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1.
World J Microbiol Biotechnol ; 40(10): 324, 2024 Sep 19.
Artículo en Inglés | MEDLINE | ID: mdl-39294482

RESUMEN

High fidelity DNA polymerase from Pyrococcus furiosus (Pfupol) is an attractive alternative to the highly popular DNA polymerase from Thermus aquaticus. Because this enzyme is in great demand for biotechnological applications, optimizing Pfupol production is essential to supplying the industry's expanding demand. T7-induced promoter expression in Escherichia coli expression systems is used to express recombinant Pfupol; however, this method is not cost-effective. Here, we have effectively developed an optimized process for the autoinduction approach of Pfupol expression in a defined medium. To better examine Pfupol's activities, its purified fraction was used. A 71 mg/L of pure Pfupol was effectively produced, resulting in a 2.6-fold increase in protein yield when glucose, glycerol, and lactose were added in a defined medium at concentrations of 0.05%, 1%, and 0.6%, respectively, and the condition for production in a 5 L bioreactor was as follow: 200 rpm, 3 vvm, and 10% inoculant. Furthermore, the protein exhibited 1445 U/mg of specific activity when synthesized in its active state. This work presents a high level of Pfupol production, which makes it an economically viable and practically useful approach.


Asunto(s)
Reactores Biológicos , Medios de Cultivo , ADN Polimerasa Dirigida por ADN , Escherichia coli , Pyrococcus furiosus , Proteínas Recombinantes , Pyrococcus furiosus/genética , Pyrococcus furiosus/enzimología , Escherichia coli/genética , Escherichia coli/metabolismo , Reactores Biológicos/microbiología , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , ADN Polimerasa Dirigida por ADN/metabolismo , ADN Polimerasa Dirigida por ADN/genética , Medios de Cultivo/química , Glucosa/metabolismo , Regiones Promotoras Genéticas , Glicerol/metabolismo , Lactosa/metabolismo
2.
Biosens Bioelectron ; 265: 116692, 2024 Dec 01.
Artículo en Inglés | MEDLINE | ID: mdl-39208510

RESUMEN

Foodborne hazardous factors pose a significant risk to public health, emphasizing the need for the development of sensitive and user-friendly detection strategies to effectively manage and control these risks in the food supply chain. Pyrococcus furiosus argonaute (PfAgo)-based biosensing approaches have been extensively explored due to its built-in signal amplification. However, the property that PfAgo is a DNA-guided DNA endonuclease has enabled almost all the existing PfAgo-based reports to be used for the detection of nucleic acids. To lend PfAgo toolbox to extended non-nucleic acid detection, we systematically investigated the mechanism characteristic of PfAgo' preference for guide DNA (gDNA) and proposed a gDNA dephosphorylation-modulated PfAgo sensor for the detection of non-nucleic acid targets. Our results indicated that PfAgo exhibits preference for 5'-phosphorylated gDNA at a specific ratio of PfAgo to gDNA concentration. Leveraging this PfAgo' preference and the dephosphorylation activity of alkaline phosphatase (ALP), ALP could be detected as low as 2.7 U/L. Furthermore, the PfAgo was coupled with immunolabelled ALP to develop a PfAgo-based fluorescence immunosensor, which achieves aflatoxins B1 detection with a detection limit of 29.89 pg/mL and exhibits satisfactory recoveries in wheat and maize samples. The developed method broadens the application scope of PfAgo toolbox, and provides a simple, sensitive, and universal detection platform for a variety targets.


Asunto(s)
Aflatoxina B1 , Fosfatasa Alcalina , Técnicas Biosensibles , Pyrococcus furiosus , Técnicas Biosensibles/métodos , Pyrococcus furiosus/enzimología , Aflatoxina B1/análisis , Fosfatasa Alcalina/metabolismo , Fosfatasa Alcalina/química , Proteínas Argonautas/metabolismo , Límite de Detección , ADN/química , Fosforilación , Fluorescencia , Contaminación de Alimentos/análisis
3.
Int J Mol Sci ; 25(16)2024 Aug 15.
Artículo en Inglés | MEDLINE | ID: mdl-39201583

RESUMEN

Hyperthermophilic archaea such as Pyrococcus furiosus survive under very aggressive environmental conditions by occupying niches inaccessible to representatives of other domains of life. The ability to survive such severe living conditions must be ensured by extraordinarily efficient mechanisms of DNA processing, including repair. Therefore, in this study, we compared kinetics of conformational changes of DNA Endonuclease Q from P. furiosus during its interaction with various DNA substrates containing an analog of an apurinic/apyrimidinic site (F-site), hypoxanthine, uracil, 5,6-dihydrouracil, the α-anomer of adenosine, or 1,N6-ethenoadenosine. Our examination of DNA cleavage activity and fluorescence time courses characterizing conformational changes of the dye-labeled DNA substrates during the interaction with EndoQ revealed that the enzyme induces multiple conformational changes of DNA in the course of binding. Moreover, the obtained data suggested that the formation of the enzyme-substrate complex can proceed through dissimilar kinetic pathways, resulting in different types of DNA conformational changes, which probably allow the enzyme to perform its biological function at an extreme temperature.


Asunto(s)
División del ADN , Pyrococcus furiosus , Pyrococcus furiosus/enzimología , Cinética , Proteínas Arqueales/metabolismo , Proteínas Arqueales/química , Especificidad por Sustrato , Conformación de Ácido Nucleico , ADN/metabolismo
4.
Mikrochim Acta ; 191(7): 439, 2024 07 02.
Artículo en Inglés | MEDLINE | ID: mdl-38954110

RESUMEN

A Pyrococcus furiosus Argonaute (PfAgo)-based biosensor is presented for alkaline phosphatase (ALP) activity detection in which the ALP-catalyzed hydrolysis of 3'-phosphate-modified functional DNA activates the strand displacement amplification, and the amplicon mediates the fluorescent reporter cleavage as a guide sequence of PfAgo. Under the dual amplification mode of PfAgo-catalyzed multiple-turnover cleavage activity and pre-amplification technology, the developed method was successfully applied to ALP activity determination with a detection limit (LOD) of 0.0013 U L-1 (3σ) and a detection range of 0.0025 to 1 U L-1 within 90 min. The PfAgo-based method exhibits satisfactory analytic performance in the presence of potential interferents and in complex human serum samples. The proposed method shows several advantages, such as rapid analysis, high sensitivity, low-cost, and easy operation, and has great potential in disease evolution fundamental studies and clinical diagnosis applications.


Asunto(s)
Fosfatasa Alcalina , Técnicas Biosensibles , Límite de Detección , Pyrococcus furiosus , Técnicas Biosensibles/métodos , Fosfatasa Alcalina/sangre , Fosfatasa Alcalina/química , Fosfatasa Alcalina/metabolismo , Humanos , Pyrococcus furiosus/enzimología , Proteínas Argonautas/metabolismo , Técnicas de Amplificación de Ácido Nucleico/métodos , Pruebas de Enzimas/métodos
5.
J Am Chem Soc ; 146(26): 18019-18031, 2024 Jul 03.
Artículo en Inglés | MEDLINE | ID: mdl-38888987

RESUMEN

The membrane-bound hydrogenase (Mbh) from Pyrococcus furiosus is an archaeal member of the Complex I superfamily. It catalyzes the reduction of protons to H2 gas powered by a [NiFe] active site and transduces the free energy into proton pumping and Na+/H+ exchange across the membrane. Despite recent structural advances, the mechanistic principles of H2 catalysis and ion transport in Mbh remain elusive. Here, we probe how the redox chemistry drives the reduction of the proton to H2 and how the catalysis couples to conformational dynamics in the membrane domain of Mbh. By combining large-scale quantum chemical density functional theory (DFT) and correlated ab initio wave function methods with atomistic molecular dynamics simulations, we show that the proton transfer reactions required for the catalysis are gated by electric field effects that direct the protons by water-mediated reactions from Glu21L toward the [NiFe] site, or alternatively along the nearby His75L pathway that also becomes energetically feasible in certain reaction steps. These local proton-coupled electron transfer (PCET) reactions induce conformational changes around the active site that provide a key coupling element via conserved loop structures to the ion transport activity. We find that H2 forms in a heterolytic proton reduction step, with spin crossovers tuning the energetics along key reaction steps. On a general level, our work showcases the role of electric fields in enzyme catalysis and how these effects are employed by the [NiFe] active site of Mbh to drive PCET reactions and ion transport.


Asunto(s)
Hidrógeno , Hidrogenasas , Simulación de Dinámica Molecular , Pyrococcus furiosus , Hidrogenasas/química , Hidrogenasas/metabolismo , Hidrógeno/química , Hidrógeno/metabolismo , Pyrococcus furiosus/enzimología , Protones , Teoría Funcional de la Densidad , Dominio Catalítico , Oxidación-Reducción
6.
Gene ; 922: 148544, 2024 Sep 05.
Artículo en Inglés | MEDLINE | ID: mdl-38734187

RESUMEN

This study introduces an efficient RPA-PfAgo detection system for the MTHFR C677T polymorphism, proposing a potential strategy to simplify the genotyping process. By optimizing recombinase polymerase amplification (RPA) with Pyrococcus furiosus Argonaute (PfAgo) nucleases, we achieved DNA amplification at a constant temperature. The assay was fine-tuned through meticulous primer and guide DNA selection, with optimal conditions established at 2.0 µL of MgAc, a reaction temperature of 42 °C, and a 10-minute reaction time for RPA. Further optimization of the PfAgo cleavage assay revealed the ideal concentrations of MnCl2, guide DNA, molecular beacon probes, the PfAgo enzyme, and the RPA product to maximize sensitivity and specificity. Clinical validation of 20 samples showed 100% concordance with Sanger sequencing, confirming the method's precision. The RPA-PfAgo system is a promising tool for on-site genotyping, with broad applications in personalized medicine and disease prevention.


Asunto(s)
Técnicas de Genotipaje , Metilenotetrahidrofolato Reductasa (NADPH2) , Humanos , Metilenotetrahidrofolato Reductasa (NADPH2)/genética , Técnicas de Genotipaje/métodos , Polimorfismo de Nucleótido Simple , Pyrococcus furiosus/genética , Pyrococcus furiosus/enzimología , Genotipo , Técnicas de Amplificación de Ácido Nucleico/métodos , Proteínas Argonautas/genética , Recombinasas/metabolismo , Recombinasas/genética
7.
Nucleic Acids Res ; 52(10): 6017-6035, 2024 Jun 10.
Artículo en Inglés | MEDLINE | ID: mdl-38709902

RESUMEN

Archaeal transcription is carried out by a multi-subunit RNA polymerase (RNAP) that is highly homologous in structure and function to eukaryotic RNAP II. Among the set of basal transcription factors, only Spt5 is found in all domains of life, but Spt5 has been shaped during evolution, which is also reflected in the heterodimerization of Spt5 with Spt4 in Archaea and Eukaryotes. To unravel the mechanistic basis of Spt4/5 function in Archaea, we performed structure-function analyses using the archaeal transcriptional machinery of Pyrococcus furiosus (Pfu). We report single-particle cryo-electron microscopy reconstructions of apo RNAP and the archaeal elongation complex (EC) in the absence and presence of Spt4/5. Surprisingly, Pfu Spt4/5 also binds the RNAP in the absence of nucleic acids in a distinct super-contracted conformation. We show that the RNAP clamp/stalk module exhibits conformational flexibility in the apo state of RNAP and that the enzyme contracts upon EC formation or Spt4/5 engagement. We furthermore identified a contact of the Spt5-NGN domain with the DNA duplex that stabilizes the upstream boundary of the transcription bubble and impacts Spt4/5 activity in vitro. This study, therefore, provides the structural basis for Spt4/5 function in archaeal transcription and reveals a potential role beyond the well-described support of elongation.


Asunto(s)
Proteínas Arqueales , ARN Polimerasas Dirigidas por ADN , Modelos Moleculares , Elongación de la Transcripción Genética , Factores de Elongación Transcripcional , Proteínas Arqueales/química , Proteínas Arqueales/metabolismo , Proteínas Arqueales/genética , Proteínas Cromosómicas no Histona/química , Proteínas Cromosómicas no Histona/genética , Proteínas Cromosómicas no Histona/metabolismo , Microscopía por Crioelectrón , ARN Polimerasas Dirigidas por ADN/metabolismo , ARN Polimerasas Dirigidas por ADN/química , ARN Polimerasas Dirigidas por ADN/genética , Unión Proteica , Pyrococcus furiosus/enzimología , Pyrococcus furiosus/genética , Factores de Elongación Transcripcional/metabolismo , Factores de Elongación Transcripcional/química , Factores de Elongación Transcripcional/genética
8.
Biotechnol Bioeng ; 121(7): 2079-2090, 2024 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-38682557

RESUMEN

Hyperthermophilic enzymes serve as an important source of industrial enzymes due to their high thermostability. Unfortunately, most hyperthermophilic enzymes suffer from reduced activity at low temperatures (e.g., ambient temperature), limiting their applicability. In addition, evolving hyperthermophilic enzymes to increase low temperature activity without compromising other desired properties is generally difficult. In the current study, a variant of ß-glucosidase from Pyrococcus furiosus (PfBGL) was engineered to enhance enzyme activity at low temperatures through the construction of a saturation mutagenesis library guided by the HotSpot Wizard analysis, followed by its screening for activity and thermostability. From this library construction and screening, one PfBGL mutant, PfBGL-A4 containing Q214S/A264S/F344I mutations, showed an over twofold increase in ß-glucosidase activity at 25 and 50°C compared to the wild type, without compromising high-temperature activity, thermostability and substrate specificity. Our experimental and computational characterizations suggest that the findings with PfBGL-A4 may be due to the elevation of local conformational flexibility around the active site, while slightly compacting the global protein structure. This study showcases the potential of HotSpot Wizard-informed engineering of hyperthermophilic enzymes and underscores the interplays among temperature, enzyme activity, and conformational flexibility in these enzymes.


Asunto(s)
Estabilidad de Enzimas , Ingeniería de Proteínas , Pyrococcus furiosus , beta-Glucosidasa , Pyrococcus furiosus/enzimología , Pyrococcus furiosus/genética , beta-Glucosidasa/genética , beta-Glucosidasa/química , beta-Glucosidasa/metabolismo , Ingeniería de Proteínas/métodos , Frío
9.
J Biochem ; 175(6): 671-676, 2024 May 31.
Artículo en Inglés | MEDLINE | ID: mdl-38302756

RESUMEN

Crystal structure of a ribonuclease for ribosomal RNA processing, FAU-1, from Pyrococcus furiosus was determined with the resolution of 2.57 Å in a homo-trimeric form. The monomer structure consists of two domains: N-terminal and C-terminal domains. C-terminal domain forms trimer and each N-terminal domain locates outside of the trimer core. In the obtained crystal, a dinucleotide, pApUp, was bound to the N-terminal domain, indicating that N-terminal domain has the RNA-binding ability. The affinities to RNA of FAU-1 and a fragment corresponding to the N-terminal domain, FAU-ΔC, were confirmed by polyacrylamide gel electrophoresis and nuclear magnetic resonance (NMR). Interestingly, well-dispersed NMR signals were observed at 318K, indicating that the FAU-ΔC-F18 complex form an ordered structure at higher temperature. As predicted in our previous works, FAU-1 and ribonuclease (RNase) E show a structural similarity in their RNA-binding regions. However, structural similarity between RNase E and FAU-1 could be found in the limited regions of the N-terminal domain. On the other hand, structural similarity between C-terminal domain and some proteins including a phosphatase was found. Thus, it is possible that the catalytic site is located in C-terminal domain.


Asunto(s)
Pyrococcus furiosus , Pyrococcus furiosus/enzimología , ARN Ribosómico/metabolismo , ARN Ribosómico/química , Modelos Moleculares , Cristalografía por Rayos X , Ribonucleasas/metabolismo , Ribonucleasas/química , Proteínas Arqueales/química , Proteínas Arqueales/metabolismo , Conformación Proteica , Multimerización de Proteína
10.
J Biol Chem ; 299(12): 105403, 2023 12.
Artículo en Inglés | MEDLINE | ID: mdl-38229399

RESUMEN

We have investigated the kinetics of NAD+-dependent NADPH:ferredoxin oxidoreductase (NfnI), a bifurcating transhydrogenase that takes two electron pairs from NADPH to reduce two ferredoxins and one NAD+ through successive bifurcation events. NADPH reduction takes place at the bifurcating FAD of NfnI's large subunit, with high-potential electrons transferred to the [2Fe-2S] cluster and S-FADH of the small subunit, ultimately on to NAD+; low-potential electrons are transferred to two [4Fe-4S] clusters of the large subunit and on to ferredoxin. Reduction of NfnI by NADPH goes to completion only at higher pH, with a limiting kred of 36 ± 1.6 s-1 and apparent KdNADPH of 5 ± 1.2 µM. Reduction of one of the [4Fe-4S] clusters of NfnI occurs within a second, indicating that in the absence of NAD+, the system can bifurcate and generate low-potential electrons without NAD+. When enzyme is reduced by NADPH in the absence of NAD+ but the presence of ferredoxin, up to three equivalents of ferredoxin become reduced, although the reaction is considerably slower than seen during steady-state turnover. Bifurcation appears to be limited by transfer of the first, high-potential electron into the high-potential pathway. Ferredoxin reduction without NAD+ demonstrates that electron bifurcation is an intrinsic property of the bifurcating FAD and is not dependent on the simultaneous presence of NAD+ and ferredoxin. The tight coupling between NAD+ and ferredoxin reduction observed under multiple-turnover conditions is instead simply due to the need to remove reducing equivalents from the high-potential electron pathway under multiple-turnover conditions.


Asunto(s)
Proteínas Arqueales , Ferredoxinas , Oxidorreductasas , Pyrococcus furiosus , Ferredoxinas/metabolismo , Cinética , NAD/metabolismo , NADP/metabolismo , Oxidación-Reducción , Oxidorreductasas/metabolismo , Pyrococcus furiosus/enzimología , Proteínas Arqueales/metabolismo
11.
Nucleic Acids Res ; 50(13): 7560-7569, 2022 07 22.
Artículo en Inglés | MEDLINE | ID: mdl-35819229

RESUMEN

5'-Adenylated oligonucleotides (AppOligos) are widely used for single-stranded DNA/RNA ligation in next-generation sequencing (NGS) applications such as microRNA (miRNA) profiling. The ligation between an AppOligo adapter and target molecules (such as miRNA) no longer requires ATP, thereby minimizing potential self-ligations and simplifying library preparation procedures. AppOligos can be produced by chemical synthesis or enzymatic modification. However, adenylation via chemical synthesis is inefficient and expensive, while enzymatic modification requires pre-phosphorylated substrate and additional purification. Here we cloned and characterized the Pfu RNA ligase encoded by the PF0353 gene in the hyperthermophilic archaea Pyrococcus furiosus. We further engineered fusion enzymes containing both Pfu RNA ligase and T4 polynucleotide kinase. One fusion enzyme, 8H-AP, was thermostable and can directly catalyze 5'-OH-terminated DNA substrates to adenylated products. The newly discovered Pfu RNA ligase and the engineered fusion enzyme may be useful tools for applications using AppOligos.


Asunto(s)
Adenosina Monofosfato/química , Técnicas Genéticas , MicroARNs , Oligonucleótidos/química , Polinucleótido 5'-Hidroxil-Quinasa , ADN/química , ADN Ligasas/metabolismo , ADN de Cadena Simple , Polinucleótido 5'-Hidroxil-Quinasa/genética , Pyrococcus furiosus/enzimología , ARN Ligasa (ATP)/metabolismo
12.
J Am Chem Soc ; 143(49): 20873-20883, 2021 12 15.
Artículo en Inglés | MEDLINE | ID: mdl-34846879

RESUMEN

The membrane-bound hydrogenase (Mbh) is a redox-driven Na+/H+ transporter that employs the energy from hydrogen gas (H2) production to catalyze proton pumping and Na+/H+ exchange across cytoplasmic membranes of archaea. Despite a recently resolved structure of this ancient energy-transducing enzyme [Yu et al. Cell 2018, 173, 1636-1649], the molecular principles of its redox-driven ion-transport mechanism remain puzzling and of major interest for understanding bioenergetic principles of early cells. Here we use atomistic molecular dynamics (MD) simulations in combination with data clustering methods and quantum chemical calculations to probe principles underlying proton reduction as well as proton and sodium transport in Mbh from the hyperthermophilic archaeon Pyrococcus furiosus. We identify putative Na+ binding sites and proton pathways leading across the membrane and to the NiFe-active center as well as conformational changes that regulate ion uptake. We suggest that Na+ binding and protonation changes at a putative ion-binding site couple to proton transfer across the antiporter-like MbhH subunit by modulating the conformational state of a conserved ion pair at the subunit interface. Our findings illustrate conserved coupling principles within the complex I superfamily and provide functional insight into archaeal energy transduction mechanisms.


Asunto(s)
Proteínas Arqueales/química , Hidrogenasas/química , Intercambiadores de Sodio-Hidrógeno/química , Proteínas Arqueales/metabolismo , Catálisis , Dominio Catalítico , Hidrogenasas/metabolismo , Transporte Iónico , Simulación de Dinámica Molecular , Unión Proteica , Protones , Pyrococcus furiosus/enzimología , Sodio/química , Sodio/metabolismo , Intercambiadores de Sodio-Hidrógeno/metabolismo , Agua/química , Agua/metabolismo
13.
Biotechnol Lett ; 43(11): 2105-2110, 2021 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-34532823

RESUMEN

OBJECTIVE: With the widespread application of CRISPR/Cas9 gene editing technology, new methods are needed to screen mutants quickly and effectively. Here, we aimed to develop a simple and cost-effective method to screen CRISPR/Cas9-induced mutants. RESULT: We report a novel method to identify CRISPR/Cas9-induced mutants through a DNA-guided Argonaute nuclease derived from the archaeon Pyrococcus furiosus. We demonstrated that the Pyrococcus furiosus Argonaute (PfAgo)-based method could distinguish among biallelic mutants, monoallelic mutants and wild type (WT). Furthermore, this method was able to identify 1 bp indel mutations. CONCLUSION: The PfAgo-based method is simple to implement and can be applied to screen biallelic mutants and mosaic mutants generated by CRISPR-Cas9 or other kinds of gene editing tools.


Asunto(s)
Proteínas Argonautas , Sistemas CRISPR-Cas/genética , Edición Génica , Mutación INDEL/genética , Animales , Proteínas Arqueales/genética , Proteínas Arqueales/metabolismo , Proteínas Argonautas/genética , Proteínas Argonautas/metabolismo , ADN/genética , Edición Génica/economía , Edición Génica/métodos , Pyrococcus furiosus/enzimología , Pyrococcus furiosus/genética
14.
Nucleic Acids Res ; 49(16): 9444-9458, 2021 09 20.
Artículo en Inglés | MEDLINE | ID: mdl-34387688

RESUMEN

The ribonucleoprotein (RNP) form of archaeal RNase P comprises one catalytic RNA and five protein cofactors. To catalyze Mg2+-dependent cleavage of the 5' leader from pre-tRNAs, the catalytic (C) and specificity (S) domains of the RNase P RNA (RPR) cooperate to recognize different parts of the pre-tRNA. While ∼250-500 mM Mg2+ renders the archaeal RPR active without RNase P proteins (RPPs), addition of all RPPs lowers the Mg2+ requirement to ∼10-20 mM and improves the rate and fidelity of cleavage. To understand the Mg2+- and RPP-dependent structural changes that increase activity, we used pre-tRNA cleavage and ensemble FRET assays to characterize inter-domain interactions in Pyrococcus furiosus (Pfu) RPR, either alone or with RPPs ± pre-tRNA. Following splint ligation to doubly label the RPR (Cy3-RPRC domain and Cy5-RPRS domain), we used native mass spectrometry to verify the final product. We found that FRET correlates closely with activity, the Pfu RPR and RNase P holoenzyme (RPR + 5 RPPs) traverse different Mg2+-dependent paths to converge on similar functional states, and binding of the pre-tRNA by the holoenzyme influences Mg2+ cooperativity. Our findings highlight how Mg2+ and proteins in multi-subunit RNPs together favor RNA conformations in a dynamic ensemble for functional gains.


Asunto(s)
Archaea/enzimología , Magnesio/metabolismo , ARN de Archaea/genética , Ribonucleasa P/genética , Conformación de Ácido Nucleico/efectos de los fármacos , Pyrococcus furiosus/enzimología , Pyrococcus furiosus/genética , Precursores del ARN/genética , ARN de Archaea/ultraestructura , ARN Catalítico , Ribonucleasa P/ultraestructura
15.
PLoS Comput Biol ; 17(6): e1009107, 2021 06.
Artículo en Inglés | MEDLINE | ID: mdl-34133419

RESUMEN

We describe an approach for integrating distance restraints from Double Electron-Electron Resonance (DEER) spectroscopy into Rosetta with the purpose of modeling alternative protein conformations from an initial experimental structure. Fundamental to this approach is a multilateration algorithm that harnesses sets of interconnected spin label pairs to identify optimal rotamer ensembles at each residue that fit the DEER decay in the time domain. Benchmarked relative to data analysis packages, the algorithm yields comparable distance distributions with the advantage that fitting the DEER decay and rotamer ensemble optimization are coupled. We demonstrate this approach by modeling the protonation-dependent transition of the multidrug transporter PfMATE to an inward facing conformation with a deviation to the experimental structure of less than 2Å Cα RMSD. By decreasing spin label rotamer entropy, this approach engenders more accurate Rosetta models that are also more closely clustered, thus setting the stage for more robust modeling of protein conformational changes.


Asunto(s)
Algoritmos , Modelos Moleculares , Conformación Proteica , Bacteriófago T4/enzimología , Biología Computacional , Espectroscopía de Resonancia por Spin del Electrón/estadística & datos numéricos , Metionina Adenosiltransferasa/química , Simulación de Dinámica Molecular/estadística & datos numéricos , Proteínas Asociadas a Resistencia a Múltiples Medicamentos/química , Muramidasa/química , Pyrococcus furiosus/enzimología , Programas Informáticos , Marcadores de Spin
16.
Sci Rep ; 11(1): 11553, 2021 06 02.
Artículo en Inglés | MEDLINE | ID: mdl-34078944

RESUMEN

Salt-bridges play a key role in the thermostability of proteins adapted in stress environments whose intrinsic basis remains to be understood. We find that the higher hydrophilicity of PfP than that of HuP is due to the charged but not the polar residues. The primary role of these residues is to enhance the salt-bridges and their ME. Unlike HuP, PfP has made many changes in its intrinsic property to strengthen the salt-bridge. First, the desolvation energy is reduced by directing the salt-bridge towards the surface. Second, it has made bridge-energy more favorable by recruiting energetically advantageous partners with high helix-propensity among the six possible salt-bridge pairs. Third, ME-residues that perform intricate interactions have increased their energy contribution by making major changes in their binary properties. The use of salt-bridge partners as ME-residues, and ME-residues' overlapping usage, predominant in helices, and energetically favorable substitution are some of the favorable features of PfP compared to HuP. These changes in PfP reduce the unfavorable, increase the favorable ME-energy. Thus, the per salt-bridge stability of PfP is greater than that of HuP. Further, unfavorable target ME-residues can be identified whose mutation can increase the stability of salt-bridge. The study applies to other similar systems.


Asunto(s)
Calor , Prolil Oligopeptidasas/metabolismo , Pyrococcus furiosus/enzimología , Estabilidad de Enzimas , Interacciones Hidrofóbicas e Hidrofílicas , Prolil Oligopeptidasas/química , Electricidad Estática , Termodinámica
17.
J Microbiol Biotechnol ; 31(4): 570-583, 2021 Apr 28.
Artículo en Inglés | MEDLINE | ID: mdl-33753701

RESUMEN

Pyrococcus furiosus α-amylase can hydrolyze α-1,4 linkages in starch and related carbohydrates under hyperthermophilic condition (~ 100°C), showing great potential in a wide range of industrial applications, while its relatively low productivity from heterologous hosts has limited the industrial applications. Bacillus subtilis, a gram-positive bacterium, has been widely used in industrial production for its non-pathogenic and powerful secretory characteristics. This study was conducted to increase production of P. furiosus α-amylase in B. subtilis through three strategies. Initial experiments showed that co-expression of P. furiosus molecular chaperone peptidyl-prolyl cis-trans isomerase through genomic integration mode, using a CRISPR/Cas9 system, increased soluble amylase production. Therefore, considering that native P. furiosus α-amylase is produced within a hyperthermophilic environment and is highly thermostable, heat treatment of intact culture at 90°C for 15 min was performed, thereby greatly increasing soluble amylase production. After optimization of the culture conditions (nitrogen source, carbon source, metal ion, temperature and pH), experiments in a 3-L fermenter yielded a soluble activity of 3,806.7 U/ml, which was 3.3- and 28.2-fold those of a control without heat treatment (1,155.1 U/ml) and an empty expression vector control (135.1 U/ml), respectively. This represents the highest P. furiosus α-amylase production reported to date and should promote innovation in the starch liquefaction process and related industrial productions. Meanwhile, heat treatment, which may promote folding of aggregated P. furiosus α-amylase into a soluble, active form through the transfer of kinetic energy, may be of general benefit when producing proteins from thermophilic archaea.


Asunto(s)
Bacillus subtilis/metabolismo , Fermentación , Chaperonas Moleculares , Pyrococcus furiosus/enzimología , alfa-Amilasas/biosíntesis , Calor , Microbiología Industrial , Almidón/metabolismo
18.
Talanta ; 227: 122154, 2021 May 15.
Artículo en Inglés | MEDLINE | ID: mdl-33714462

RESUMEN

Infectious diseases caused by viruses such as SARS-CoV-2 and HPV have greatly endangered human health. The nucleic acid detection is essential for the early diagnosis of diseases. Here, we propose a method called PLCR (PfAgo coupled with modified Ligase Chain Reaction for nucleic acid detection) which utilizes PfAgo to only use DNA guides longer than 14-mer to specifically cleave DNA and LCR to precisely distinguish single-base mismatch. PLCR can detect DNA or RNA without PCR at attomolar sensitivities, distinguish single base mutation between the genome of wild type SARS-CoV-2 and its mutant spike D614G, effectively distinguish the novel coronavirus from other coronaviruses and finally achieve multiplexed detection in 70 min. Additionally, LCR products can be directly used as DNA guides without additional input guides to simplify primer design. With desirable sensitivity, specificity and simplicity, the method can be extended for detecting other pathogenic microorganisms.


Asunto(s)
Proteínas Argonautas/química , ADN Viral/análisis , Reacción en Cadena de la Ligasa/métodos , Pyrococcus furiosus/enzimología , ARN Viral/análisis , Alphapapillomavirus/química , Alphapapillomavirus/aislamiento & purificación , COVID-19/diagnóstico , ADN Viral/química , Humanos , Límite de Detección , Mutación , Infecciones por Papillomavirus/diagnóstico , ARN Viral/química , SARS-CoV-2/química , SARS-CoV-2/aislamiento & purificación , Sensibilidad y Especificidad , Glicoproteína de la Espiga del Coronavirus/genética
19.
Proc Natl Acad Sci U S A ; 118(10)2021 03 09.
Artículo en Inglés | MEDLINE | ID: mdl-33658373

RESUMEN

Spontaneous deamination of DNA cytosine and adenine into uracil and hypoxanthine, respectively, causes C to T and A to G transition mutations if left unrepaired. Endonuclease Q (EndoQ) initiates the repair of these premutagenic DNA lesions in prokaryotes by cleaving the phosphodiester backbone 5' of either uracil or hypoxanthine bases or an apurinic/apyrimidinic (AP) lesion generated by the excision of these damaged bases. To understand how EndoQ achieves selectivity toward these structurally diverse substrates without cleaving undamaged DNA, we determined the crystal structures of Pyrococcus furiosus EndoQ bound to DNA substrates containing uracil, hypoxanthine, or an AP lesion. The structures show that substrate engagement by EndoQ depends both on a highly distorted conformation of the DNA backbone, in which the target nucleotide is extruded out of the helix, and direct hydrogen bonds with the deaminated bases. A concerted swing motion of the zinc-binding and C-terminal helical domains of EndoQ toward its catalytic domain allows the enzyme to clamp down on a sharply bent DNA substrate, shaping a deep active-site pocket that accommodates the extruded deaminated base. Within this pocket, uracil and hypoxanthine bases interact with distinct sets of amino acid residues, with positioning mediated by an essential magnesium ion. The EndoQ-DNA complex structures reveal a unique mode of damaged DNA recognition and provide mechanistic insights into the initial step of DNA damage repair by the alternative excision repair pathway. Furthermore, we demonstrate that the unique activity of EndoQ is useful for studying DNA deamination and repair in mammalian systems.


Asunto(s)
Proteínas Arqueales/química , ADN de Archaea/química , Endonucleasas/química , Pyrococcus furiosus/enzimología , Proteínas Arqueales/genética , Dominio Catalítico , ADN de Archaea/genética , Desaminación , Endonucleasas/genética , Pyrococcus furiosus/genética
20.
Protein Expr Purif ; 182: 105843, 2021 06.
Artículo en Inglés | MEDLINE | ID: mdl-33631310

RESUMEN

Commercial applications of ß-glucosidase (BGL) demands its purity and availability on a large scale. In the present study, we aim to optimize the expression and secretion of a thermostable BGL from Pyrococcus furiosus (PfuBGL) in B. subtilis strain RIK1285. Initial studies with base strain BV002 harboring aprE signal peptide (aprESP) showed PfuBGL yield of 0.743 ± 0.19 pNP U/ml only. A library of 173 different homologous SPs from B. subtilis 168 genome was fused with target PfuBGL gene (PF0073) in pBE-S vector and extracellularly expressed in RIK1285 strain to identify optimal SP for PfuBGL secretion. High-throughput screening of the resulting SP library for BGL activity with a synthetic substrate followed by systematic scaling of the clones yielded a gene construct with CitHSP reporting a sixteen fold enhancement of PfuBGL secretion in comparison to base strain. Batch fermentation (7.5 L scale) PfuBGL yield of the BV003 strain with CitHSP-PF0073 fusion was observed to be 12.08 ± 0.21 pNP U/ml with specific activity of 35.52 ± 0.53 U/mg. Thus, the study represents report on the secretory expression of thermostable PfuBGL using B. subtilis as a host organism and demonstrating its high potential for industrial production of any protein/enzyme.


Asunto(s)
Proteínas Arqueales , Bacillus subtilis , Señales de Clasificación de Proteína/genética , Pyrococcus furiosus , beta-Glucosidasa , Proteínas Arqueales/biosíntesis , Proteínas Arqueales/química , Proteínas Arqueales/genética , Proteínas Arqueales/aislamiento & purificación , Bacillus subtilis/genética , Bacillus subtilis/metabolismo , Pyrococcus furiosus/enzimología , Pyrococcus furiosus/genética , Proteínas Recombinantes/biosíntesis , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/aislamiento & purificación , beta-Glucosidasa/biosíntesis , beta-Glucosidasa/química , beta-Glucosidasa/genética , beta-Glucosidasa/aislamiento & purificación
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