Astrobiological implications of the organic and inorganic cyanide utilization by a novel Antarctic hyperthermophilic Pyrococcus strain.

Organic and inorganic cyanides are widely distributed in nature, yet not much is known about the ability of microorganisms to use these compounds as a source of nitrogen and/or carbon at high temperatures (>80 °C). Here we studied the capacity of organic and inorganic cyanides to support growth of an hyperthermophilic Pyrococcus strain isolated from Deception Island, Antarctica. This microorganism was capable of growing with aromatic nitriles, aliphatic nitriles, heterocyclic nitriles, amino aromatic nitriles and inorganic cyanides as nitrogen and/or carbon source. This is the first report of an hyperthermophilic microorganism able to incorporate these compounds in its nitrogen and carbon metabolism. Based on enzymatic activity and genomic information, it is possibly that cells of this Pyrococcus strain growing with nitriles or cyanide, might use the carboxylic acid and/or the ammonia generated through the nitrilase enzymatic activity, as a carbon and/or nitrogen source respectively. This work expands the temperature range at which microorganisms can use organic and inorganic cyanides to growth, having important implications to understand microbial metabolisms that can support life on Earth and the possibility to support life elsewhere.

Improving the thermal stability and branching efficiency of Pyrococcus horikoshii OT3 glycogen branching enzyme.

In practical applications, the gelatinisation temperature of starch is high. Most current glycogen branching enzymes (GBEs, EC 2.4.1.18) exhibit optimum activity at moderate or low temperatures and quickly lose their activity at higher temperatures, limiting the application of GBEs in starch modification. Therefore, we used the PROSS strategy combined with PDBePISA analysis of the dimer interface to further improve the heat resistance of hyperthermophilic bacteria Pyrococcus horikoshii OT3 GBE. The results showed that the melting temperature of mutant T508K increased by 3.1 °C compared to wild-type (WT), and the optimum reaction temperature increased by 10 °C for all mutants except V140I. WT almost completely lost its activity after incubation at 95 °C for 60 h, while all of the combined mutants maintained >40 % of their residual activity. Further, the content of the α-1,6 glycosidic bond of corn starch modified by H415W and V140I/H415W was approximately 2.68-fold and 1.92-fold higher than that of unmodified corn starch and corn starch modified by WT, respectively. Additionally, the glucan chains of DP < 13 were significantly increased in mutant modified corn starch. This method has potential for improving the thermal stability of GBE, which can be applied in starch branching in the food industry.

Structural, Thermodynamic and Enzymatic Characterization of N,N-Diacetylchitobiose Deacetylase from Pyrococcus chitonophagus.

Chitin is a major source of energy and macroelements for many organisms. An important step in its degradation is the deacetylation of chitin or its fragments. Deacetylase from the extremophile Pyrococcus chitonophagus has been analyzed by X-ray crystallography, small-angle X-ray scattering, differential scanning calorimetry, isothermal titration calorimetry and NMR to determine its structure, thermodynamics and enzymatic properties. It is a hexameric, zinc-containing metalloenzyme that retains its structural integrity up to temperatures slightly exceeding 100 °C. It removes the acetyl group specifically from the non-reducing end of the sugar substrate. Its main substrate is N,N-diacetylchitobiose but it also active, at a reduced level, toward N-acetyl-d-glucosamine or a trimer of N-acetyl-d-glucosamine units. Crystallographic analysis includes the structure of the enzyme with its main substrate approaching the active site in a monodentate manner, replacing the single water molecule that is bound at the Zn2+ cation when the ligand is absent. The Zn2+ cation remains tetrahedrally coordinated, with three of its ligands provided by the protein's conserved His-Asp-His triad. The crystal structures are consistent with the reaction mechanism proceeding via an anhydride intermediate. Hydrolysis as the first step cannot be ruled out in a hydrated environment but no defined 'hydrolytic water' site can be identified in the analyzed structures.

Modulating the pH profile of the pullulanase from Pyrococcus yayanosii CH1 by synergistically engineering the active center and surface.

A preferable pullulanase with high thermostability and catalytic activity at pH 4.5-5 is desired to match with glucoamylase in the starch-saccharification process. However, most of them exhibit low activity under such low pH conditions. Here, the optimal pH of the hyperthermostable pullulanase from Pyrococcus yayanosii (PulPY2) was successfully shifted from 6.4 to 5 with a 2-fold increase in the specific activity based on synergistic engineering of the active center and surface. Synergistic engineering was performed by introducing histidine within 6 Å of the active sites, and by enhancing negative charges on the enzymatic surface. Two single-site mutants of PulPY2-Q13H and PulPY2-I25E with higher hydrolytic activity were obtained, the optimal pH of which was shifted to pH 5 and 5.4, respectively; the combined mutant PulPY2-Q13H/I25E exhibited the optimal pH of 5, 3.2-fold increasing catalytic efficiency at pH 5, and high thermostability compared to PulPY2. These results not only obtained an applicable pullulanase for industrial application, but also provided a strategy for shifting the optimal pH of the enzyme based on synergistic engineering of the active center and surface.

Biosynthesis of Chuangxinmycin Featuring a Deubiquitinase-like Sulfurtransferase.

The knowledge on sulfur incorporation mechanism involved in sulfur-containing molecule biosynthesis remains limited. Chuangxinmycin is a sulfur-containing antibiotic with a unique thiopyrano[4,3,2-cd]indole (TPI) skeleton and selective inhibitory activity against bacterial tryptophanyl-tRNA synthetase. Despite the previously reported biosynthetic gene clusters and the recent functional characterization of a P450 enzyme responsible for C-S bond formation, the enzymatic mechanism for sulfur incorporation remains unknown. Here, we resolve this central biosynthetic problem by in vitro biochemical characterization of the key enzymes and reconstitute the TPI skeleton in a one-pot enzymatic reaction. We reveal that the JAMM/MPN+ protein Cxm3 functions as a deubiquitinase-like sulfurtransferase to catalyze a non-classical sulfur-transfer reaction by interacting with the ubiquitin-like sulfur carrier protein Cxm4GG. This finding adds a new mechanism for sulfurtransferase in nature.

Structure and Function of Piezophilic Hyperthermophilic Pyrococcus yayanosii pApase.

3'-Phosphoadenosine 5'-monophosphate (pAp) is a byproduct of sulfate assimilation and coenzyme A metabolism. pAp can inhibit the activity of 3'-phosphoadenosine 5'-phosphosulfate (PAPS) reductase and sulfotransferase and regulate gene expression under stress conditions by inhibiting XRN family of exoribonucleases. In metazoans, plants, yeast, and some bacteria, pAp can be converted into 5'-adenosine monophosphate (AMP) and inorganic phosphate by CysQ. In some bacteria and archaea, nanoRNases (Nrn) from the Asp-His-His (DHH) phosphoesterase superfamily are responsible for recycling pAp. In addition, histidinol phosphatase from the amidohydrolase superfamily can hydrolyze pAp. The bacterial enzymes for pAp turnover and their catalysis mechanism have been well studied, but these processes remain unclear in archaea. Pyrococcus yayanosii, an obligate piezophilic hyperthermophilic archaea, encodes a DHH family pApase homolog (PyapApase). Biochemical characterization showed that PyapApase can efficiently convert pAp into AMP and phosphate. The resolved crystal structure of apo-PyapApase is similar to that of bacterial nanoRNaseA (NrnA), but they are slightly different in the α-helix linker connecting the DHH and Asp-His-His associated 1 (DHHA1) domains. The longer α-helix of PyapApase leads to a narrower substrate-binding cleft between the DHH and DHHA1 domains than what is observed in bacterial NrnA. Through mutation analysis of conserved amino acid residues involved in coordinating metal ion and binding substrate pAp, it was confirmed that PyapApase has an ion coordination pattern similar to that of NrnA and slightly different substrate binding patterns. The results provide combined structural and functional insight into the enzymatic turnover of pAp, implying the potential function of sulfate assimilation in hyperthermophilic cells.

When anaerobes encounter oxygen: mechanisms of oxygen toxicity, tolerance and defence.

The defining trait of obligate anaerobes is that oxygen blocks their growth, yet the underlying mechanisms are unclear. A popular hypothesis was that these microorganisms failed to evolve defences to protect themselves from reactive oxygen species (ROS) such as superoxide and hydrogen peroxide, and that this failure is what prevents their expansion to oxic habitats. However, studies reveal that anaerobes actually wield most of the same defences that aerobes possess, and many of them have the capacity to tolerate substantial levels of oxygen. Therefore, to understand the structures and real-world dynamics of microbial communities, investigators have examined how anaerobes such as Bacteroides, Desulfovibrio, Pyrococcus and Clostridium spp. struggle and cope with oxygen. The hypoxic environments in which these organisms dwell - including the mammalian gut, sulfur vents and deep sediments - experience episodic oxygenation. In this Review, we explore the molecular mechanisms by which oxygen impairs anaerobes and the degree to which bacteria protect their metabolic pathways from it. The emergent view of anaerobiosis is that optimal strategies of anaerobic metabolism depend upon radical chemistry and low-potential metal centres. Such catalytic sites are intrinsically vulnerable to direct poisoning by molecular oxygen and ROS. Observations suggest that anaerobes have evolved tactics that either minimize the extent to which oxygen disrupts their metabolism or restore function shortly after the stress has dissipated.

Crystal structure of PYCH_01220 from Pyrococcus yayanosii potentially involved in binding nucleic acid.

We report the crystal structure of PYCH_01220, a hypothetical protein in Pyrococcus yayanosii CH1. This protein is composed of two domains, named Domain A and Domain B. While Domain B is not significantly homologous to known protein structures, Domain A is structurally analogous to the C-terminal ribonuclease domain of Escherichia coli colicin D. Domain A has a positively charged surface patch rendered by 13 basic residues, eight arginine or lysine residues of which are evolutionarily conserved. Electrophoretic mobility shift assays showed that PYCH_01220 binds to DNA, and charge-inversion mutations on this patch negatively affect the DNA binding, suggesting that the function of PYCH_01220 might involve nucleic acid-binding via the positively charged patch.

Novel Intact Polar and Core Lipid Compositions in the Pyrococcus Model Species, P. furiosus and P. yayanosii, Reveal the Largest Lipid Diversity Amongst Thermococcales.

Elucidating the lipidome of Archaea is essential to understand their tolerance to extreme environmental conditions. Previous characterizations of the lipid composition of Pyrococcus species, a model genus of hyperthermophilic archaea belonging to the Thermococcales order, led to conflicting results, which hindered the comprehension of their membrane structure and the putative adaptive role of their lipids. In an effort to clarify the lipid composition data of the Pyrococcus genus, we thoroughly investigated the distribution of both the core lipids (CL) and intact polar lipids (IPL) of the model Pyrococcus furiosus and, for the first time, of Pyrococcus yayanosii, the sole obligate piezophilic hyperthermophilic archaeon known to date. We showed a low diversity of IPL in the lipid extract of P. furiosus, which nonetheless allowed the first report of phosphatidyl inositol-based glycerol mono- and trialkyl glycerol tetraethers. With up to 13 different CL structures identified, the acid methanolysis of Pyrococcus furiosus revealed an unprecedented CL diversity and showed strong discrepancies with the IPL compositions reported here and in previous studies. By contrast, P. yayanosii displayed fewer CL structures but a much wider variety of polar heads. Our results showed severe inconsistencies between IPL and CL relative abundances. Such differences highlight the diversity and complexity of the Pyrococcus plasma membrane composition and demonstrate that a large part of its lipids remains uncharacterized. Reassessing the lipid composition of model archaea should lead to a better understanding of the structural diversity of their lipidome and of their physiological and adaptive functions.

On the Thermal Stability of O6-Methylguanine-DNA Methyltransferase from Archaeon Pyrococcus kodakaraensis by Molecular Dynamics Simulations.

We have employed molecular dynamics simulations to analyze the thermal stability of the O6-methylguanine-DNA methyltransferase (MGMT) protein, both hyperthermophilic archaeon Pyrococcus kodakaraensis (Pk-MGMT) and its mesophilic homologue pair, obtained from enterobacterium Escherichia coli (AdaC). This theoretical study was done at three different temperatures: 302, 371, and 450 K. The molecular dynamics has been performed in explicit aqueous solvent during a period of time of 95 ns, including periodic boundary conditions and constant pressure. The same procedure has been used for both proteins, and each simulation has been carried out by triplicate. Hence, we performed 18 simulations. In this way, we have done different analyses to explore the factors that may affect the thermal stability of Pk-MGMT. The structural behavior was analyzed using indicators such as root-mean-square deviation, radius of gyration, solvent-accessible surface area, hydrogen bonds, native contacts, secondary structure, and salt bridge formation. The results showed that when the temperature increases, the global atomic fluctuations increase too, which suggests that both proteins lose thermal stability, but as expected, this fact is highlighted in AdaC. Moreover, the contacts of the native state in AdaC are considerably lower than those found in Pk-MGMT at 450 K. Also, the structural studies showed that conserved and nonconserved salt bridges kept close contacts with the Pk-MGMT protein at high temperatures. These interaction types act as molecular staples and are mainly responsible to provide thermostability to the hyperthermophilic protein.

Simultaneously Improved Thermostability and Hydrolytic Pattern of Alpha-Amylase by Engineering Central Beta Strands of TIM Barrel.

This study reported simultaneously improved thermostability and hydrolytic pattern of α-amylase from Bacillus subtilis CN7 by rationally engineering the mostly conserved central beta strands in TIM barrel fold. Nine single point mutations and a double mutation were introduced at the 2nd site of the ß7 strand and 3rd site of the ß5 strand to rationalize the weak interactions in the beta strands of the TIM barrel of α-amylase. All the five active mutants changed the compositions and percentages of maltooligosaccharides in final hydrolytic products compared to the product spectrum of the wild-type. A mutant Y204V produced only maltose, maltotriose, and maltopentaose without any glucose and maltotetraose, indicating a conversion from typical endo-amylase to novel maltooligosaccharide-producing amylase. A mutant V260I enhanced the thermal stability by 7.1 °C. To our best knowledge, this is the first report on the simultaneous improvement of thermostability and hydrolytic pattern of α-amylase by engineering central beta strands of TIM barrel and the novel "beta strands" strategy proposed here may be useful for the protein engineering of other TIM barrel proteins.

Enzymatic Synthesis of 2-(ß-Galactosyl)-ethyl Methacrylate by ß-Galactosidase from Pyrococcus woesei and Application for Glycopolymer Synthesis and Lectin Studies.

Glycosidases have long been used for the synthesis of glycosides by transglycosylation reactions. Especially glycosidases from hyperthermophilic bacteria are useful for reactions under extreme reaction conditions, e.g., in the presence of organic solvents. We herein report the facile enzymatic synthesis and purification of 2-(ß-galactosyl)-ethyl methacrylate (Gal-EMA) with the recombinant hyperthermostable glycosidase from Pyrococcus woesei in high yields. Optimized reaction conditions resulted in gram-scale synthesis of the galactosylated monomer with 88% transglycosylation yield. The product Gal-EMA was characterized by high-performance liquid chromatography-electrospray ionization-mass spectrometry (HPLC-ESI-MS), nuclear magnetic resonance (NMR) spectroscopy, and infrared (IR) spectroscopy. Gal-EMA was utilized to synthesize sugar-functionalized acrylate polymers with defined amounts of incorporated galactose (0-100%). Analysis of the binding affinity of the lectin RCA120 from Ricinus communis to the glycopolymers using an enzyme-linked lectin assay (ELLA) revealed KD values between 0.24 and 6.2 nM, depending on the amount of incorporated Gal-EMA. The potential of Gal-EMA for the synthesis of acrylate-functionalized glycan oligomers was demonstrated by sequential elongation of the terminal galactose by two glycosyltransferases, resulting in the terminal glycan N-acetyllactosamine (LacNAc) epitope. In conclusion, the enzymatic synthesis of Gal-EMA opens new routes to a series of novel monomeric building blocks for the synthesis of glycan-functionalized polyacrylates.

[Comparison of pretreatment methods in lipid analysis and ultra-performance liquid chromatography-mass spectrometry analysis of archaea].

Archaea are single-cell microorganisms, structurally and biochemically similar to bacteria and fungi. Most of them live in extreme environments, such as high salt, extremely acidic, extremely hot, and anaerobicenvironments. The membrane structure and related metabolic pathways of archaea are different from those of other microorganisms. Therefore, studying the lipid metabolism of archaea is of great significance for exploring the life activities in extreme environments. As the first step in lipidomic analysis, lipid extraction and pretreatment methods play an important role, as they influence the accuracy and reliability of the final results. We harnessed ultra-performance liquid chromatography coupled with high-resolution mass spectrometry (UPLC-HRMS) to detect the total normal lipids. The hyperthermophilic archaeon Pyrococcus yayanosii was selected as the model. The Bligh-Dyer acidic method, Folch method, methyl tert-butyl ether (MTBE) method, and solid-phase extraction (SPE) method were compared by multi-component analysis in terms of extraction efficiency, reproducibility, and extraction discrimination. Comprehensive analysis revealed that the SPE and MTBE methods showed the best extraction repeatability and extraction efficiency, and were suitable for high-throughput microbial lipid extraction. Finally, normal lipid components of P. yayanosii were comprehensively analyzed by SPE coupled with UPLC-HRMS. A total of 1402 lipid components were identified. This article aims to provide a reference for non-targeted lipidomic analysis of archaea and other microorganisms towards understanding their lipid metabolism.

A Hyperthermostable Type II Pullulanase from a Deep-Sea Microorganism Pyrococcus yayanosii CH1.

Pullulanase is a commonly used debranching enzyme in the starch processing industry. Because the starch liquefaction process requires high temperature, a thermostable pullulanase is desired. Here, a novel hyperthermostable type II pullulanase gene (pulPY) was cloned from Pyrococcus yayanosii CH1, isolated from a deep-sea hydrothermal site. PulPY was optimally active at pH 6.6 and 95 °C, retaining more than 50% activity after incubation at 95 °C for 10 h. The thermostability was significantly higher than those of most pullulanases reported previously. To further improve its activity and thermostability, the N-terminal and C-terminal domains of PulPY were truncated. The optimum temperature of the combined truncation mutant Δ28N + Δ791C increased to 100 °C with a specific activity of 32.18 U/mg, which was six times higher than that of wild-type PulPY. PulPY and the truncation mutant enzyme could realize the combined use of pullulanase with α-amylase during the starch liquefaction process to improve hydrolysis efficiency.

Beyond the Second Coordination Sphere: Engineering Dirhodium Artificial Metalloenzymes To Enable Protein Control of Transition Metal Catalysis.

Transition metal catalysis is a powerful tool for chemical synthesis, a standard by which understanding of elementary chemical processes can be measured, and a source of awe for those who simply appreciate the difficulty of cleaving and forming chemical bonds. Each of these statements is amplified in cases where the transition metal catalyst controls the selectivity of a chemical reaction. Enantioselective catalysis is a challenging but well-established phenomenon, and regio- or site-selective catalysis is increasingly common. On the other hand, transition-metal-catalyzed reactions are typically conducted under highly optimized conditions. Rigorous exclusion of air and water is common, and it is taken for granted that only a single substrate (of a particular class) will be present in a reaction, a desired site selectivity can be achieved by installing a directing group, and undesired reactivity can be blocked with protecting groups. These are all reasonable synthetic strategies, but they also highlight limits to catalyst control. The utility of transition metal catalysis could be greatly expanded if catalysts possessed the ability to regulate which molecules they encounter and the relative orientation of those molecules. The rapid and widespread adoption of stoichiometric bioorthogonal reactions illustrates the utility of robust reactions that proceed with high selectivity and specificity under mild reaction conditions. Expanding this capability beyond preprogrammed substrate pairs via catalyst control could therefore have an enormous impact on molecular science. Many metalloenzymes exhibit this level of catalyst control, and directed evolution can be used to rapidly improve the catalytic properties of these systems. On the other hand, the range of reactions catalyzed by enzymes is limited relative to that developed by chemists. The possibility of imparting enzyme-like activity, selectivity, and evolvability to reactions catalyzed by synthetic transition metal complexes has inspired the creation of artificial metalloenzymes (ArMs). The increasing levels of catalyst control exhibited by ArMs developed to date suggest that these systems could constitute a powerful platform for bioorthogonal transition metal catalysis and for selective catalysis in general. This Account outlines the development of a new class of ArMs based on a prolyl oligopeptidase (POP) scaffold. Studies conducted on POP ArMs containing a covalently linked dirhodium cofactor have shown that POP can impart enantioselectivity to a range of dirhodium-catalyzed reactions, increase reaction rates, and improve the specificity for reaction of dirhodium carbene intermediates with targeted organic substrates over components of cell lysate, including bulk water. Several design features of these ArMs enabled their evolution via random mutagenesis, which revealed that mutations throughout the POP scaffold, beyond the second sphere of the dirhodium cofactor, were important for ArM activity and selectivity. While it was anticipated that the POP scaffold would be capable of encapsulating and thus controlling the selectivity of bulky cofactors, molecular dynamics studies also suggest that POP conformational dynamics plays a role in its unique efficacy. These advances in scaffold selection, bioconjugation, and evolution form the basis of our ongoing efforts to control transition metal reactivity using protein scaffolds with the goal of enabling unique synthetic capabilities, including bioorthogonal catalysis.

Induction of a Toxin-Antitoxin Gene Cassette under High Hydrostatic Pressure Enables Markerless Gene Disruption in the Hyperthermophilic Archaeon Pyrococcus yayanosii.

The discovery of hyperthermophiles has dramatically changed our understanding of the habitats in which life can thrive. However, the extreme high temperatures in which these organisms live have severely restricted the development of genetic tools. The archaeon Pyrococcus yayanosii A1 is a strictly anaerobic and piezophilic hyperthermophile that is an ideal model for studies of extreme environmental adaptation. In the present study, we identified a high hydrostatic pressure (HHP)-inducible promoter (P hhp ) that controls target gene expression under HHP. We developed an HHP-inducible toxin-antitoxin cassette (HHP-TAC) containing (i) a counterselectable marker in which a gene encoding a putative toxin (virulence-associated protein C [PF0776 {VapC}]) controlled by the HHP-inducible promoter was used in conjunction with the gene encoding antitoxin PF0775 (VapB), which was fused to a constitutive promoter (P hmtB ), and (ii) a positive marker with the 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase-encoding gene from P. furiosus controlled by the constitutive promoter P gdh The HHP-TAC was constructed to realize markerless gene disruption directly in P. yayanosii A1 in rich medium. The pop-out recombination step was performed using an HHP-inducible method. As proof, the PYCH_13690 gene, which encodes a 4-α-glucanotransferase, was successfully deleted from the strain P. yayanosii A1. The results showed that the capacity for starch hydrolysis in the Δ1369 mutant decreased dramatically compared to that in the wild-type strain. The inducible toxin-antitoxin system developed in this study greatly increases the genetic tools available for use in hyperthermophiles.IMPORTANCE Genetic manipulations in hyperthermophiles have been studied for over 20 years. However, the extremely high temperatures under which these organisms grow have limited the development of genetic tools. In this study, an HHP-inducible promoter was used to control the expression of a toxin. Compared to sugar-inducible and cold-shock-inducible promoters, the HHP-inducible promoter rarely has negative effects on the overall physiology and central metabolism of microorganisms, especially piezophilic hyperthermophiles. Previous studies have used auxotrophic strains as hosts, which may interfere with studies of adaptation and metabolism. Using an inducible toxin-antitoxin (TA) system as a counterselectable marker enables the generation of a markerless gene disruption strain without the use of auxotrophic mutants and counterselection with 5-fluoroorotic acid. TA systems are widely distributed in bacteria and archaea and can be used to overcome the limitations of high growth temperatures and dramatically extend the selectivity of genetic tools in hyperthermophiles.

Simultaneous cell disruption and semi-quantitative activity assays for high-throughput screening of thermostable L-asparaginases.

L-asparaginase, which catalyses the hydrolysis of L-asparagine to L-aspartate, has attracted the attention of researchers due to its expanded applications in medicine and the food industry. In this study, a novel thermostable L-asparaginase from Pyrococcus yayanosii CH1 was cloned and over-expressed in Bacillus subtilis 168. To obtain thermostable L-asparaginase mutants with higher activity, a robust high-throughput screening process was developed specifically for thermophilic enzymes. In this process, cell disruption and enzyme activity assays are simultaneously performed in 96-deep well plates. By combining error-prone PCR and screening, six brilliant positive variants and four key amino acid residue mutations were identified. Combined mutation of the four residues showed relatively high specific activity (3108 U/mg) that was 2.1 times greater than that of the wild-type enzyme. Fermentation with the mutant strain in a 5-L fermenter yielded L-asparaginase activity of 2168 U/mL.

Crystal structures of an archaeal chitinase ChiD and its ligand complexes.

Chitinase D (designated as Pc-ChiD) was found in a hyperthermophilic archaeon, Pyrococcus chitonophagus (previously described as Thermococcus chitonophagus), that was isolated from media containing only chitin as carbon source. Pc-ChiD displays chitinase activity and is thermostable at temperatures up to 95°C, suggesting its potential for industrial use. Pc-ChiD has a secretion signal peptide and two chitin-binding domains (ChBDs) in the N-terminal domain. However, the C-terminal domain shares no sequence similarity with previously identified saccharide-degrading enzymes and does not contain the DXDXE motif conserved in the glycoside hydrolase (GH) 18 family chitinases. To elucidate its overall structure and reaction mechanism, we determined the first crystal structures of Pc-ChiD, both in the ligand-free form and in complexes with substrates. Structure analyses revealed that the C-terminal domain of Pc-ChiD, Pc-ChiD(ΔBD), consists of a third putative substrate-binding domain, which cannot be predicted from the amino acid sequence, and a catalytic domain structurally similar to that found in not the GH18 family but the GH23 family. Based on the similarity with GH23 family chitinase, the catalytic residues of Pc-ChiD were predicted and confirmed by mutagenesis analyses. Moreover, the specific C-terminal 100 residues of Pc-ChiD are important to fix the putative substrate-binding domain next to the catalytic domain, contributing to the structure stability as well as the long chitin chain binding. Our findings reveal the structure of a unique archaeal chitinase that is distinct from previously known members of the GH23 family.

Identification of a functional toxin-antitoxin system located in the genomic island PYG1 of piezophilic hyperthermophilic archaeon Pyrococcus yayanosii.

Toxin-antitoxin (TA) system is bacterial or archaeal genetic module consisting of toxin and antitoxin gene that be organized as a bicistronic operon. TA system could elicit programmed cell death, which is supposed to play important roles for the survival of prokaryotic population under various physiological stress conditions. The phage abortive infection system (AbiE family) belongs to bacterial type IV TA system. However, no archaeal AbiE family TA system has been reported so far. In this study, a putative AbiE TA system (PygAT), which is located in a genomic island PYG1 in the chromosome of Pyrococcus yayanosii CH1, was identified and characterized. In Escherichia coli, overexpression of the toxin gene pygT inhibited its growth while the toxic effect can be suppressed by introducing the antitoxin gene pygA in the same cell. PygAT also enhances the stability of shuttle plasmids with archaeal plasmid replication protein Rep75 in E. coli. In P. yayanosii, disruption of antitoxin gene pygA cause a significantly growth delayed under high hydrostatic pressure (HHP). The antitoxin protein PygA can specifically bind to the PygAT promoter region and regulate the transcription of pygT gene in vivo. These results show that PygAT is a functional TA system in P. yayanosii, and also may play a role in the adaptation to HHP environment.

Heterologous expression of an engineered protein domain acts as chaperone and enhances thermotolerance of Escherichia coli.

Heat shock proteins (HSPs) are known to confer protection to the stressed cells by rescuing vital host cell proteins. In the present study we have demonstrated that heterologous expression of N-terminal domain of hyperthermophilic L-asparaginase (NPfA) confers thermotolerance to E. coli. The recombinant expression of NPfA enabled E. coli to demonstrate typical growth behavior at 52°C and survive a thermal shock up to 62°C, both being the highest reported temperatures for growth and heat shock survival. To understand the basis of protection proteome analysis of these cells was carried out which showed that NPfA guards a battery of proteins, especially related to gene regulations and repair, providing definite survival advantage to the stressed cells. Thus NPfA a non-canonical, non-natural chaperone has been shown to render E. coli cells with selective growth advantage under extremes of conditions. We propose that such modified, heat stabilized hosts could be utilized in developing heat-induced expression systems as well for the recombinant expression of thermophilic proteins.