Pyrobaculum Research Articles

Triple Enzymatic Cascade Reaction to Produce Hydroxytyrosol Acetate from Olive Leaves Using Integrated Membrane Bioreactors.

An integrated system of three membrane bioreactors (MBRs) has been developed that cascades three different enzymatic reactions. The integrated system was applied to produce hydroxytyrosol acetate from oleuropein extracted from olive leaves. Different reactor configurations for each reaction were tested and individually optimized to select the MBR to ensure high conversion and continuous production of oleuropein aglycone (OA), hydroxytyrosol (HY) and hydroxytyrosol acetate (HA). Based on this study, the most performing configuration of the integrated system was identified. In the first reaction, oleuropein was converted to OA using a biocatalytic membrane reactor (BMR) with immobilized β-glucosidase in polymeric membranes (conversion 95 %). The OA was then fed to another BMR, where it was converted to HY (conversion: 70 %) by an immobilized mutant of the promiscuous hydrolase/acyltransferase (PestE) (from the thermophilic archaeon Pyrobaculum calidifontis VA1). The HY produced was then acetylated using PestE immobilized on magnetic nanoparticles in a multiphase MBR (conversion: 98 %) and simultaneously extracted (extraction: 98 %) in ethyl acetate. The work demonstrates that continuous cascade enzymatic reactions can be engineered using artificial membranes to tailor enzyme compartmentalization, mass transport and phase contact according to reaction requirements. Besides, environmental factors proved the sustainability of the integrated membrane bioreactive system.

Development of the esterase PestE for amide bond synthesis under aqueous conditions: Enzyme cascades for converting waste PET into tamibarotene.

A growing number of hydrolase enzymes show promiscuous acyltransferase activity, even under aqueous conditions. Here we report, for the first time, the ability of Pyrobaculum calidifontis VA1 esterase (PestE) to catalyse the formation of a wide range of amides in buffer, where the acyl donor forms a significant structural component in the amide product. The reactions occur under mild conditions and can achieve conversions up to 97% in 6 h for formation of N-benzylfuranamide as the model reaction. We demonstrate PestE's potential in enzyme cascades to make amides from waste PET plastic and the conversion of the terephthalic acid product to tamibarotene, a drug with activity against acute leukemia. Rational mutagenesis led to identification of PestE variants F33L_F289A and F33L. F33L_F289A increased conversion of N-benzylfuranamide by 1.2-fold, and F33L gave a 4-fold increase in conversion to tamibarotene.

Development of the esterase PestE for amide bond synthesis under aqueous conditions: Enzyme cascades for converting waste PET into tamibarotene.

A growing number of hydrolase enzymes show promiscuous acyltransferase activity, even under aqueous conditions. Here we report, for the first time, the ability of Pyrobaculum calidifontis VA1 esterase (PestE) to catalyse the formation of a wide range of amides in buffer, where the acyl donor forms a significant structural component in the amide product. The reactions occur under mild conditions and can achieve conversions up to 97% in 6 h for formation of N‐benzylfuranamide as the model reaction. We demonstrate PestE’s potential in enzyme cascades to make amides from waste PET plastic and the conversion of the terephthalic acid product to tamibarotene, a drug with activity against acute leukemia. Rational mutagenesis led to identification of PestE variants F33L_F289A and F33L. F33L_F289A increased conversion of N‐benzylfuranamide by 1.2‐fold, and F33L gave a 4‐fold increase in conversion to tamibarotene.

Computer-Aided Flexible Loops Engineering of Glutamate Dehydrogenase for Asymmetric Synthesis of Chiral Pesticides l-phosphinothricin.

The access to the enantiopure noncanonical amino acid l-phosphinothricin (l-PPT) by applying biocatalysts is highly appealing in organic chemistry. In this study, a NADH-dependent glutamate dehydrogenase from Lachnospiraceae bacterium (LbGluDH) was chosen for the asymmetric synthesis of l-PPT. Three flexible loops undergoing big conformational shifts during the catalysis were identified and rationally engineered following the initial mutagenesis. The enzyme's specific activity toward the key precursor of l-PPT, 2-oxo-4-[(hydroxy) (methyl) phosphinyl] butyric acid (PPO), was improved from negligible to 9 U/mg, and the Km value was reduced to 17 mM. The computational analysis showed that the modified loops broadened the enzyme's narrow tunnels, allowing the substrate to access the binding pocket and get closer to the crucial residue D165, thereby enhancing the catalytic process. Utilizing the variant as the catalyst, the preparation of l-PPT achieved a 100% conversion rate within 60 min, coupled with a stereoselectivity exceeding 99.9%, demonstrating its practical capacity for industrial application. Similar enhancement in catalytic activity was obtained applying the same strategy to a typical NADH-dependent GluDH from Pyrobaculum islandicum (PisGluDH), indicating the effectiveness of our strategy for the protein engineering of GluDHs targeted to the biosynthesis of unnatural compounds.

Structural and functional investigations of Pcal_0606, a bifunctional phosphoglucose/phosphomannose isomerase from Pyrobaculum calidifontis

We are investigating the glycolytic pathway in Pyrobaculum calidifontis whose genome sequence contains homologues of all the enzymes involved in this pathway. We have characterized most of them. An open reading frame, Pcal_0606, annotated as a putative phosphoglucose/phosphomannose isomerase has to be characterized yet. In silico analysis indicated the presence of more than one substrate binding pockets at the dimeric interface of Pcal_0606. The gene encoding Pcal_0606 was cloned and expressed in Escherichia coli. Recombinant Pcal_0606, produced in soluble form, exhibited highest enzyme activity at 90 °C and pH 8.5. Presence or absence of metal ions or EDTA did not significantly affect the enzyme activity. Under optimal conditions, Pcal_0606 displayed apparent Km values of 0.33, 0.34, and 0.29 mM against glucose 6-phosphate, mannose 6-phosphate and fructose 6-phosphate, respectively. In the same order, Vmax values against these substrates were 290, 235, and 240 μmol min−1 mg−1, indicating that Pcal_0606 catalyzed the reversible isomerization of these substrates with nearly same catalytic efficiency. These results characterize Pcal_0606 a bifunctional phosphoglucose/phosphomannose isomerase, which displayed high thermostability with a half-life of ∼50 min at 100 °C. To the best of our knowledge, Pcal_0606 is the most active and thermostable bifunctional phosphoglucose/phosphomannose isomerase characterized to date.

Effiziente enzymatische Synthese von Carbamaten in Wasser durch promiskuitive Esterasen/Acyltransferasen

AbstractDie Biokatalyse bietet einen attraktiven Ansatz, um synthetische Reaktionen in wässriger Lösung zu ermöglichen. Motiviert durch die Entdeckung der vielseitigen Aminolyseaktivität von Esterasen haben wir die Esterase aus Pyrobaculum calidifontis VA1 (PestE) für die Synthese von Carbamaten aus verschiedenen aliphatischen, aromatischen und arylaliphatischen Aminen sowie einer Reihe von Carbonaten wie Dimethyl‐, Dibenzyl‐ oder Diallylcarbonat genutzt. So konnten Anilin‐ und Benzylaminderivate, aliphatische und sogar sekundäre Amine effizient in die entsprechenden Benzyloxycarbonyl (Cbz)‐ oder Allyloxycarbonyl (Alloc)‐geschützten Produkte in wässriger Lösung, mit (isolierten) Ausbeuten von bis zu 99 % umgesetzt werden.

Enzymatic Synthesis of Hydroxycinnamic Acid Amides in Water Using the Promiscuous Hydrolase/Acyltransferase PestE from Pyrobaculum calidifontis VA1

AbstractHydroxycinnamic acid amides are believed to have antioxidant, antidiabetic, cytotoxic, anticancer, neuroprotective, and antiinflammatory properties, making them interesting target molecules for potential applications in the food, cosmetics, and pharmaceutical industries. Here, we describe the synthesis of hydroxycinnamic acid amides starting from hydroxycinnamic acid esters and the corresponding amines by using variants of the promiscuous hydrolase/acyltransferase from Pyrobaculum calidifontis VA1 (PestE) in water as a solvent. Up to 97% conversion within two hours at 60 °C was achieved with methyl ferulate and tyramine as substrates. This is a promising, environmentally friendly alternative strategy to established chemical synthesis routes or enzymatic methods using lipases in nonaqueous organic solvents.

Enzymatic depolymerization of plastic materials by a highly efficient two-enzyme system

Advancing the efficiency of polyethylene terephthalate (PET) degradation is pivotal for sustainable and versatile PET recycling. In this study, we initially screened eight esterases, pinpointing Pyrobaculum calidifontis VA1 esterase (PCEST) as markedly effective in decomposing PET intermediate products. Building on this discovery, we engineered fusion proteins combining a robust cutinase (HRC) with PCEST, connected by flexible glycine-serine linkers. We further optimized the linker length, the sequential arrangement and the enzymatic conditions of the conjugated enzymes. Notably, the synergistic activity of the HRC-PCEST fusion protein significantly enhanced the breakdown of PET, thereby promising to streamline recycling processes. Collectively, this methodology not only propels the efficiency of PET degradation but also broadens the horizons for sustainable and versatile PET waste management protocols.

Extremophile enzyme activity lab: using catalase from Pyrobaculum calidifontis to highlight temperature sensitivity and thermostable enzyme activity.

There are places on earth that are considered to possess extreme physico-chemical characteristics as they relate to life. Surprisingly, there are microbes that have adapted various strategies that enable them to form robust communities in these environments. The microbes that live in these environments, called extremophiles, are described as being thermophilic, psychrophilic, halophilic, acidophilic, alkaliphilic, barophilic, and so on. Given that extremophiles were not discovered until relatively recently due to a view point that the environments in which they inhabited were not conducive to life, it is reasonable to conclude that the concept of extremophiles may be hard to grasp for students. Herein is described a laboratory exercise adapted from laboratory exercises that use mesophilic catalase enzymes to illustrate the influence of physico-chemical parameters on enzyme activity. Catalase is an enzyme that accelerates the degradation of hydrogen peroxide to water and oxygen gas. In addition to mesophilic catalases, the catalase from Pyrobaculum calidifontis, a hyperthermophile with an optimal growth temperature of 90°C, is used to highlight the adaptation of an enzyme to an extreme environment. A visual comparison of bubble production by the hyperthermophilic and mesophilic enzymes after heating at high temperatures dramatically illustrates differences in thermostability that will likely reinforce concepts that are given in a pre-laboratory lecture that discusses not only the extremophiles themselves but also their applications in biotechnology and possible role in the field of astrobiology.

Molecular cloning and characterization of Pcal_0039, an ATP-/NAD+-independent DNA ligase from hyperthermophilic archaeon Pyrobaculum calidifontis

The genome sequence of hyperthermophilic archaeon Pyrobaculum calidifontis contains an open reading frame, Pcal_0039, which encodes a putative DNA ligase. Structural analysis disclosed the presence of signature sequences of ATP-dependent DNA ligases. We have heterologously expressed Pcal_0039 gene in Escherichia coli. The recombinant protein, majorly produced in soluble form, was purified and functionally characterized. Recombinant Pcal_0039 displayed nick-joining activity between 40 and 85 °C. Optimal activity was observed at 70 °C and pH 5.5. Nick-joining activity was retained even after heating for 1 h at 90 °C, indicating highly thermostable nature of Pcal_0039. The nick-joining activity, displayed by Pcal_0039, was metal ion dependent and Mg2+ was the most preferred. NaCl and KCl inhibited the nick-joining activity at or above 200 mmol/L. The activity catalyzed by recombinant Pcal_0039 was independent of addition of ATP or NAD+ or any other nucleotide cofactor. A mismatch adjacent to the nick, either at 3′- or 5′-end, abolished the nick-joining activity. These characteristics make Pcal_0039 a potential candidate for applications in DNA diagnostics. To the best of our knowledge, Pcal_0039 is the only DNA ligase, characterized from genus Pyrobaculum, which exhibits optimum nick-joining activity at pH below 6.0 and independent of any nucleotide cofactor.

Enzymatic Nitrogen Incorporation Using Hydroxylamine.

Hydroxylamine-derived reagents have enabled versatile nitrene transfer reactions for introducing nitrogen-containing functionalities in small-molecule catalysis, as well as biocatalysis. These reagents, however, result in a poor atom economy and stoichiometric organic waste. Activating hydroxylamine (NH2OH) for nitrene transfer offers a low-cost and sustainable route to amine synthesis, since water is the sole byproduct. Despite its presence in nature, hydroxylamine is not known to be used for enzymatic nitrogen incorporation in biosynthesis. Here, we report an engineered heme enzyme that can utilize hydroxylammonium chloride, an inexpensive commodity chemical, for nitrene transfer. Directed evolution of Pyrobaculum arsenaticum protoglobin generated efficient enzymes for benzylic C-H primary amination and styrene aminohydroxylation. Mechanistic studies supported a stepwise radical pathway involving rate-limiting hydrogen atom transfer. This unprecedented activity is a useful addition to the "nitrene transferase" repertoire and hints at possible future discovery of natural enzymes that use hydroxylamine for amination chemistry.

The evolution of archaeal flagellar filaments

Flagellar motility has independently arisen three times during evolution: in bacteria, archaea, and eukaryotes. In prokaryotes, the supercoiled flagellar filaments are composed largely of a single protein, bacterial or archaeal flagellin, although these two proteins are not homologous, while in eukaryotes, the flagellum contains hundreds of proteins. Archaeal flagellin and archaeal type IV pilin are homologous, but how archaeal flagellar filaments (AFFs) and archaeal type IV pili (AT4Ps) diverged is not understood, in part, due to the paucity of structures for AFFs and AT4Ps. Despite having similar structures, AFFs supercoil, while AT4Ps do not, and supercoiling is essential for the function of AFFs. We used cryo-electron microscopy to determine the atomic structure of two additional AT4Ps and reanalyzed previous structures. We find that all AFFs have a prominent 10-strand packing, while AT4Ps show a striking structural diversity in their subunit packing. A clear distinction between all AFF and all AT4P structures involves the extension of the N-terminal α-helix with polar residues in the AFFs. Additionally, we characterize a flagellar-like AT4P from Pyrobaculum calidifontis with filament and subunit structure similar to that of AFFs which can be viewed as an evolutionary link, showing how the structural diversity of AT4Ps likely allowed for an AT4P to evolve into a supercoiling AFF.

Structural and functional analyses of Pcal_0917, an α-glucosidase from hyperthermophilic archaeon Pyrobaculum calidifontis

Genome analysis of Pyrobaculum calidifontis revealed the presence of α-glucosidase (Pcal_0917) gene. Structural analysis affirmed the presence of signature sequences of Type II α-glucosidases in Pcal_0917. We have heterologously expressed the gene and produced recombinant Pcal_0917 in Escherichia coli. Biochemical characteristics of the recombinant enzyme resembled to that of Type I α-glucosidases, instead of Type II. Recombinant Pcal_0917 existed in a tetrameric form in solution and displayed highest activity at 95 °C and pH 6.0, independent of any metal ions. A short heat-treatment at 90 °C resulted in a 35 % increase in enzyme activity. A slight structural shift was observed by CD spectrometry at this temperature. Half-life of the enzyme was >7 h at 90 °C. Pcal_0917 exhibited apparent Vmax values of 1190 ± 5 and 3.9 ± 0.1 U/mg against p-nitrophenyl α-D-glucopyranoside and maltose, respectively. To the best of our knowledge, Pcal_0917 displayed the highest ever reported p-nitrophenyl α-D-glucopyranosidase activity among the characterized counterparts. Moreover, Pcal_0917 displayed transglycosylation activity in addition to α-glucosidase activity. Furthermore, in combination with α-amylase, Pcal_0917 was capable of producing glucose syrup from starch with >40 % glucose content. These properties make Pcal_0917 a potential candidate for starch hydrolyzing industry.

Efficient decolorization of melanoidin in raw molasses wastewater by thermophilic esterase in actual extreme conditions

This work was developed to explore the versatility of thermophilic esterase for decolorizing raw molasses wastewater at high temperature and acidic pH. Combining covalent crosslinking method with deep eutectic solvent, a thermophilic esterase from Pyrobaculum calidifontis was immobilized on chitosan/macroporous resin composite carrier. The application of this immobilized thermophilic esterase eliminated 92.35% of colorants in raw molasses wastewater, achieving maximal decolorization efficiency across all the enzymes tested. Strikingly, this immobilized thermophilic esterase was capable of engaging in continuous activity for a 5-day period while removing 76.23% of pigments from samples. It effectively and continuously eliminated BOD5 and COD, effectively and directly facilitating raw molasses wastewater decolorization under extreme conditions more readily than control group. In addition, this thermophilic esterase was believed to achieve decolorization through an addition reaction that disrupted conjugated system of melanoidins. Together, these results highlight an efficient and practical means of achieving enzyme-based molasses wastewater decolorization.

Molecular cloning and production of recombinant Pcal_0672, a family GH57 glycoside hydrolase from Pyrobaculum calidifontis

Molecular cloning and production of recombinant Pcal_0672, a family GH57 glycoside hydrolase from Pyrobaculum calidifontis

Archaeal DNA-import apparatus is homologous to bacterial conjugation machinery

Conjugation is a major mechanism of horizontal gene transfer promoting the spread of antibiotic resistance among human pathogens. It involves establishing a junction between a donor and a recipient cell via an extracellular appendage known as the mating pilus. In bacteria, the conjugation machinery is encoded by plasmids or transposons and typically mediates the transfer of cognate mobile genetic elements. Much less is known about conjugation in archaea. Here, we determine atomic structures by cryo-electron microscopy of three conjugative pili, two from hyperthermophilic archaea (Aeropyrum pernix and Pyrobaculum calidifontis) and one encoded by the Ti plasmid of the bacterium Agrobacterium tumefaciens, and show that the archaeal pili are homologous to bacterial mating pili. However, the archaeal conjugation machinery, known as Ced, has been ‘domesticated’, that is, the genes for the conjugation machinery are encoded on the chromosome rather than on mobile genetic elements, and mediates the transfer of cellular DNA.

Engineering a DNA polymerase from Pyrobaculum calidifontis for improved activity, processivity and extension rate

Positively charged amino acids in the DNA polymerase domain are important for interaction with DNA. Two potential residues in the palm domain of Pca-Pol, a DNA polymerase from Pyrobaculum calidifontis, were identified and mutated to arginine in order to improve the properties of this enzyme. The mutant proteins were heterologously produced in Escherichia coli. Biochemical characterization revealed that there was no significant difference in pH, metal ion, buffer preferences, 3′ − 5′ exonuclease activity and error rate of the wild-type and the mutant enzymes. However, the specific activity, processivity and extension rate of the mutant enzymes increased significantly. Specific activity of one of the mutants (G522R-E555R) was nearly 9-fold higher than that of the wild-type enzyme. These properties make G522R-E555R mutant enzyme a potential candidate for commercial applications.

The evolution of archaeal flagellar filaments

Eukaryotes, archaea, and bacteria each independently evolved flagellar-based motility systems allowing cells to swim in solution. The two prokaryotic flagellar systems involve the motor-driven rotation of supercoiled flagellar filaments, which function as propellers providing the thrust needed to swim. Despite being unrelated to each other, archaeal and bacterial flagellar filaments have convergently evolved to form similar supercoils with pitches around 1 to 2.5 µm and diameters around 0.2 to 0.6 µm. The recent discovery of 11 protofilament states in the supercoiled bacterial flagella and 10 in archaeal flagella [Kreutzberger et al., Cell (2022)] further highlights the analogous mechanism of supercoiling shared by these two structures. It is known that archaeal flagellar filaments are homologous to archaeal type IV pili (T4P), and the N-terminal domains in these archaeal T4P and flagellar filaments are homologous to the N-terminal domains in bacterial T4P. However, the features which distinguish archaeal flagellar filaments from archaeal T4P remained unclear. Here, we report several new structures of archaeal T4Ps and archaeal flagellar filaments and compare these with existing structures. We find that archaeal T4Ps have highly variable symmetries with nearly all of their helical twists varying by about 1-5 degrees and having either 7 or no protofilaments. All archaeal flagellar filament structures have helical twists within ∼0.2 degrees of each other and have 10 protofilaments. Strikingly, one of our new structures from Pyrobaculum calidifontis is of a flagellar-like filament with a pilin-like sequence which has a symmetry most similar to archaeal flagellar filaments assembling into a 10-protofilament structure. This provides the basis for proposing that archaeal flagellar filaments arose from such P.calidifontis-like T4P with symmetries very similar to those of the extant archaeal flagellar filaments, with supercoiled structures arising following the emergence of the filaments with 10 protofilaments.

Domesticated conjugation machinery promotes DNA exchange in hyperthermophilic archaea.

Conjugation, a major mechanism of horizontal gene transfer promoting the spread of antibiotic resistance among human pathogens, involves establishing a junction between a donor and a recipient cell. The mating pilus plays a prominent role in this process. In bacteria, the conjugation machinery is encoded by plasmids or transposons and typically mediates the transfer of cognate mobile genetic elements. Much less has been known about conjugation in archaea, with no homologs of bacterial mating pilins having been identified in sequence searches. Here, using cryo-electron microscopy, we determined high-resolution structures of three conjugative pili, two from hyperthermophilic archaea, Aeropyrum pernix and Pyrobaculum calidifontis, and one encoded by the Ti plasmid of the bacterium Agrobacterium tumefaciens. We show that the archaeal pili are homologous to bacterial mating pili and display intricate pilin-lipid interaction networks. Unlike in bacteria, the conjugation machinery in hyperthermophilic archaea has been domesticated and mediates the transfer of cellular DNA. We suggest that the constitutive expression of the pili may be due to the chronic damage of DNA at high temperatures that is constantly being repaired using homologous recombination.

Functional analyses of a highly thermostable hexokinase from Pyrobaculum calidifontis

The gene encoding a repressor open reading frame sugar kinase (ROK) family protein from hyperthermophilic crenarchaeon Pyrobaculum calidifontis, Pcal-HK, was cloned and expressed in Escherichia coli. The recombinant protein was produced in soluble and highly active form. Purified Pcal-HK was highly thermostable and existed in a monomeric form in solution. The enzyme was specific to ATP as phosphoryl donor but showed broad specificity to phosphoryl acceptors. It catalyzed the phosphorylation of a number of hexoses, including glucose, glucosamine, N-acetyl glucosamine, fructose and mannose, at nearly the same rate and similar affinity. The enzyme was metal ion dependent exhibiting highest activity at 90–95 °C and pH 8.5. Mg2+ was most effective metal ion, which could be partially replaced by Mn2+, Ni2+ or Zn2+. Kinetic parameters were determined at 90 °C and the enzyme showed almost similar catalytic efficiency (kcat/Km) towards the above mentioned hexoses. To the best of our knowledge, Pcal-HK is the most active thermostable ROK family hexokinase characterized to date which catalyzes the phosphorylation of various hexoses with nearly similar affinity.