scholarly journals Prediction and characterization of enzymatic activities guided by sequence similarity and genome neighborhood networks

eLife ◽  
2014 ◽  
Vol 3 ◽  
Author(s):  
Suwen Zhao ◽  
Ayano Sakai ◽  
Xinshuai Zhang ◽  
Matthew W Vetting ◽  
Ritesh Kumar ◽  
...  
Keyword(s):  
Metabolic Pathways ◽  
Large Scale ◽  
Sequence Similarity ◽  
Gene Clusters ◽  
Enzymatic Activities ◽  
Or Gene ◽  
Enzyme Functions

Metabolic pathways in eubacteria and archaea often are encoded by operons and/or gene clusters (genome neighborhoods) that provide important clues for assignment of both enzyme functions and metabolic pathways. We describe a bioinformatic approach (genome neighborhood network; GNN) that enables large scale prediction of the in vitro enzymatic activities and in vivo physiological functions (metabolic pathways) of uncharacterized enzymes in protein families. We demonstrate the utility of the GNN approach by predicting in vitro activities and in vivo functions in the proline racemase superfamily (PRS; InterPro IPR008794). The predictions were verified by measuring in vitro activities for 51 proteins in 12 families in the PRS that represent ~85% of the sequences; in vitro activities of pathway enzymes, carbon/nitrogen source phenotypes, and/or transcriptomic studies confirmed the predicted pathways. The synergistic use of sequence similarity networks3 and GNNs will facilitate the discovery of the components of novel, uncharacterized metabolic pathways in sequenced genomes.

scholarly journals Characterization of an L-Ascorbate Catabolic Pathway with Unprecedented Enzymatic Transformations

2019 ◽  
Author(s):  
Tyler Stack ◽  
Katelyn Morrison ◽  
Thomas Dettmer ◽  
Brendan Wille ◽  
Chan Kim ◽  
...  
Keyword(s):  
Ralstonia Eutropha ◽  
Sequence Similarity ◽  
Catabolic Genes ◽  
Genes Encoding ◽  
Benzilic Acid ◽  
Amidohydrolase Superfamily ◽  
Sequence Similarity Networks

<p>L-Ascorbate (vitamin C) is ubiquitous in both our diet and the environment. <i>Ralstonia eutropha </i>H16 (<i>Cupriavidus necator </i>ATCC 17699) uses L-ascorbate as sole carbon source but lacks the genes encoding the known catabolic pathways. RNAseq identified eight candidate catabolic genes. Sequence similarity networks and genome neighborhood networks guided predictions for function of the encoded proteins; the predictions were confirmed by <i>in vitro</i> assays and <i>in vivo</i> growth phenotypes of gene deletion mutants. L-Ascorbate, a lactone, is oxidized and ring-opened by enzymes in the cytochrome b<sub>561</sub> and gluconolactonase families, respectively, to form 2,3-diketo-L-gulonate. A protein predicted to have a WD40-like fold catalyzes an unprecedented benzilic acid rearrangement involving migration of a carboxylate group to form 2-carboxy-L-lyxonolactone; the lactone is hydrolyzed by a member of the amidohydrolase superfamily to yield 2-carboxy-L-lyxonate. A member of the PdxA family of oxidative decarboxylases catalyzes a novel decarboxylation that uses NAD<sup>+</sup> catalytically. The product, L-lyxonate, is catabolized to alpha-ketoglutarate by a previously characterized pathway.</p>

scholarly journals The semi-phosphorylative Entner–Doudoroff pathway in hyperthermophilic archaea: a re-evaluation

2005 ◽  
Vol 390 (2) ◽  
pp. 529-540 ◽  
Author(s):  
Hatim Ahmed ◽  
Thijs J. G. Ettema ◽  
Britta Tjaden ◽  
Ans C. M. Geerling ◽  
John van der Oost ◽  
...  
Keyword(s):  
Metabolic Pathways ◽  
Sulfolobus Solfataricus ◽  
Gene Clusters ◽  
Hyperthermophilic Archaea ◽  
Biochemical Studies ◽  
Key Enzyme ◽  
Comparative Genomics Analysis ◽  
Thermoproteus Tenax

Biochemical studies have suggested that, in hyperthermophilic archaea, the metabolic conversion of glucose via the ED (Entner–Doudoroff) pathway generally proceeds via a non-phosphorylative variant. A key enzyme of the non-phosphorylating ED pathway of Sulfolobus solfataricus, KDG (2-keto-3-deoxygluconate) aldolase, has been cloned and characterized previously. In the present study, a comparative genomics analysis is described that reveals conserved ED gene clusters in both Thermoproteus tenax and S. solfataricus. The corresponding ED proteins from both archaea have been expressed in Escherichia coli and their specificity has been identified, revealing: (i) a novel type of gluconate dehydratase (gad gene), (ii) a bifunctional 2-keto-3-deoxy-(6-phospho)-gluconate aldolase (kdgA gene), (iii) a 2-keto-3-deoxygluconate kinase (kdgK gene) and, in S. solfataricus, (iv) a GAPN (non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase; gapN gene). Extensive in vivo and in vitro enzymatic analyses indicate the operation of both the semi-phosphorylative and the non-phosphorylative ED pathway in T. tenax and S. solfataricus. The existence of this branched ED pathway is yet another example of the versatility and flexibility of the central carbohydrate metabolic pathways in the archaeal domain.

scholarly journals The In Vivo Transcriptomic Blueprint of Mycobacterium tuberculosis in the Lung

2021 ◽  
Vol 12 ◽  
Author(s):  
Mariateresa Coppola ◽  
Rachel P-J. Lai ◽  
Robert J. Wilkinson ◽  
Tom H. M. Ottenhoff
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Metabolic Pathways ◽  
Large Scale ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Genes Encoding ◽  
High Concordance ◽  
Lower Correlation

Mycobacterium tuberculosis (Mtb) genes encoding proteins targeted by vaccines and drugs should be expressed in the lung, the main organ affected by Mtb, for these to be effective. However, the pulmonary expression of most Mtb genes and their proteins remains poorly characterized. The aim of this study is to fill this knowledge gap. We analyzed large scale transcriptomic datasets from specimens of Mtb-infected humans, TB-hypersusceptible (C3H/FeJ) and TB-resistant (C57BL/6J) mice and compared data to in vitro cultured Mtb gene-expression profiles. Results revealed high concordance in the most abundantly in vivo expressed genes between pulmonary Mtb transcriptomes from different datasets and different species. As expected, this contrasted with a lower correlation found with the highest expressed Mtb genes from in vitro datasets. Among the most consistently and highly in vivo expressed genes, 35 have not yet been explored as targets for vaccination or treatment. More than half of these genes are involved in protein synthesis or metabolic pathways. This first lung-oriented multi-study analysis of the in vivo expressed Mtb-transcriptome provides essential data that considerably increase our understanding of pulmonary TB infection biology, and identifies novel molecules for target-based TB-vaccine and drug development.

Proliferative enteropathy: a global enteric disease of pigs caused byLawsonia intracellularis

2005 ◽  
Vol 6 (2) ◽  
pp. 173-197 ◽  
Author(s):  
Jeremy J. Kroll ◽  
Michael B. Roof ◽  
Lorraine J. Hoffman ◽  
James S. Dickson ◽  
D. L. Hank Harris
Keyword(s):  
Metabolic Pathways ◽  
Vaccine Development ◽  
Diagnostic Tools ◽  
Lawsonia Intracellularis ◽  
Genetic Sequencing ◽  
Host Interactions ◽  
Proliferative Enteropathy

AbstractProliferative enteropathy (PE; ileitis) is a common intestinal disease affecting susceptible pigs raised under various management systems around the world. Major developments in the understanding of PE and its causative agent,Lawsonia intracellularis, have occurred that have led to advances in the detection of this disease and methods to control and prevent it. Diagnostic tools that have improved overall detection and early onset of PE in pigs include various serological and molecular-based assays. Histological tests such as immunohistochemistry continue to be the gold standard in confirmingLawsonia-specific lesions in pigspost mortem. Despite extreme difficulties in isolatingL. intracellularis, innovations in the cultivation and the development of pure culture challenge models, have opened doors to better characterization of the pathogenesis of PE throughin vivoandin vitro L. intracellularis–host interactions. Advancements in molecular research such as the genetic sequencing of the entireLawsoniagenome have provided ways to identify various immunogens, metabolic pathways and methods for understanding the epidemiology of this organism. The determinations of immunological responsiveness in pigs to virulent and attenuated isolates ofL. intracellularisand identification of various immunogens have led to progress in vaccine development.

Characterization of in vitro and in vivo metabolic pathways of the investigational anticancer agent, 2‐methoxyestradiol

2007 ◽  
Vol 96 (7) ◽  
pp. 1821-1831 ◽  
Author(s):  
Nehal J. Lakhani ◽  
Alex Sparreboom ◽  
X.i.a. Xu ◽  
Timothy D. Veenstra ◽  
Jürgen Venitz ◽  
...  
Keyword(s):  
Metabolic Pathways ◽  
Anticancer Agent

scholarly journals Bacille Calmette-Guérin vaccine reprograms human neonatal lipid metabolism in vitro and in vivo

2021 ◽  
Author(s):  
Joann Diray-Arce ◽  
Asimenia Angelidou ◽  
Kristoffer Jarlov Jensen ◽  
Maria Giulia Conti ◽  
Rachel S. Kelly ◽  
...  
Keyword(s):  
Metabolic Pathways ◽  
Early Life ◽  
Mycobacterial Antigen ◽  
Bacille Calmette Guerin ◽  
Tlr Agonist ◽  
Induced Changes ◽  
Insight Into

SummaryVaccines have generally been developed with limited insight into their molecular impact. While systems vaccinology, including metabolomics, enables new characterization of vaccine mechanisms of action, these tools have yet to be applied to infants at high risk of infection and receive the most vaccines. Bacille Calmette-Guérin (BCG) protects infants against disseminated tuberculosis (TB) and TB-unrelated infections via incompletely understood mechanisms. We employed mass spectrometry-based metabolomics of blood plasma to profile BCG-induced infant responses in Guinea Bissau in vivo and the U.S. in vitro. BCG selectively altered plasma lipid pathways, including lysophospholipids. BCG-induced lysophosphatidylcholines (LPCs) correlated with both TLR agonist- and purified protein derivative (PPD, mycobacterial antigen)-induced blood cytokine production in vitro, raising the possibility that LPCs contribute to BCG immunogenicity. Analysis of an independent newborn cohort from The Gambia demonstrated shared vaccine-induced metabolites such as phospholipids and sphingolipids. BCG-induced changes to the plasma lipidome and LPCs may contribute to its immunogenicity and inform the discovery and development of early life vaccines.HighlightsNeonatal BCG immunization generates distinct metabolic shifts in vivo and in vitro across multiple independent cohorts.BCG induces prominent changes in concentrations of plasma lysophospholipids (LPLs)BCG induced changes in plasma lysophosphatidylcholines (LPCs) correlate with BCG effects on TLR agonist- and mycobacterial antigen-induced cytokine responses.Characterization of vaccine-induced changes in metabolism may define predictive signatures of vaccine responses and inform early life vaccine development.Abstract FigureGraphical abstract:BCG vaccination perturbs metabolic pathways in vivo and in vitro.Vaccines have traditionally been developed empirically, with limited insight into their impact on molecular pathways. Metabolomics provides a new approach to characterizing vaccine mechanisms but has not yet been applied to human newborns, who are at the highest risk of infection and receive the most vaccines. Bacille Calmette-Guérin (BCG) prevents disseminated mycobacterial disease in children and can induce broad protection to reduce mortality due to non-TB infections. Underlying mechanisms are incompletely characterized. Employing mass spectrometry-based metabolomics, we demonstrate that early BCG administration alters the human neonatal plasma metabolome, especially lipid metabolic pathways such as lysophosphatidylcholines (LPCs), both in vivo and in vitro. Plasma LPCs correlated with both innate TLR-mediated and PPD antigen-induced cytokine responses suggesting that BCG-induced lipids might contribute to the immunogenicity of this vaccine. Vaccine-induced metabolic changes may provide fresh insights into vaccine immunogenicity and inform the discovery and development of early life vaccines.

scholarly journals Characterization of an L-Ascorbate Catabolic Pathway with Unprecedented Enzymatic Transformations

2019 ◽  
Author(s):  
Tyler Stack ◽  
Katelyn Morrison ◽  
Thomas Dettmer ◽  
Brendan Wille ◽  
Chan Kim ◽  
...  
Keyword(s):  
Ralstonia Eutropha ◽  
Sequence Similarity ◽  
Catabolic Genes ◽  
Genes Encoding ◽  
Benzilic Acid ◽  
Amidohydrolase Superfamily ◽  
Sequence Similarity Networks

<p>L-Ascorbate (vitamin C) is ubiquitous in both our diet and the environment. <i>Ralstonia eutropha </i>H16 (<i>Cupriavidus necator </i>ATCC 17699) uses L-ascorbate as sole carbon source but lacks the genes encoding the known catabolic pathways. RNAseq identified eight candidate catabolic genes. Sequence similarity networks and genome neighborhood networks guided predictions for function of the encoded proteins; the predictions were confirmed by <i>in vitro</i> assays and <i>in vivo</i> growth phenotypes of gene deletion mutants. L-Ascorbate, a lactone, is oxidized and ring-opened by enzymes in the cytochrome b<sub>561</sub> and gluconolactonase families, respectively, to form 2,3-diketo-L-gulonate. A protein predicted to have a WD40-like fold catalyzes an unprecedented benzilic acid rearrangement involving migration of a carboxylate group to form 2-carboxy-L-lyxonolactone; the lactone is hydrolyzed by a member of the amidohydrolase superfamily to yield 2-carboxy-L-lyxonate. A member of the PdxA family of oxidative decarboxylases catalyzes a novel decarboxylation that uses NAD<sup>+</sup> catalytically. The product, L-lyxonate, is catabolized to alpha-ketoglutarate by a previously characterized pathway.</p>

Purification of the Antihemophilic Factor by Gel Filtration on Agarose

1969 ◽  
Vol 22 (03) ◽  
pp. 577-583 ◽  
Author(s):  
M.M.P Paulssen ◽  
A.C.M.G.B Wouterlood ◽  
H.L.M.A Scheffers
Keyword(s):  
Factor Viii ◽  
Plasma Proteins ◽  
Large Scale ◽  
Gel Filtration ◽  
Large Scale Preparation ◽  
Scale Preparation ◽  
Antihemophilic Factor

SummaryFactor VIII can be isolated from plasma proteins, including fibrinogen by chromatography on agarose. The best results were obtained with Sepharose 6B. Large scale preparation is also possible when cryoprecipitate is separated by chromatography. In most fractions containing factor VIII a turbidity is observed which may be due to the presence of chylomicrons.The purified factor VIII was active in vivo as well as in vitro.

A Comparison of the Effect of Decorsin and Two Disintegrins, Albolabrin and Eristostatin, on Platelet Function

1995 ◽  
Vol 74 (05) ◽  
pp. 1316-1322 ◽  
Author(s):  
Mary Ann McLane ◽  
Jagadeesh Gabbeta ◽  
A Koneti Rao ◽  
Lucia Beviglia ◽  
Robert A Lazarus ◽  
...  
Keyword(s):  
Platelet Aggregation ◽  
Platelet Function ◽  
Sequence Similarity ◽  
Platelet Aggregation Inhibitors ◽  
Antiplatelet Drug ◽  
Rgd Sequence ◽  
Fibrinogen Receptor ◽  
Activated Platelets

SummaryNaturally-occurring fibrinogen receptor antagonists and platelet aggregation inhibitors that are found in snake venom (disintegrins) and leeches share many common features, including an RGD sequence, high cysteine content, and low molecular weight. There are, however, significant selectivity and potency differences. We compared the effect of three proteins on platelet function: albolabrin, a 7.5 kDa disintegrin, eristostatin, a 5.4 kDa disintegrin in which part of the disintegrin domain is deleted, and decorsin, a 4.5 kDa non-disintegrin derived from the leech Macrobdella decora, which has very little sequence similarity with either disintegrin. Decorsin was about two times less potent than albolabrin and six times less potent than eristostatin in inhibiting ADP- induced human platelet aggregation. It had a different pattern of interaction with glycoprotein IIb/IIIa as compared to the two disintegrins. Decorsin bound with a low affinity to resting platelets (409 nM) and to ADP-activated platelets (270 nM), and with high affinity to thrombin- activated platelets (74 nM). At concentrations up to 685 nM, it did not cause expression of a ligand-induced binding site epitope on the (β3 subunit of the GPIIb/IIIa complex. It did not significantly inhibit isolated GPIIb/IIIa binding to immobilized von Willebrand Factor. At low doses (1.5-3.0 μg/mouse), decorsin protected mice against death from pulmonary thromboembolism, showing an effect similar to eristostatin. This suggested that decorsin is a much more potent inhibitor of platelet aggregation in vivo than in vitro, and it may have potential as an antiplatelet drug.

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