theoretical applications to practical use in food production. The key properties, such as stability, substrate specificity, and catalytic efficiency in cold environments, are also discussed. Although psychrozymes show considerable promise, their large-scale application in the food industry remains largely unexplored. This review emphasizes the need for further research to unlock the full potential of psychrozymes, encouraging their broader integration into the food sector to contribute to more sustainable food production processes.

Increase of ATP synthesis and amino acids absorption contributes to cold adaptation in Antarctic bacterium Poseidonibacter antarcticus SM1702T

Numerous psychrophiles inhabit the cold environments that are prevalent across the global biosphere. The adaptation of psychrophiles to cold conditions has been widely studied in strains from the archaeal phylum Euryarchaeota and the bacterial class Gamma-proteobacteria. However, given the vast diversity of microorganisms in cold environments, many microbial lineages with potentially unique cold-adaptation strategies remain largely unexplored. This study investigates the cold responses of the Antarctic strain Poseidonibacter antarcticus SM1702T, a cold-adapted bacterium belonging to the class Epsilon-proteobacteria within the phylum Campylobacterota. Proteomic analysis revealed that this strain responds to low temperatures by overexpressing proteins involved in energy production and amino acid transport. Experimental results confirmed that intracellular ATP concentrations increased at low temperatures compared to higher temperatures. Low temperatures significantly reduced the strain's amino acid absorption rates, a condition that was mitigated by increased expression of membrane transporters. We propose that the impairment of membrane protein function due to low temperatures is the primary factor affecting cell growth. As a result, the strain enhances ATP synthesis and upregulates membrane transporter expression to counteract cold stress. These findings contribute to a deeper understanding of cold adaptation strategies in psychrophiles.

Extremophiles and Extremophilic Behaviour-New Insights and Perspectives

Extremophiles, throughout evolutionary time, have evolved a plethora of unique strategies to overcome hardships associated with the environments they are found in. Modifying their genome, showing a bias towards certain amino acids, redesigning their proteins, and enhancing their membranes and other organelles with specialised chemical compounds are only some of those strategies. Scientists can utilise such attributes of theirs for a plethora of biotechnological and astrobiological applications. Moreover, the rigorous study of such microorganisms regarding their evolution and ecological niche can offer deep insight into science's most paramount inquiries such as how life originated on Earth and whether we are alone in the universe. The intensification of studies involving extremophiles in the future can prove to be highly beneficial for humanity, even potentially ameliorating modern problems such as those related to climate change while also expanding our knowledge about the complex biochemical reactions that ultimately resulted in life as we know it today.

Evolutionary-Scale Enzymology Enables Biochemical Constant Prediction Across a Multi-Peaked Catalytic Landscape

Quantitatively mapping enzyme sequence-catalysis landscapes remains a critical challenge in understanding enzyme function, evolution, and design. Here, we expand an emerging microfluidic platform to measure catalytic constants-k cat and K M-for hundreds of diverse naturally occurring sequences and mutants of the model enzyme Adenylate Kinase (ADK). This enables us to dissect the sequence-catalysis landscape's topology, navigability, and mechanistic underpinnings, revealing distinct catalytic peaks organized by structural motifs. These results challenge long-standing hypotheses in enzyme adaptation, demonstrating that thermophilic enzymes are not slower than their mesophilic counterparts. Combining the rich representations of protein sequences provided by deep-learning models with our custom high-throughput kinetic data yields semi-supervised models that significantly outperform existing models at predicting catalytic parameters of naturally occurring ADK sequences. Our work demonstrates a promising strategy for dissecting sequence-catalysis landscapes across enzymatic evolution and building family-specific models capable of accurately predicting catalytic constants, opening new avenues for enzyme engineering and functional prediction.

A Novel Cold-Adapted Nitronate Monooxygenase from Psychrobacter sp. ANT206: Identification, Characterization and Degradation of 2-Nitropropane at Low Temperature

Aliphatic nitro compounds cause environmental pollution by being discharged into water with industrial waste. Biodegradation needs to be further explored as a green and pollution-free method of environmental remediation. In this study, we successfully cloned a novel nitronate monooxygenase gene (psnmo) from the genomic DNA library of Psychrobacter sp. ANT206 and investigated its ability to degrade 2-nitropropane (2-NP). Homology modeling demonstrated that PsNMO had a typical I nitronate monooxygenase catalytic site and cold-adapted structural features, such as few hydrogen bonds. The specific activity of purified recombinant PsNMO (rPsNMO) was 97.34 U/mg, rPsNMO exhibited thermal instability and reached maximum catalytic activity at 30 °C. Moreover, rPsNMO was most active in 1.5 M NaCl and remained at 104% of its full activity in 4.0 M NaCl, demonstrating its significant salt tolerance. Based on this finding, a novel bacterial cold-adapted enzyme was obtained in this work. Furthermore, rPsNMO protected E. coli BL21 (DE3)/pET28a(+) from the toxic effects of 2-NP at 30 °C because the 2-NP degradation rate reached 96.1% at 3 h and the final product was acetone. These results provide a reliable theoretical basis for the low-temperature degradation of 2-NP by NMO.

Novel, cold-adapted D-laminaribiose- and D-glucose-releasing GH16 endo-β-1,3-glucanase from Hymenobacter siberiensis PAMC 29290, a psychrotolerant bacterium from Arctic marine sediment

Endo-β-1,3-glucanase is a glycoside hydrolase (GH) that plays an essential role in the mineralization of β-glucan polysaccharides. In this study, the novel gene encoding an extracellular, non-modular GH16 endo-β-1,3-glucanase (GluH) from Hymenobacter siberiensis PAMC 29290 isolated from Arctic marine sediment was discovered through an in silico analysis of its whole genome sequence and subsequently overexpressed in Escherichia coli BL21. The 870-bp GluH gene encoded a protein featuring a single catalytic GH16 domain that shared over 61% sequence identity with uncharacterized endo-β-1,3-glucanases from diverse Hymenobacter species, as recorded in the National Center for Biotechnology Information database. The purified recombinant endo-β-1,3-glucanase (rGluH: 31.0 kDa) demonstrated peak activity on laminarin at pH 5.5 and 40°C, maintaining over 40% of its maximum endo-β-1,3-glucanase activity even at 25°C. rGluH preferentially hydrolyzed D-laminarioligosaccharides and β-1,3-linked polysaccharides, but did not degrade D-laminaribiose or structurally unrelated substrates, confirming its specificity as a true endo-β-1,3-glucanase without ancillary GH activities. The biodegradability of various substrate polymers by the enzyme was evaluated in the following sequence: laminarin > barley β-glucan > carboxymethyl-curdlan > curdlan > pachyman. Notably, the specific activity (253.1 U mg-1) and catalytic efficiency (k cat /K m : 105.72 mg-1 s-1 mL) of rGluH for laminarin closely matched its specific activity (250.2 U mg-1) and k cat /K m value (104.88 mg-1 s-1 mL) toward barley β-glucan. However, the k cat /K m value (9.86 mg-1 s-1 mL) of rGluH for insoluble curdlan was only about 9.3% of the value for laminarin, which correlates well with the observation that rGluH displayed weak binding affinity (< 40%) to the insoluble polymer. The biocatalytic hydrolysis of D-laminarioligosaccharides with a degree of polymerization between 3 and 6 and laminarin generally resulted in the formation of D-laminaribiose as the predominant product and D-glucose as the secondary product, with a ratio of approximately 4:1. These findings suggest that highly active rGluH is an acidic, cold-adapted D-laminaribiose- and D-glucose-releasing GH16 endo-β-1,3-glucanase, which can be exploited as a valuable biocatalyst for facilitating low temperature preservation of foods.

Computer-aided mining of a psychrophilic cellobiose 2-epimerase from the Qinghai-Tibet Plateau gene catalogue

Cellobiose 2-epimerase (CE) catalyzes the conversion of the lactose into its high-value derivatives, epilactose and lactulose, which has great prospects in food applications. In this study, CE sequences from the Qinghai-Tibet Plateau gene catalogue, we screened these for structural flexibility through molecular dynamics simulation to identify potential psychrophilic CE candidates. One such psychrophilic CE we termed psyCE demonstrated exceptional epimerization activity, achieving an optimum activity of 122.2 ± 1.6 U/mg. Its kinetic parameters (Kcat and Km) for epimerization activity were 219.9 ± 5.6 s-1 and 261.9 ± 18.1 mM, respectively, representing the highest Kcat recorded among known cold-active CEs. Notably, this is the first report of a psychrophilic CE. The psyCE can effectively produce epilactose at 8 °C, converting 20.3 % of 200 mM lactose into epilactose within four hours. These findings suggest that psyCE is highly suitable for cryogenic food processing, and glaciers may serve as a valuable repository of psychrophilic enzymes.

Enhanced degradation of phenolic pollutants by a novel cold-adapted laccase from Peribacillus simplex

Laccase (EC 1.10.3.2), as eco-friendly biocatalysts, holds immense potential for sustainable applications across various environmental and industrial sectors. Despite the growing interest, the exploration of cold-adapted laccases, especially their unique properties and applicability, remains limited. In this study, we have isolated, cloned, expressed, and purified a novel laccase from Peribacillus simplex (GenBank: PP430751), which was derived from permafrost layer. The recombinant laccase (PsLac) exhibited optimal activity at 30 °C and a pH optimum of 3.5. Remarkably, PsLac exhibited remarkable stability in the presence of organic solvents, with its enzyme activity increasing by 20 % after being incubated in a 30 % trichloromethane solution for 12 h, compared to its initial activity. Furthermore, the enzyme preserved 100 % of its activity after undergoing eight freeze-thaw cycles. Notably, the catalytic center of PsLac contains Zn2+ instead of the typically observed Cu2+ found in other laccases, and metal-ion substitution experiments raised the catalytic efficiency to 3-fold when Zn2+ was replaced with Fe2+. Additionally, PsLac has demonstrated a proficient ability to degrade phenolic pollutants, such as hydroquinone, even at a low temperature of 16 °C, positioning it as a promising candidate for environmental bioremediation and contributing to cleaner production processes.

Extreme makeover: the incredible cell membrane adaptations of extremophiles to harsh environments

The existence of life beyond Earth has long captivated humanity, and the study of extremophiles-organisms surviving and thriving in extreme environments-provides crucial insights into this possibility. Extremophiles overcome severe challenges such as enzyme inactivity, protein denaturation, and damage of the cell membrane by adopting several strategies. This feature article focuses on the molecular strategies extremophiles use to maintain the cell membrane's structure and fluidity under external stress. Key strategies include homeoviscous adaptation (HVA), involving the regulation of lipid composition, and osmolyte-mediated adaptation (OMA), where small organic molecules protect the lipid membrane under stress. Proteins also have direct and indirect roles in protecting the lipid membrane. Examining the survival strategies of extremophiles provides scientists with crucial insights into how life can adapt and persist in harsh conditions, shedding light on the origins of life. This article examines HVA and OMA and their mechanisms in maintaining membrane stability, emphasizing our contributions to this field. It also provides a brief overview of the roles of proteins and concludes with recommendations for future research directions.

Heterologous Expression and Characterization of a Novel Mesophilic Maltogenic α-Amylase AmyFlA from Flavobacterium sp. NAU1659

A novel amylase AmyFlA from Flavobacterium sp. NAU1659, AmyFlA, was cloned and expressed in Esherichia coli. Based on phylogenetic and functional analysis, it was identified as a novel member of the subfamily GH13_46, sharing high sequence identity. The protein was predicted to consist of 620 amino acids, with a putative signal peptide of 25 amino acids. The enzyme was able to hydrolyze soluble starch with a specific activity of 352.97 U/mg at 50 °C in 50 mM phosphate buffer (pH 6.0). The Km and Vmax values of AmyFlA were respectively 3.15 mg/ml and 566.36 µmol·ml-1·min-1 under optimal conditions. Its activity towards starch was enhanced by 63% in the presence of 1 mM Ca2+, indicating that AmyFlA was a Ca2+-dependent amylase. Compared to the reported maltogenic amylases, AmyFlA produced a lower variety of intermediate oligosaccharides at the start of the reaction so that the product mixture contained a higher proportion of maltose. These results indicate that AmyFlA may be potential application value in the production of high-maltose syrup.

Evolution of Pyrrolysyl-tRNA Synthetase: From Methanogenesis to Genetic Code Expansion

Over 20 years ago, the pyrrolysine encoding translation system was discovered in specific archaea. Our Review provides an overview of how the once obscure pyrrolysyl-tRNA synthetase (PylRS) tRNA pair, originally responsible for accurately translating enzymes crucial in methanogenic metabolic pathways, laid the foundation for the burgeoning field of genetic code expansion. Our primary focus is the discussion of how to successfully engineer the PylRS to recognize new substrates and exhibit higher in vivo activity. We have compiled a comprehensive list of ncAAs incorporable with the PylRS system. Additionally, we also summarize recent successful applications of the PylRS system in creating innovative therapeutic solutions, such as new antibody-drug conjugates, advancements in vaccine modalities, and the potential production of new antimicrobials.

Temperature-Dependent tRNA Modifications in Bacillales

Transfer RNA (tRNA) modifications are essential for the temperature adaptation of thermophilic and psychrophilic organisms as they control the rigidity and flexibility of transcripts. To further understand how specific tRNA modifications are adjusted to maintain functionality in response to temperature fluctuations, we investigated whether tRNA modifications represent an adaptation of bacteria to different growth temperatures (minimal, optimal, and maximal), focusing on closely related psychrophilic (P. halocryophilus and E. sibiricum), mesophilic (B. subtilis), and thermophilic (G. stearothermophilus) Bacillales. Utilizing an RNA sequencing approach combined with chemical pre-treatment of tRNA samples, we systematically profiled dihydrouridine (D), 4-thiouridine (s4U), 7-methyl-guanosine (m7G), and pseudouridine (Ψ) modifications at single-nucleotide resolution. Despite their close relationship, each bacterium exhibited a unique tRNA modification profile. Our findings revealed increased tRNA modifications in the thermophilic bacterium at its optimal growth temperature, particularly showing elevated levels of s4U8 and Ψ55 modifications compared to non-thermophilic bacteria, indicating a temperature-dependent regulation that may contribute to thermotolerance. Furthermore, we observed higher levels of D modifications in psychrophilic and mesophilic bacteria, indicating an adaptive strategy for cold environments by enhancing local flexibility in tRNAs. Our method demonstrated high effectiveness in identifying tRNA modifications compared to an established tool, highlighting its potential for precise tRNA profiling studies.

Biochemical and Structural Characterization of a Novel Psychrophilic Laccase (Multicopper Oxidase) Discovered from Oenococcus oeni 229 (ENOLAB 4002)

Recently, prokaryotic laccases from lactic acid bacteria (LAB), which can degrade biogenic amines, were discovered. A laccase enzyme has been cloned from Oenococcus oeni, a very important LAB in winemaking, and it has been expressed in Escherichia coli. This enzyme has similar characteristics to those previously isolated from LAB as the ability to oxidize canonical substrates such as 2,2-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), 2,6-dimethoxyphenol (2,6-DMP), and potassium ferrocyanide K4[Fe(CN6)], and non-conventional substrates as biogenic amines. However, it presents some distinctiveness, the most characteristic being its psychrophilic behaviour, not seen before among these enzymes. Psychrophilic enzymes capable of efficient catalysis at low temperatures are of great interest due to their potential applications in various biotechnological processes. In this study, we report the discovery and characterization of a new psychrophilic laccase, a multicopper oxidase (MCO), from the bacterium Oenococcus oeni. The psychrophilic laccase gene, designated as LcOe 229, was identified through the genomic analysis of O. oeni, a Gram-positive bacterium commonly found in wine fermentation. The gene was successfully cloned and heterologously expressed in Escherichia coli, and the recombinant enzyme was purified to homogeneity. Biochemical characterization of the psychrophilic laccase revealed its optimal activity at low temperatures, with a peak at 10 °C. To our knowledge, this is the lowest optimum temperature described so far for laccases. Furthermore, the psychrophilic laccase demonstrated remarkable stability and activity at low pH (optimum pH 2.5 for ABTS), suggesting its potential for diverse biotechnological applications. The kinetic properties of LcOe 229 were determined, revealing a high catalytic efficiency (kcat/Km) for several substrates at low temperatures. This exceptional cold adaptation of LcOe 229 indicates its potential as a biocatalyst in cold environments or applications requiring low-temperature processes. The crystal structure of the psychrophilic laccase was determined using X-ray crystallography demonstrating structural features similar to other LAB laccases, such as an extended N-terminal and an extended C-terminal end, with the latter containing a disulphide bond. Also, the structure shows two Met residues at the entrance of the T1Cu site, common in LAB laccases, which we suggest could be involved in substrate binding, thus expanding the substrate-binding pocket for laccases. A structural comparison of LcOe 229 with Antarctic laccases has not revealed specific features assigned to cold-active laccases versus mesophilic. Thus, further investigation of this psychrophilic laccase and its engineering could lead to enhanced cold-active enzymes with improved properties for future biotechnological applications. Overall, the discovery of this novel psychrophilic laccase from O. oeni expands our understanding of cold-adapted enzymes and presents new opportunities for their industrial applications in cold environments.

Hydrolytic enzyme activity in high-rate anaerobic reactors treating municipal wastewater in temperate climates

Particulate matter hydrolysis is the bottleneck in anaerobic treatment of municipal wastewater in temperate climates. Low temperatures theoretically slow enzyme-substrate interactions, hindering utilization kinetics, but this remains poorly understood. β-glucosidase, protease, and lipase activities were evaluated in two pilot-scale upflow anaerobic sludge blanket (UASB) reactors, inoculated with different sludges and later converted to anaerobic membrane bioreactors (AnMBRs). Despite similar methane production and solids hydrolysis rates, significant differences emerged. Specific activity peaked at 37 °C, excluding the predominance of psychrophilic enzymes. Nevertheless, the Michaelis-Menten constant (Km) indicated high enzyme-substrate affinity at the operational temperature of 15-20 °C, notably greater in AnMBRs. It is shown, for the first time, that different seed sludges can equally adapt, as hydrolytic enzymatic affinity to the substrate reached similar values in the two reactors at the operational temperature and identified that membrane ultrafiltration impacted hydrolysis by a favourable enzyme Michaelis-Menten constant.

Genomics-based identification of a cold adapted clade in Deinococcus

BACKGROUND

Microbes in the cold polar and alpine environments play a critical role in feedbacks that amplify the effects of climate change. Defining the cold adapted ecotype is one of the prerequisites for understanding the response of polar and alpine microbes to climate change.

RESULTS

Here, we analysed 85 high-quality, de-duplicated genomes of Deinococcus, which can survive in a variety of harsh environments. By leveraging genomic and phenotypic traits with reverse ecology, we defined a cold adapted clade from eight Deinococcus strains isolated from Arctic, Antarctic and high alpine environments. Genome-wide optimization in amino acid composition and regulation and signalling enable the cold adapted clade to produce CO2 from organic matter and boost the bioavailability of mineral nitrogen.

CONCLUSIONS

Based primarily on in silico genomic analysis, we defined a potential cold adapted clade in Deinococcus and provided an updated view of the genomic traits and metabolic potential of Deinococcus. Our study would facilitate the understanding of microbial processes in the cold polar and alpine environments.

Structural determinants of cold activity and glucose tolerance of a family 1 glycoside hydrolase (GH1) from Antarctic Marinomonas sp. ef1

Cold-active enzymes support life at low temperatures due to their ability to maintain high activity in the cold and can be useful in several biotechnological applications. Although information on the mechanisms of enzyme cold adaptation is still too limited to devise general rules, it appears that very diverse structural and functional changes are exploited in different protein families and within the same family. In this context, we studied the cold adaptation mechanism and the functional properties of a member of the glycoside hydrolase family 1 (GH1) from the Antarctic bacterium Marinomonas sp. ef1. This enzyme exhibits all typical functional hallmarks of cold adaptation, including high catalytic activity at 5 °C, broad substrate specificity, low thermal stability, and higher lability of the active site compared to the overall structure. Analysis of the here-reported crystal structure (1.8 Å resolution) and molecular dynamics simulations suggest that cold activity and thermolability may be due to a flexible region around the active site (residues 298-331), whereas the dynamic behavior of loops flanking the active site (residues 47-61 and 407-413) may favor enzyme-substrate interactions at the optimal temperature of catalysis (Topt) by tethering together protein regions lining the active site. Stapling of the N-terminus onto the surface of the β-barrel is suggested to partly counterbalance protein flexibility, thus providing a stabilizing effect. The tolerance of the enzyme to glucose and galactose is accounted for by the presence of a "gatekeeping" hydrophobic residue (Leu178), located at the entrance of the active site.

Microbial Ecology of an Arctic Travertine Geothermal Spring: Implications for Biosignature Preservation and Astrobiology

Jotun springs in Svalbard, Norway, is a rare warm environment in the Arctic that actively forms travertine. In this study, we assessed the microbial ecology of Jotun's active (aquatic) spring and dry spring transects. We evaluated the microbial preservation potential and mode, as well as the astrobiological relevance of the travertines to marginal carbonates mapped at Jezero Crater on Mars (the Mars 2020 landing site). Our results revealed that microbial communities exhibited spatial dynamics controlled by temperature, fluid availability, and geochemistry. Amorphous carbonates and silica precipitated within biofilm and on the surface of filamentous microorganisms. The water discharged at the source is warm, with near neutral pH, and undersaturated in silica. Hence, silicification possibly occurred through cooling, dehydration, and partially by a microbial presence or activities that promote silica precipitation. CO2 degassing and possible microbial contributions induced calcite precipitation and travertine formation. Jotun revealed that warm systems that are not very productive in carbonate formation may still produce significant carbonate buildups and provide settings favorable for fossilization through silicification and calcification. Our findings suggest that the potential for amorphous silica precipitation may be essential for Jezero Crater's marginal carbonates because it significantly increases the preservation potential of putative martian organisms.

Exploring the Frozen Armory: Antiphage Defense Systems in Cold-Adapted Bacteria with a Focus on CRISPR-Cas Systems

Our understanding of the antiphage defense system arsenal in bacteria is rapidly expanding, but little is known about its occurrence in cold-adapted bacteria. In this study, we aim to shed light on the prevalence and distribution of antiphage defense systems in cold-adapted bacteria, with a focus on CRISPR-Cas systems. Using bioinformatics tools, Prokaryotic Antiviral Defense LOCator (PADLOC) and CRISPRCasTyper, we mapped the presence and diversity of antiphage defense systems in 938 available genomes of cold-adapted bacteria from diverse habitats. We confirmed that CRISPR-Cas systems are less frequent in cold-adapted bacteria, compared to mesophilic and thermophilic species. In contrast, several antiphage defense systems, such as dXTPases and DRTs, appear to be more frequently compared to temperate bacteria. Additionally, our study provides Cas endonuclease candidates with a potential for further development into cold-active CRISPR-Cas genome editing tools. These candidates could have broad applications in research on cold-adapted organisms. Our study provides a first-time map of antiphage defense systems in cold-adapted bacteria and a detailed overview of CRISPR-Cas diversity.

Bacterial diversity and biopotentials of Hamtah glacier cryoconites, Himalaya

Cryoconite is a granular structure present on the glaciers and ice sheets found in polar regions including the Himalayas. It is composed of organic and inorganic matter which absorb solar radiations and reduce ice surface albedo, therefore impacting the melting and retreat of glaciers. Though climate warming has a serious impact on Himalayan glaciers, the biodiversity of sub-glacier ecosystems is poorly understood. Moreover, cryoconite holes are unique habitats for psychrophile biodiversity hotspots in the NW Himalayas, but unfortunately, studies on the microbial diversity of such habitats remain elusive. Therefore, the current study was designed to explore the bacterial diversity of the Hamtah Glacier Himalaya using both culturable and non-culturable approaches. The culturable bacterial count ranged from 2.0 × 103 to 8.8 × 105 colony-forming units (CFUs)/g at the different locations of the glacier. A total of 88 bacterial isolates were isolated using the culturable approach. Based on the 16S ribosomal RNA gene (16S rRNA), the identified species belong to seven genera, namely, Cryobacterium, Duganella, Janthinobacterium, Pseudomonas, Peribacillus, Psychrobacter, and Sphingomonas. In the non-culturable approach, high-throughput sequencing of 16S rRNA genes (using MiSeq) showed unique bacterial community profiles and represented 440 genera belonging to 20 phyla, namely, Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes, Chloroflexi, Acidobacteria, Planctomycetes, Cyanobacteria, Verrucomicrobia, Spirochaetes, Elusimicrobia, Armatimonadetes, Gemmatimonadetes, Deinococcus-Thermus, Nitrospirae, Chlamydiae, Chlorobi, Deferribacteres, Fusobacteria, Lentisphaerae, and others. High relative abundances of Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes were observed in the samples. Phototrophic (Cyanobacteria and Chloroflexi) and nitrifier (Nitrospirae) in bacterial populations indicated sustenance of the micro-ecosystem in the oligotrophic glacier environment. The isolates varied in their phenotypic characteristics, enzyme activities, and antibiotic sensitivity. Furthermore, the fatty acid profiles of bacterial isolates indicate the predominance of branched fatty acids. Iso-, anteiso-, unsaturated and saturated fatty acids together constituted a major proportion of the total fatty acid composition. High cold-adapted enzyme activities such as lipase and cellulase expressed by Cryobacterium arcticum (KY783365) and protease and cellulase activities by Pseudomonas sp. strains (KY783373, KY783377-79, KY783382) provide evidence of the possible applications of these organisms. Additionally, antibiotic tests indicated that most isolates were sensitive to antibiotics. In conclusion, the present study contributed for the first time to bacterial diversity and biopotentials of cryoconites of Hamtah Glacier, Himalayas. Furthermore, the cold-adapted enzymes and polyunsaturated fatty acids (PUFAs) may provide an opportunity for biotechnology in the Himalayas. Inductively coupled plasma mass spectrometry (ICPMS) analyses showed the presence of several elements in cryoconites, providing a clue for the accelerating melting and retreating of the Hamtah glacier.

Comparative molecular dynamics simulations provided insights into the mechanisms of cold-adaption of alginate lyases from the PL7 family

Alginate is an important polysaccharide that is abundant in the marine environments, including the Polar Regions, and bacterial alginate lyases play key roles in its degradation. Many reported alginate lyases show characteristics of cold-adapted enzymes, including relatively low temperature optimum of activities (Topt) and low thermal stabilities. However, the cold-adaption mechanisms of alginate lyases remain unclear. Here, we studied the cold-adaptation mechanisms of alginate lyases by comparing four members of the PL7 family from different environments: AlyC3 from the Arctic ocean (Psychromonas sp. C-3), AlyA1 from the temperate ocean (Zobellia galactanivorans), PA1167 from the human pathogen (Pseudomonas aeruginosa PAO1), and AlyQ from the tropic ocean (Persicobacter sp. CCB-QB2). Sequence comparison and comparative molecular dynamics (MD) simulations revealed two main strategies of cold adaptation. First, the Arctic AlyC3 and temperate AlyA1 increased the flexibility of the loops close to the catalytic center by introducing insertions at these loops. Second, the Arctic AlyC3 increased the electrostatic attractions with the negatively charged substrate by introducing a high portion of positively charged lysine at three of the insertions mentioned above. Furthermore, our study also revealed that the root mean square fluctuation (RMSF) increased greatly when the temperature was increased to Topt or higher, suggesting the RMSF increase temperature as a potential indicator of the cold adaptation level of the PL7 family. This study provided new insights into the cold-adaptation mechanisms of bacterial alginate lyases and the marine carbon cycling at low temperatures.

Cold-active microbial enzymes and their biotechnological applications

Microorganisms known as psychrophiles/psychrotrophs, which survive in cold climates, constitute majority of the biosphere on Earth. Their capability to produce cold-active enzymes along with other distinguishing characteristics allows them to survive in the cold environments. Due to the relative ease of large-scale production compared to enzymes from plants and animals, commercial uses of microbial enzyme are alluring. The ocean depths, polar, and alpine regions, which make up over 85% of the planet, are inhabited to cold ecosystems. Microbes living in these regions are important for their metabolic contribution to the ecosphere as well as for their enzymes, which may have potential industrial applications. Cold-adapted microorganisms are a possible source of cold-active enzymes that have high catalytic efficacy at low and moderate temperatures at which homologous mesophilic enzymes are not active. Cold-active enzymes can be used in a variety of biotechnological processes, including food processing, additives in the detergent and food industries, textile industry, waste-water treatment, biopulping, environmental bioremediation in cold climates, biotransformation, and molecular biology applications with great potential for energy savings. Genetically manipulated strains that are suitable for producing a particular cold-active enzyme would be crucial in a variety of industrial and biotechnological applications. The potential advantage of cold-adapted enzymes will probably lead to a greater annual market than for thermo-stable enzymes in the near future. This review includes latest updates on various microbial source of cold-active enzymes and their biotechnological applications.

Low-Temperature Adaptive Single-Atom Iron Nanozymes against Viruses in the Cold Chain

Outbreaks of viral infectious diseases, such as the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza A virus (IAV), pose a great threat to human health. Viral spread is accelerated worldwide by the development of cold chain logistics; Therefore, an effective antiviral approach is required. In this study, it is aimed to develop a distinct antiviral strategy using nanozymes with low-temperature adaptability, suitable for cold chain logistics. Phosphorus (P) atoms are added to the remote counter position of Fe-N-C center to prepare FeN4P2-single-atom nanozymes (SAzymes), exhibiting lipid oxidase (OXD)-like activity at cold chain temperatures (-20, and 4 °C). This feature enables FeN4P2-SAzymes to disrupt multiple enveloped viruses (human, swine, and avian coronaviruses, and H1-H11 subtypes of IAV) by catalyzing lipid peroxidation of the viral lipid envelope. Under the simulated conditions of cold chain logistics, FeN4P2-SAzymes are successfully applied as antiviral coatings on outer packaging and personal protective equipment; Therefore, FeN4P2-SAzymes with low-temperature adaptability and broad-spectrum antiviral properties may serve as key materials for developing specific antiviral approaches to interrupt viral transmission through the cold chain.

High temperature delays and low temperature accelerates evolution of a new protein phenotype

Since the origin of life, temperatures on earth have fluctuated both on short and long time scales. How such changes affect the rate at which Darwinian evolution can bring forth new phenotypes remains unclear. On the one hand, high temperature may accelerate phenotypic evolution because it accelerates most biological processes. On the other hand, it may slow phenotypic evolution, because proteins are usually less stable at high temperatures and therefore less evolvable. Here, to test these hypotheses experimentally, we evolved a green fluorescent protein in E. coli towards the new phenotype of yellow fluorescence at different temperatures. Yellow fluorescence evolved most slowly at high temperature and most rapidly at low temperature, in contradiction to the first hypothesis. Using high-throughput population sequencing, protein engineering, and biochemical assays, we determined that this is due to the protein-destabilizing effect of neofunctionalizing mutations. Destabilization is highly detrimental at high temperature, where neofunctionalizing mutations cannot be tolerated. Their detrimental effects can be mitigated through excess stability at low temperature, leading to accelerated adaptive evolution. By modifying protein folding stability, temperature alters the accessibility of mutational paths towards high-fitness genotypes. Our observations have broad implications for our understanding of how temperature changes affect evolutionary adaptations and innovations.

Chapter 6: The Breadth and Limits of Life on Earth

Scientific ideas about the potential existence of life elsewhere in the universe are predominantly informed by knowledge about life on Earth. Over the past ∼4 billion years, life on Earth has evolved into millions of unique species. Life now inhabits nearly every environmental niche on Earth that has been explored. Despite the wide variety of species and diverse biochemistry of modern life, many features, such as energy production mechanisms and nutrient requirements, are conserved across the Tree of Life. Such conserved features help define the operational parameters required by life and therefore help direct the exploration and evaluation of habitability in extraterrestrial environments. As new diversity in the Tree of Life continues to expand, so do the known limits of life on Earth and the range of environments considered habitable elsewhere. The metabolic processes used by organisms living on the edge of habitability provide insights into the types of environments that would be most suitable to hosting extraterrestrial life, crucial for planning and developing future astrobiology missions. This chapter will introduce readers to the breadth and limits of life on Earth and show how the study of life at the extremes can inform the broader field of astrobiology.

Characterization of novel mevalonate kinases from the tardigrade Ramazzottius varieornatus and the psychrophilic archaeon Methanococcoides burtonii

Mevalonate kinase is central to the isoprenoid biosynthesis pathway. Here, high-resolution X-ray crystal structures of two mevalonate kinases are presented: a eukaryotic protein from Ramazzottius varieornatus and an archaeal protein from Methanococcoides burtonii. Both enzymes possess the highly conserved motifs of the GHMP enzyme superfamily, with notable differences between the two enzymes in the N-terminal part of the structures. Biochemical characterization of the two enzymes revealed major differences in their sensitivity to geranyl pyrophosphate and farnesyl pyrophosphate, and in their thermal stabilities. This work adds to the understanding of the structural basis of enzyme inhibition and thermostability in mevalonate kinases.

A Manganese-Based Metal-Organic Framework as a Cold-Adapted Nanozyme

The development of cold-adapted enzymes with high efficiency and good stability is an advanced strategy to overcome the limitations of catalytic medicine in low and cryogenic temperatures. In this work, inspired by natural enzymes, a novel cold-adapted nanozyme based on a manganese-based nanosized metal-organic framework (nMnBTC) is designed and synthesized. The nMnBTC as an oxidase mimetic not only exhibits excellent activity at 0 °C, but also presents almost no observable activity loss as the temperature is increased to 45 °C. This breaks the traditional recognition that enzymes show maximum activity only under specific psychrophilic or thermophilic condition. The superior performance of nMnBTC as a cold-adapted nanozyme can be attributed to its high-catalytic efficiency at low temperature, good substrate affinity, and flexible conformation. Based on the robust performance of nMnBTC, a low-temperature antiviral strategy is developed to inactivate influenza virus H1N1 even at -20 °C. These results not only provide an important guide for the rational design of highly efficient artificial cold-adapted enzymes, but also pave a novel way for biomedical application in cryogenic fields.

Structural and functional characterization of cold-active sialidase isolated from Antarctic fungus Penicillium griseofulvum P29

The fungal strain, Penicillium griseofulvum P29, isolated from a soil sample taken from Terra Nova Bay, Antarctica, was found to be a good producer of sialidase (P29). The present study was focused on the purification and structural characterization of the enzyme. P29 enzyme was purified using a Q-Sepharose column and fast performance liquid chromatography separation on a Mono Q column. The determined molecular mass of the purified enzyme of 40 kDa by SDS-PAGE and 39924.40 Da by matrix desorption/ionization mass spectrometry (MALDI-TOF/MS) analysis correlated well with the calculated mass (39903.75 kDa) from the amino acid sequence of the enzyme. P29 sialidase shows a temperature optimum of 37 °C and low-temperature stability, confirming its cold-active nature. The enzyme is more active towards α(2 → 3) sialyl linkages than those containing α(2 → 6) linkages. Based on the determined amino acid sequence and 3D structural modeling, a 3D model of P29 sialidase was presented, and the properties of the enzyme were explained. The conformational stability of the enzyme was followed by fluorescence spectroscopy, and the new enzyme was found to be conformationally stable in the neutral pH range of pH 6 to pH 9. In addition, the enzyme was more stable in an alkaline environment than in an acidic environment. The purified cold-active enzyme is the only sialidase produced and characterized from Antarctic fungi to date.

Disconnected active layers and unfrozen permafrost: A discussion of permafrost-related terms and definitions

Permafrost is ground that remains at or below 0 °C for two or more consecutive years. It is overlain by an active layer which thaws and freezes annually. The difference between these definitions - the active layer based on pore water phase and permafrost based on soil temperature - leads to challenges when monitoring and modelling permafrost environments. Contrary to its definition, the key properties of permafrost including hardness, bearing capacity, permeability, unfrozen water content, and energy content, depend primarily on the ice content of permafrost and not its temperature. Temperature-based measurements in permafrost systems often overlook key features, e.g. taliks and cryopegs, and comparisons between measured and modelled systems can differ energetically by up to 90 % while reporting the same temperature. Due to the shortcomings of the temperature-based definition, it is recommended that an estimate of ice content be reported alongside temperature in permafrost systems for both in-situ measurements and modelling applications. PLAIN LANGUAGE SUMMARY: Permafrost is ground that remains at or below 0 °C for two or more consecutive years. Above it sits an active layer which thaws and freezes annually (meaning that the water in the ground changes to ice each winter). The difference between these definitions - the active layer based on the state or water in the ground and permafrost based on ground temperature - leads to challenges when measuring (in the field) and modelling (using computers) permafrost environments. In addition to these challenges, the key properties of permafrost including its ability to support infrastructure, convey water, and absorb energy depend more on its ice content than its temperature. Due to the shortcomings of the temperature-based definition, it is recommended that an estimate of ice content be reported alongside temperature in permafrost systems for both field measurements and modelling applications.

An inhibitor of the adaptability of Pseudomonas fluorescens in a high-salt environment. Phenomenon and mechanism of inhibition

Pseudomonas fluorescens is a spoilage bacterium in food that has the ability to maintain growth and reproduction in high-salt environments. It acts as a defence mechanism through the exclusion of ions and the formation of biofilms. Hence, disrupting this defence mechanism may be a good way to control food spoilage. In this study, a specific flavonoid small molecule baicalin was found, which was able to dismantle the defence mechanism of the bacteria at a lower concentration (400 μM) of treatment. In synergy with salt, baicalin showed a significant inhibitory effect on the growth, c-di-gmp synthetics and biofilm formation of Pseudomonas fluorescens Pf08. Through transcriptomics, we also found that baicalein interfered with bacterial transport and polysaccharide production functions. Through molecular docking and QPCR, we found that baicalin is able to binding with the RpoS protein through hydrogen bonding and thus interfere with its function.

Living in trinity of extremes: Genomic and proteomic signatures of halophilic, thermophilic, and pH adaptation

Since nucleic acids and proteins of unicellular prokaryotes are directly exposed to extreme environmental conditions, it is possible to explore the genomic-proteomic compositional determinants of molecular mechanisms of adaptation developed by them in response to harsh environmental conditions. Using a wealth of currently available complete genomes/proteomes we were able to explore signatures of adaptation to three environmental factors, pH, salinity, and temperature, observing major trends in compositions of their nucleic acids and proteins. We derived predictors of thermostability, halophilic, and pH adaptations and complemented them by the principal components analysis. We observed a clear difference between thermophilic and salinity/pH adaptations, whereas latter invoke seemingly overlapping mechanisms. The genome-proteome compositional trade-off reveals an intricate balance between the work of base paring and base stacking in stabilization of coding DNA and r/tRNAs, and, at the same time, universal requirements for the stability and foldability of proteins regardless of the nucleotide biases. Nevertheless, we still found hidden fingerprints of ancient evolutionary connections between the nucleotide and amino acid compositions indicating their emergence, mutual evolution, and adjustment. The evolutionary perspective on the adaptation mechanisms is further studied here by means of the comparative analysis of genomic/proteomic traits of archaeal and bacterial species. The overall picture of genomic/proteomic signals of adaptation obtained here provides a foundation for future engineering and design of functional biomolecules resistant to harsh environments.

Catalase from the Antarctic Fungus Aspergillus fumigatus I-9-Biosynthesis and Gene Characterization

Extremely cold habitats are a serious challenge for the existing there organisms. Inhabitants of these conditions are mostly microorganisms and lower mycetae. The mechanisms of microbial adaptation to extreme conditions are still unclear. Low temperatures cause significant physiological and biochemical changes in cells. Recently, there has been increasing interest in the relationship between low-temperature exposure and oxidative stress events, as well as the importance of antioxidant enzymes for survival in such conditions. The catalase is involved in the first line of the cells' antioxidant defense. Published information supports the concept of a key role for catalase in antioxidant defense against cold stress in a wide range of organisms isolated from the Antarctic. Data on representatives of microscopic fungi, however, are rarely found. There is scarce information on the characterization of catalase synthesized by adapted to cold stress organisms. Overall, this study aimed to observe the role of catalase in the survival strategy of filamentous fungi in extremely cold habitats and to identify the gene encoded catalase enzyme. Our results clearly showed that catalase is the main part of antioxidant enzyme defense in fungal cells against oxidative stress caused by low temperature exposure.

Exploring the molecular mechanism of cold-adaption of an alkaline protease mutant by molecular dynamics simulations and residue interaction network

Psychrophilic proteases have attracted enormous attention in past decades, due to their high catalytic activity at low temperatures in a wide range of industrial processes, especially in the detergent and leather industries. Among them, H5 is an alkaline protease mutant, which featuring psychrophilic-like behavior, but the reasons that H5 with higher activity at low temperatures are still poorly understood. Herein, the molecular dynamics (MD) simulations combined with residue interaction network (RIN) were utilized to investigate the mechanisms of the cold-adaption of mutant H5. The results demonstrated that two loops involved in the substrate binding G100-S104 and S125-S129 in H5 had higher mobility, and the distance enlargement between the two loops modulated the substrate's accessibility compared with wild type counterpart. Besides, H5 enhanced conformational flexibility by weakening salt bridges and increasing interaction with the solvent. In particular, the absence of Lys251-Asp197-Arg247 salt bridge network may contribute to the structural mobility. Based on the free energy landscape and molecular mechanics Poisson-Boltzmann surface area of the wild type and H5, it was elucidated that H5 possessed a large population of interconvertible conformations, resulting in the weaker substrate binding free energy. The calculated RIN topology parameters such as the average degree, average cluster coefficient, and average path length further verified that the mutant H5 attenuated residue-to-residue interactions. The investigation of the mechanisms by which how the residue mutation affects the stability and activity of enzymes provides a theoretical basis for the development of cold-adapted protease.

Helping proteins come in from the cold: 5 burning questions about cold-active enzymes

Enzymes from psychrophilic (cold-loving) organisms have attracted considerable interest over the past decades for their potential in various low-temperature industrial processes. However, we still lack large-scale commercialization of their activities. Here, we review their properties, limitations and potential. Our review is structured around answers to 5 central questions: 1. How do cold-active enzymes achieve high catalytic rates at low temperatures? 2. How is protein flexibility connected to cold-activity? 3. What are the sequence-based and structural determinants for cold-activity? 4. How does the thermodynamic stability of psychrophilic enzymes reflect their cold-active capabilities? 5. How do we effectively identify novel cold-active enzymes, and can we apply them in an industrial context? We conclude that emerging screening technologies combined with big-data handling and analysis make it reasonable to expect a bright future for our understanding and exploitation of cold-active enzymes.

Resonance Raman spectra of blue copper proteins: Variable temperature spectra of Thermus thermophilus HB27 laccase

The resonance Raman (rR) spectra of the oxidized type 1 copper active site (CuT1) in Thermus thermophilus HB27 laccase (Tth-lac) has been determined in the 20 to 80 °C temperature range using 633-nm excitation. The positions and relative intensities of rR peaks are virtually independent of temperature, indicating that CuT1 ligation is robust over the investigated range. The intensity-weighted average of Tth-lac Cu-SCys vibrations (<ν(Cu-SCys)>) = 423 cm-1) is higher than those of most cupredoxins but is comparable to those of other multicopper oxidases (MCOs). <ν(Cu-SCys)> values for Tth-lac and several CuT1 centers in cupredoxins and MCOs do not correlate well with Cu-SCys bond lengths but do exhibit systematic trends with redox thermodynamic properties. PROLOGUE: F. Ann Walker was a great scholar and dear friend. While at Columbia in the early 1960s, I (HBG) followed her graduate work at Brown on the effects of axial ligands on vanadyl ion EPR spectra. Dick Carlin, her thesis adviser, invited me to serve as external member of her thesis committee. I joined, made my way to Providence, met her just before the exam, and greatly admired (enjoyed!) her thoughtful responses to questions from physical chemists about metal-oxo electronic structures. Our friendship grew stronger over the years, enhanced by lively discussions of heme protein chemistry in San Francisco, Pasadena, Tucson, and at Gordon Research Conferences. Ann was a superstar in biological inorganic chemistry. She will be sorely missed but not forgotten.

Temperature activated transient receptor potential ion channels from Antarctic fishes

Antarctic notothenioid fishes (cryonotothenioids) live in waters that range between -1.86°C and an extreme maximum +4°C. Evidence suggests these fish sense temperature peripherally, but the molecular mechanism of temperature sensation in unknown. Previous work identified transient receptor potential (TRP) channels TRPA1b, TRPM4 and TRPV1a as the top candidates for temperature sensors. Here, cryonotothenioid TRPA1b and TRPV1a are characterized using Xenopus oocyte electrophysiology. TRPA1b and TRPV1a showed heat-evoked currents with Q10s of 11.1 ± 2.2 and 20.5 ± 2.4, respectively. Unexpectedly, heat activation occurred at a threshold of 22.9 ± 1.3°C for TRPA1b and 32.1 ± 0.6°C for TRPV1a. These fish have not experienced such temperatures for at least 15 Myr. Either (1) another molecular mechanism underlies temperature sensation, (2) these fishes do not sense temperatures below these thresholds despite having lethal limits as low as 5°C, or (3) native cellular conditions modify the TRP channels to function at relevant temperatures. The effects of osmolytes, pH, oxidation, phosphorylation, lipids and accessory proteins were tested. No conditions shifted the activity range of TRPV1a. Oxidation in combination with reduced cholesterol significantly dropped activation threshold of TRPA1b to 11.3 ± 2.3°C, it is hypothesized the effect may be due to lipid raft disruption.

Biochemical Insights into a Novel Family 2 Glycoside Hydrolase with Both β-1,3-Galactosidase and β-1,4-Galactosidase Activity from the Arctic

A novel GH2 (glycoside hydrolase family 2) β-galactosidase from Marinomonas sp. BSi20584 was successfully expressed in E. coli with a stable soluble form. The recombinant enzyme (rMaBGA) was purified to electrophoretic homogeneity and characterized extensively. The specific activity of purified rMaBGA was determined as 96.827 U mg-1 at 30 °C using ONPG (o-nitrophenyl-β-D-galactopyranoside) as a substrate. The optimum pH and temperature of rMaBGA was measured as 7.0 and 50 °C, respectively. The activity of rMaBGA was significantly enhanced by some divalent cations including Zn2+, Mg2+ and Ni2+, but inhibited by EDTA, suggesting that some divalent cations might play important roles in the catalytic process of rMaBGA. Although the enzyme was derived from a cold-adapted strain, it still showed considerable stability against various physical and chemical elements. Moreover, rMaBGA exhibited activity both toward Galβ-(1,3)-GlcNAc and Galβ-(1,4)-GlcNAc, which is a relatively rare occurrence in GH2 β-galactosidase. The results showed that two domains in the C-terminal region might be contributed to the β-1,3-galactosidase activity of rMaBGA. On account of its fine features, this enzyme is a promising candidate for the industrial application of β-galactosidase.