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Results for “extracellular enzyme”

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At least 145 records · Page 8
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Spectroscopic and computational investigations of organometallic complexation of group 12 transition metals by methanobactins from Methylocystis sp. SB2

Methanotrophic bacteria catalyze the aerobic oxidation of methane to methanol using Cu-containing enzymes, thereby exerting a modulating influence on the global methane cycle. To facilitate the acquisition of Cu ions, some methanotrophic bacteria secrete small modified peptides known as “methanobactins,” which strongly bind Cu and function as an extracellular Cu recruitment relay, analogous to siderophores and Fe. In addition to Cu, methanobactins form complexes with other late transition metals, including the Group 12 transition metals Zn, Cd, and Hg, although the interplay among solution-phase configurations, metal interactions, and the spectroscopic signatures of methanobactin-metal complexes remains ambiguous. In this study, the complexation of Zn, Cd, and Hg by methanobactin from Methylocystis sp. strain SB2 was studied using a combination of absorbance, fluorescence, extended x-ray absorption fine structure (EXAFS) spectroscopy, and time-dependent density functional theory (TD-DFT) calculations. We report changes in sample absorbance and fluorescence spectral dynamics, which occur on a wide range of experimental timescales and characterize a clear stoichiometric complexation dependence. Mercury L3-edge EXAFS and TD-DFT calculations suggest a linear model for Hg--S coordination, and TD-DFT suggests a tetrahedral model for Zn 2+ and Cd 2+ . We observed an enhancement in the fluorescence of methanobactin upon interaction with transition metals and propose a mechanism of complexation-hindered isomerization drawing inspiration from the wild-type Green Fluorescent Protein active site. Collectively, our results represent the first combined computational and experimental spectroscopy study of methanobactins and shed new light on molecular interactions and dynamics that characterize complexes of methanobactins with Group 12 transition metals.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Production and characterization of extracellular cellulases from a native strain of Trichoderma harzianum using wheat straw from the Mexicali valley as the carbon source. Producción y caracterización de celulasas Extracelulares a partir de cepa nativa de Trichoderma harzianum usando como fuente de Carbono paja de trigo del valle de Mexicali

The purpose of this study was to produce cellulase enzyme from a native strain Trichoderma harzianum, isolated from crop soil. Cellulase production was carried out by two different methods of fermentation, submerging and solid state fermentation. Mandels mineral medium was used as a source of nitrogen and ammonium sulfate. Dry and ground wheat straw was used in fermentation as a carbon source. Cellulase activity was determined using the 3,5-dinitrosalicylic acid (DNS) method. The results showed that wheat straw has the potential to be used as a substrate in the production of cellulases. Trichoderma harzianum showed enzymatic activity of 0.125 FPU / ml (filter paper units) and 1. 35 U / ml CMC (carboxymethyl cellulose units) by solid state fermentation (FSS) after 96 hours of fermentation. The optimum pH for the two substrates was determined by testing with citrate buffers (pH 4 to 6), phosphates (pH 6 to 7) and tris-HCL (pH 8 to 9). To determine the optimum temperature the range of 30 ° C to 80 ° C was investigated. Storage tests were performed every seven days over a period of 6 weeks. The optimum activity pH on paper and CMC was found to be 6. The optimum activity temperature is 70 ° C for PF and 80 ° C for CMC. El propósito de este estudio fue producir enzima celulasa a partir de una cepa nativa Trichoderma harzianum, aislada de suelo de cultivo. La producción de celulasa se realizó por dos métodos diferentes de fermentación, sumergida y fermentación en estado sólido. Se utilizó medio mineral Mandels y como fuentes de nitrógeno urea y sulfato de amonio. Se utilizó paja de trigo seca y molida en las fermentaciones como fuente de carbono. La actividad de la celulasa se determinó por medición de azúcares reductores al papel filtro y a la carboximetilcelulosa usando el método del ácido 3,5- dinitrosalicílico (DNS). Los resultados mostraron que la paja de trigo tiene el potencial para usarse como sustrato en la producción de celulasas. Trichoderma harzianum mostró actividad enzimática de 0.125 FPU/ml (unidades de papel filtro) y 1.35 U/ml a la CMC (unidades de carboximetilcelulosa) por fermentación en estado sólido (FSS) después de 96 horas de fermentación. El pH óptimo para los dos sustratos se determinó realizando pruebas con buffers de citratos (pH 4 a 6), de fosfatos (pH 6 a 7) y tris- HCL (pH 8 a 9). Para la determinación de la temperatura óptima se manejó el rango de 30°C a 80°C. Las pruebas de almacenamiento se realizaron cada siete días en un periodo de 6 semanas. Se encontró que el pH óptimo de actividad en papel y CMC es de 6. La temperatura óptima de actividad es de 70°C para PF y de 80°C para CMC.

09 BIOMASS FUELS↗
DOE OSTI2026

Convergent evolution of aerobic fermentation through divergent mechanisms acting on the same key glycolytic genes

Expression profiling by high throughput sequencing The model yeast Saccharomyces cerevisiae has evolved aerobic fermentation in part through a whole genome duplication and subsequent retention of glycolytic genes. To identify independent yeast lineages with a high glycolytic rate phenotype we developed an assay measuring extracellular acidification rates (ECAR) to evaluate the glycolytic rates across diverse yeast species. This assay identified a novel group of yeasts in the genus Saturnispora with rapid glycolytic rates. Through comparative approaches, we found that several glycolytic genes encoding hexokinases and enzymes in lower glycolysis had higher expression and modifications in promoter sequences in rapid ECAR species. Intriguingly, many of the upregulated genes are the same genes that are duplicated in S. cerevisiae. When the transcription factor required for their activation was deleted, the mutants had a slow glycolytic rate and more respiratory phenotype. This work shows how the aerobic fermentation phenotype has convergently evolved in Saturnispora through transcriptional rewiring. This divergent mechanism nevertheless impacts the same glycolytic genes, which suggests that there are evolutionary constraints on how aerobic fermentation can arise.

Horianopoulos, Linda C. [Department of Food Scienc↗
DOE OSTI2023

Soluble Iron Enhances Extracellular Electron Uptake by Shewanella oneidensis MR‐1

Abstract Extracellular electron transfer (EET) is a process that microorganisms use to reduce or oxidize external insoluble electron acceptors or donors. Much of our mechanistic understanding of this process is derived from studies of transmembrane cytochrome complexes and extracellular redox shuttles that mediate outward EET to anodes and external electron acceptors. In contrast, there are knowledge gaps concerning the reverse process of inward EET from external electron donors to cells. Here, we describe a role for soluble iron (exogenous FeCl 2 ) in enhancing EET from cathodes to the model EET bacterium Shewanella oneidensis MR‐1, with fumarate serving as the intracellular electron acceptor. This iron concentration‐dependent electron uptake was eradicated upon addition of an iron chelator and occurred only in the presence of fumarate reductase, confirming an electron pathway from cathodes to this periplasmic enzyme. Moreover, S. oneidensis mutants lacking specific outer membrane and periplasmic cytochromes exhibited significantly decreased current levels relative to wild‐type. These results indicate that soluble iron can function as an electron carrier to the EET machinery of S. oneidensis .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Multi-omics of NET formation and correlations with CNDP1, PSPB, and L-cystine levels in severe and mild COVID-19 infections

We report that we performed a multi-omics analysis of an immunologically naïve SARS-CoV-2 clinical cohort to characterize overall changes in plasma among control (uninfected), mild, and severe infections. A comparison of healthy controls and patient samples showed activation of neutrophil degranulation pathways. Consistent with this observation, we characterized neutrophil extracellular trap (NET) complexes that were partially initiated in a subset of the mild infections (showing partially formed NETs) and fully-formed NETs in a subset of severe infections (containing multiple NET proteins in individual patient samples). As a potential mechanism to suppress NET formation, multiple redox enzymes were elevated in the mild and severe population. Analysis of metabolites from the same cohort showed a 24 and 60-fold elevation in plasma L-cystine, the oxidized form of cysteine and substrate of the powerful antioxidant glutathione in mild and severe patients, respectively. Unique to patients with mild infections, the carnosine dipeptidase modifying enzyme (CNDP1) was up-regulated. The strong protein and metabolite oxidation signatures suggest multiple compensatory pathways working to suppress both free radical and NET formation in SARS-CoV-2 infections.

60 APPLIED LIFE SCIENCES↗
NASA NTRS1992

Endochondral bone formation in embryonic mouse pre-metatarsals

Long term exposure to a reduced gravitational environment has a deleterious effect on bone. The developmental events which occur prior to initial bone deposition will provide insight into the regulation of mature bone physiology. We have characterized a system in which the events preceding bone formation take place in an isolated in vitro organ culture environment. We show that cultured pre-metatarsal tissue parallels development of pre-metatarsal tissue in the embryo. Both undergo mesenchyme differentiation and morphogenesis to form a cartilage rod, which resembles the future bone, followed by terminal chondrocyte differentiation in a definite morphogenetic pattern. These sequential steps occur prior to osteoblast maturation and bone matrix deposition in the developing organism. Alkaline phosphatase (ALP) activity is a distinctive enzymatic marker for mineralizing tissues. We have measured this activity throughout pre-metatarsal development and show (a) where in the tissue it is predominantly found, and (b) that this is indeed the mineralizing isoform of the enzyme.

NASA Discipline Number 93-10↗
DOE OSTI2020

Exoproteomics Reveals Outer Membrane Vesicle Mediated Catabolism of Lignin-Derived Aromatics by P. putida KT2440

Lignin is an abundant component of plant cell walls which is heterogeneous and highly resistant to degradation. Biological funneling of lignin via microbes represents an efficient approach for reducing chemical heterogeneity and generating molecules which can be valorized into performance-advantaged materials. Pseudomonas putida KT2440 (P. putida) catabolizes lignin-derived aromatic monomers rapidly and efficiently via the b-ketoadipate (bKA) pathway and our data suggest P. putida may depolymerize HMW lignin as well [1]. The mechanism by which HMW lignin is depolymerized by bacteria remains unknown. Intriguingly, we found that P. putida secretes outer membrane vesicles (OMVs) of two distinct sizes in the presence of lignin. Here, we describe the temporal proteome of OMVs and the vesicle-free secretome (VFS) in the presence or absence of lignin. Enzymes involved in aromatic catabolism via the bKA pathway are temporally enriched into OMVs in the presence of lignin. Isolated OMVs enhance growth of P. putida mutants unable to grow on model lignin-derived aromatics, and turnover protocatechuic acid in vitro. Together, this work leads us to hypothesize mechanisms by which OMVs contribute to extracellular aromatic catabolism by P. putida. Ongoing and future work seeks to further understand this phenomena in the context of both fundamental an applied lignin conversion research areas.

09 BIOMASS FUELS↗
DOE OSTI2022

Activation of the plant mevalonate pathway by extracellular ATP

The mevalonate pathway plays a critical role in multiple cellular processes in both animals and plants. In plants, the products of this pathway impact growth and development, as well as the response to environmental stress. A forward genetic screen of Arabidopsis thaliana using Ca 2+ -imaging identified mevalonate kinase (MVK) as a critical component of plant purinergic signaling. MVK interacts directly with the plant extracellular ATP (eATP) receptor P2K1 and is phosphorylated by P2K1 in response to eATP. Mutation of P2K1-mediated phosphorylation sites in MVK eliminates the ATP-induced cytoplasmic calcium response, MVK enzymatic activity, and suppresses pathogen defense. The data demonstrate that the plasma membrane associated P2K1 directly impacts plant cellular metabolism by phosphorylation of MVK, a key enzyme in the mevalonate pathway. The results underline the importance of purinergic signaling in plants and the ability of eATP to influence the activity of a key metabolite pathway with global effects on plant metabolism.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1994

Experiment K-7-29: Connective Tissue Studies: Changes in Muscle Serine Proteases, Serpins and Matrix Molecules - Part 2

In zero or micro-gravity, type 1 muscle fibers atrophy and lose predominance, especially in slow-twitch muscles. No increase in mononuclear cells has been observed, just as in simple denervation, where both types 1 and 2 fibers atrophy, again without infiltration of cells, but with clear satellite cell proliferation. However, extracellular matrix (ECM) degradation takes place after denervation and if re-innervation is encouraged, functional recovery to near control levels may be achieved. No information is available concerning the ECM milieu, the activation of serine proteases, their efficacy in degrading ECM components and the production of locally-derived natural protease inhibitors (serpins) in effecting surface proteolytic control. In addition, no studies are available concerning the activation of these enzymes in micro- or zero gravity or their response to muscle injury on the ground and what alterations, if any, occur in space. These studies were the basis for the experiments in Cosmos 2044.

Festoff, B. W.↗
DOE OSTI2023

Structural basis for heparan sulfate co-polymerase action by the EXT1–2 complex

Heparan sulfate (HS) proteoglycans are extended (-GlcAβ1,4GlcNAcα1,4-)n co-polymers containing decorations of sulfation and epimerization that are linked to cell surface and extracellular matrix proteins. In mammals, HS repeat units are extended by an obligate heterocomplex of two exostosin family members, EXT1 and EXT2, where each protein monomer contains distinct GT47 (GT-B fold) and GT64 (GT-A fold) glycosyltransferase domains. In this study, we generated human EXT1–EXT2 (EXT1–2) as a functional heterocomplex and determined its structure in the presence of bound donor and acceptor substrates. Structural data and enzyme activity of catalytic site mutants demonstrate that only two of the four glycosyltransferase domains are major contributors to co-polymer syntheses: the EXT1 GT-B fold β1,4GlcA transferase domain and the EXT2 GT-A fold α1,4GlcNAc transferase domain. Furthermore, the two catalytic sites are over 90 Å apart, indicating that HS is synthesized by a dissociative process that involves a single catalytic site on each monomer.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Three-dimensional traction microscopy accounting for cell-induced matrix degradation

Tractions exerted by cells on the extracellular matrix (ECM) are critical in many important physiological and pathological processes such as embryonic morphogenesis, wound healing, and cancer metastasis. Three-dimensional Traction Microscopy (3DTM) is a tool to quantify cellular tractions by first measuring the displacement field in the ECM in response to these tractions, and then using this measurement to infer tractions. Most applications of 3DTM have assumed that the ECM has spatially-uniform mechanical properties, but cells secrete enzymes that can locally degrade the ECM. In this work, a novel computational method is developed to quantify both cellular tractions and ECM degradation. In particular, the ECM is modeled as a hyperelastic, Neo-Hookean solid, whose material parameters are corrupted by a single degradation parameter. The feasibility of determining both the traction and the degradation parameter is first demonstrated by showing the existence and uniqueness of the solution. An inverse problem is then formulated to determine the nodal values of the traction vector and the degradation parameter, with the objective of minimizing the difference between a predicted and measured displacement field, under the constraint that the predicted displacement field satisfies the equation of equilibrium. The inverse problem is solved by means of a gradient-based optimization approach, and the gradient is computed efficiently using appropriately derived adjoint fields. The computational method is validated in-silico using a geometrically realistic neuronal cell model and synthetic traction and degradation fields. It is found that the method accurately recovers both the traction and degradation fields. Moreover, it is found that neglecting ECM degradation can yield significant errors in traction measurements. Finally, our method can extend the range of context where tractions can be appropriately measured.

42 ENGINEERING↗
NASA NTRS1993

How do plant cell walls extend?

This article briefly summarizes recent work that identifies the biophysical and biochemical processes that give rise to the extension of plant cell walls. I begin with the biophysical notion of stress relaxation of the wall and follow with recent studies of wall enzymes thought to catalyze wall extension and relaxation. Readers should refer to detailed reviews for more comprehensive discussion of earlier literature (Taiz, 1984; Carpita and Gibeaut, 1993; Cosgrove, 1993).

Review, Tutorial↗
NASA NTRS2004

Cloning and Characterization of an alpha-amylase Gene from the Hyperthermophilic Archaeon Thermococcus Thioreducens

The gene encoding an extracellular alpha-amylase, TTA, from the hyperthermophilic archaeon Thermococcus thioreducens was cloned and expressed in Escherichia coli. Primary structural analysis revealed high similarity with other a-amylases from the Thermococcus and Pyrococcus genera, as well as the four highly conserved regions typical for a-amylases. The 1374 bp gene encodes a protein of 457 amino acids, of which 435 constitute the mature protein preceded by a 22 amino acid signal peptide. The molecular weight of the purified recombinant enzyme was estimated to be 43 kDa by denaturing gel electrophoresis. Maximal enzymatic activity of recombinant TTA was observed at 90 C and pH 5.5 in the absence of exogenous Ca(2+), and the enzyme was considerably stable even after incubation at 90 C for 2 hours. The thermostability at 90 and 102 C was enhanced in the presence of 5 mM Ca(2+). The extraordinarily high specific activity (about 7.4 x 10(exp 3) U/mg protein at 90 C, pH 5.5 with soluble starch as substrate) together with its low pH optimum makes this enzyme an interesting candidate for starch processing applications.

Bernhardsdotter, Eva C. M. J.↗
NASA NTRS2004

Cloning and Characterization of an Alpha-amylase Gene from the Hyperthermophilic Archaeon Thermococcus Thioreducens

The gene encoding an extracellular a-amylase, TTA, from the hyperthermophilic archaeon Thermococcus thioreducens was cloned and expressed in Escherichia coli. Primary structural analysis revealed high similarity with other a-amylases from the Thermococcus and Pyrococcus genera, as well as the four highly conserved regions typical for a-amylases. The 1374 bp gene encodes a protein of 457 amino acids, of which 435 constitute the mature protein preceded by a 22 amino acid signal peptide. The molecular weight of the purified recombinant enzyme was estimated to be 43 kDa by denaturing gel electrophoresis. Maximal enzymatic activity of recombinant TTA was observed at 90 C and pH 5.5 in the absence of exogenous Ca(2+), and the enzyme was considerably stable even after incubation at 90 C for 2 hours. The thermostability at 90 and 102 C was enhanced in the presence of 5 mM Ca(2+). The extraordinarily high specific activity (about 7.4 x 10(exp 3) U/mg protein at 90 C, pH 5.5 with soluble starch as substrate) together with its low pH optimum makes this enzyme an interesting candidate for starch processing applications.

Bernhardsdotter, Eva C. M. J.↗
DOE OSTI2022

Cross-Kingdom Comparative Genomics of Aromatic Catabolic Pathways in Fungi and Bacteria

The overall goal of this project is to test the hypothesis that white-rot fungi can simultaneously depolymerize lignin extracellularly and catabolize depolymerization products intracellularly as carbon and energy sources. The results from this project will lead to improved understanding of lignin utilization by white-rot fungi, and enable identification of promising fungal strains for lignin catabolism and valorization. As part of this effort, we have conducted a comparative genomic study to investigate a diversity of aromatic catabolic pathways in the fungal and bacterial kingdoms. Furthermore, we have combined genomic and phylogenetic approaches to decipher the evolution of certain aromatic catabolic enzymes and discover new classes of enzymes, which represents a foundation for future biochemical and molecular genetic studies.

aromatic compounds↗
NASA NTRS1999

The Role of Calcium in the Response of Osteoblasts to Mechanical Stimulation

A major biomedical concern in the exploration and development of space is the rapid loss of bone associated with extended periods of spaceflight. Mineral content, bone formation, matrix protein production and total body calcium are all reduced during long-term periods of weightlessness. These effects of weightlessness appears to be due to decreases in the anabolic function of osteoblasts and osteocytes rather than changes in the resorptive activity of osteoclasts. Conversely, subjecting the skeleton to exogenous mechanical loading increases matrix protein synthesis and bone formation rate, a process which also appears mediated through osteogenic cells. Osteoblasts have been shown to respond to a number of types of mechanical stimulation. However recently we have demonstrated that osteoblasts respond to fluid shear, but not physiologic levels of mechanical strain, with increases in expression of the matrix protein, osteopontin. We have also shown similar responses in other markers for the anabolic response in bone. The expression of the early response gene, c-fos, and the inducible-isoform of the prostaglandin synthetic enzyme, cyclooygenase-2 (COX-2), both increase rapidly in response to fluid shear, but not strain. How osteoblasts and osteocytes perceive mechanical stimuli and convert this stimulus into a biochemical event within the cell is still unknown. However, examination of the cellular events following mechanical stimulation indicate that two of the earliest responses are a rapid increase in intracellular calcium ([Ca(2+)](sub i)) and a reorganization of the actin cytoskeleton. The increase in [Ca(2+)](sub i) is dependent on the presence of extracellular Ca(2+), suggesting the activation of membrane Ca(2+) channel. We have previously characterized a mechanosensitive, cation-selective channel (MSCC) in osteoblast-like clonal cells, which we postulate is important in this early response to mechanical loading. Using an antisense oligodeoxynucleotide strategy, we have tentatively identified this channel as an isoform of the alc subunit of the dihydropyridine-sensitive, voltage sensitive Ca(2+) channel (VSCC). However, a major component in this mechanically induced rise in [Ca(2+)](sub i) is the release of Ca(2+) from intracellular stores. The actin cytoskeleton also rapidly responds to fluid shear with an increase in stress fiber formation and a realignment of the cell parallel to the direction of flow. To ascertain whether these two observations are related and how they effect shear-induced gene expression, we examined the role of Ca(2+) channels and intracellular Ca(2+) release on cytoskeletal reorganization and the resultant increases in the expression and production of c-fos and COX-2 in response to fluid shear.

Duncan, R. L.↗
DOE OSTI2024

Comprehensive characterization of extracellular vesicles produced by environmental (Neff) and clinical (T4) strains of Acanthamoeba castellanii

We conducted a comprehensive comparative analysis of extracellular vesicles (EVs) from two Acanthamoeba castellanii strains, Neff (environmental) and T4 (clinical). Morphological analysis via transmission electron microscopy revealed slightly larger Neff EVs (average = 194.5 nm) compared to more polydisperse T4 EVs (average = 168.4 nm). Nanoparticle tracking analysis (NTA) and dynamic light scattering validated these differences. Proteomic analysis of the EVs identified 1,352 proteins, with 1,107 common, 161 exclusive in Neff, and 84 exclusively in T4 EVs. Gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) mapping revealed distinct molecular functions and biological processes and notably, the T4 EVs enrichment in serine proteases, aligned with its pathogenicity. Lipidomic analysis revealed a prevalence of unsaturated lipid species in Neff EVs, particularly triacylglycerols, phosphatidylethanolamines (PEs), and phosphatidylserine, while T4 EVs were enriched in diacylglycerols and diacylglyceryl trimethylhomoserine, phosphatidylcholine and less unsaturated PEs, suggesting differences in lipid metabolism and membrane permeability. Metabolomic analysis indicated Neff EVs enrichment in glycerolipid metabolism, glycolysis, and nucleotide synthesis, while T4 EVs, methionine metabolism. Furthermore, RNA-seq of EVs revealed differential transcript between the strains, with Neff EVs enriched in transcripts related to gluconeogenesis and translation, suggesting gene regulation and metabolic shift, while in the T4 EVs transcripts were associated with signal transduction and protein kinase activity, indicating rapid responses to environmental changes. In this novel study, data integration highlighted the differences in enzyme profiles, metabolic processes, and potential origins of EVs in the two strains shedding light on the diversity and complexity of A. castellanii EVs and having implications for understanding host-pathogen interactions and developing targeted interventions for Acanthamoeba-related diseases.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Structural features of Dnase1L3 responsible for serum antigen clearance

Autoimmunity develops when extracellular DNA released from dying cells is not cleared from serum. While serum DNA is primarily digested by Dnase1 and Dnase1L3, Dnase1 cannot rescue autoimmunity arising from Dnase1L3 deficiencies. Dnase1L3 uniquely degrades antigenic forms of cell-free DNA, including DNA complexed with lipids and proteins. The distinct activity of Dnase1L3 relies on its unique C-terminal Domain (CTD), but the mechanism is unknown. We used multiple biophysical techniques and functional assays to study the interplay between the core catalytic domain and the CTD. While the core domain resembles Dnase1, there are key structural differences between the two enzymes. First, Dnase1L3 is not inhibited by actin due to multiple differences in the actin recognition site. Second, the CTD augments the ability of the core to bind DNA, thereby facilitating the degradation of complexed DNA. Together, these structural insights will inform the development of Dnase1L3-based therapies for autoimmunity.

59 BASIC BIOLOGICAL SCIENCES↗