scholarly journals Cofactors revisited – predicting the impact of flavoprotein-related diseases on a genome scale

2018 ◽  
Author(s):  
Agnieszka B. Wegrzyn ◽  
Sarah Stolle ◽  
Rienk A. Rienksma ◽  
Vítor A. P. Martins dos Santos ◽  
Barbara M. Bakker ◽  
...  
Keyword(s):  
Degrees Of Freedom ◽  
Screening Tests ◽  
Flavin Mononucleotide ◽  
A Genome ◽  
Genes Encoding ◽  
Functional Consequences ◽  
Biomarker Research ◽  
Genome Scale ◽  
The Impact ◽  
Computational Predictions

ABSTRACTFlavin adenine dinucleotide (FAD) and its precursor flavin mononucleotide (FMN) are redox cofactors that are required for the activity of more than hundred human enzymes. Mutations in the genes encoding these proteins cause severe phenotypes, including a lack of energy supply and accumulation of toxic intermediates. Ideally, patients should be diagnosed before they show symptoms so that treatment and/or preventive care can start immediately. This can be achieved by standardized newborn screening tests. However, many of the flavin-related diseases lack appropriate biomarker profiles. Genome-scale metabolic models can aid in biomarker research by predicting altered profiles of potential biomarkers. Unfortunately, current models, including the most recent human metabolic reconstructions Recon and HMR, typically treat enzyme-bound flavins incorrectly as free metabolites. This in turn leads to artificial degrees of freedom in pathways that are strictly coupled. Here, we present a reconstruction of human metabolism with a curated and extended flavoproteome. To illustrate the functional consequences, we show that simulations with the curated model – unlike simulations with earlier Recon versions - correctly predict the metabolic impact of multiple-acyl-CoA-dehydrogenase deficiency as well as of systemic flavin-depletion. Moreover, simulations with the new model allowed us to identify a larger number of biomarkers in flavoproteome-related diseases, without loss of accuracy. We conclude that adequate inclusion of cofactors in constraint-based modelling contributes to higher precision in computational predictions.

scholarly journals Arabidopsis Genes Essential for Seedling Viability: Isolation of Insertional Mutants and Molecular Cloning

Genetics ◽  
2001 ◽  
Vol 159 (4) ◽  
pp. 1765-1778
Author(s):  
Gregory J Budziszewski ◽  
Sharon Potter Lewis ◽  
Lyn Wegrich Glover ◽  
Jennifer Reineke ◽  
Gary Jones ◽  
...  
Keyword(s):  
Large Scale ◽  
Protein Translocation ◽  
Gene Families ◽  
Mutant Phenotype ◽  
Lethal Mutant ◽  
A Genome ◽  
Genes Encoding ◽  
High Level ◽  
Mutant Lines ◽  
Genome Scale

Abstract We have undertaken a large-scale genetic screen to identify genes with a seedling-lethal mutant phenotype. From screening ~38,000 insertional mutant lines, we identified >500 seedling-lethal mutants, completed cosegregation analysis of the insertion and the lethal phenotype for >200 mutants, molecularly characterized 54 mutants, and provided a detailed description for 22 of them. Most of the seedling-lethal mutants seem to affect chloroplast function because they display altered pigmentation and affect genes encoding proteins predicted to have chloroplast localization. Although a high level of functional redundancy in Arabidopsis might be expected because 65% of genes are members of gene families, we found that 41% of the essential genes found in this study are members of Arabidopsis gene families. In addition, we isolated several interesting classes of mutants and genes. We found three mutants in the recently discovered nonmevalonate isoprenoid biosynthetic pathway and mutants disrupting genes similar to Tic40 and tatC, which are likely to be involved in chloroplast protein translocation. Finally, we directly compared T-DNA and Ac/Ds transposon mutagenesis methods in Arabidopsis on a genome scale. In each population, we found only about one-third of the insertion mutations cosegregated with a mutant phenotype.

scholarly journals Cofactors revisited – Predicting the impact of flavoprotein-related diseases on a genome scale

2019 ◽  
Vol 1865 (2) ◽  
pp. 360-370 ◽  
Author(s):  
Agnieszka B. Wegrzyn ◽  
Sarah Stolle ◽  
Rienk A. Rienksma ◽  
Vítor A.P. Martins dos Santos ◽  
Barbara M. Bakker ◽  
...  
Keyword(s):  
A Genome ◽  
Genome Scale ◽  
The Impact

scholarly journals A genome-wide analysis of Escherichia coli responses to fosfomycin using TraDIS-Xpress reveals novel roles for phosphonate degradation and phosphate transport systems

2020 ◽  
Vol 75 (11) ◽  
pp. 3144-3151 ◽  
Author(s):  
A Keith Turner ◽  
Muhammad Yasir ◽  
Sarah Bastkowski ◽  
Andrea Telatin ◽  
Andrew J Page ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Sugar Metabolism ◽  
Phosphate Transport ◽  
Transport Systems ◽  
Loss Of Function ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Genes Encoding ◽  
The Impact

Abstract Background Fosfomycin is an antibiotic that has seen a revival in use due to its unique mechanism of action and efficacy against isolates resistant to many other antibiotics. In Escherichia coli, fosfomycin often selects for loss-of-function mutations within the genes encoding the sugar importers, GlpT and UhpT. There has, however, not been a genome-wide analysis of the basis for fosfomycin susceptibility reported to date. Methods Here we used TraDIS-Xpress, a high-density transposon mutagenesis approach, to assay the role of all genes in E. coli involved in fosfomycin susceptibility. Results The data confirmed known fosfomycin susceptibility mechanisms and identified new ones. The assay was able to identify domains within proteins of importance and revealed essential genes with roles in fosfomycin susceptibility based on expression changes. Novel mechanisms of fosfomycin susceptibility that were identified included those involved in glucose metabolism and phosphonate catabolism (phnC-M), and the phosphate importer, PstSACB. The impact of these genes on fosfomycin susceptibility was validated by measuring the susceptibility of defined inactivation mutants. Conclusions This work reveals a wider set of genes that contribute to fosfomycin susceptibility, including core sugar metabolism genes and two systems involved in phosphate uptake and metabolism previously unrecognized as having a role in fosfomycin susceptibility.

scholarly journals Genome-scale phylogenetic analysis finds extensive gene transfer among fungi

2015 ◽  
Vol 370 (1678) ◽  
pp. 20140335 ◽  
Author(s):  
Gergely J. Szöllősi ◽  
Adrián Arellano Davín ◽  
Eric Tannier ◽  
Vincent Daubin ◽  
Bastien Boussau
Keyword(s):  
Gene Transfer ◽  
Gene Tree ◽  
Gene Duplications ◽  
Compelling Evidence ◽  
Gene Trees ◽  
A Genome ◽  
Genome Scale ◽  
Gains And Losses ◽  
The Impact

Although the role of lateral gene transfer is well recognized in the evolution of bacteria, it is generally assumed that it has had less influence among eukaryotes. To explore this hypothesis, we compare the dynamics of genome evolution in two groups of organisms: cyanobacteria and fungi. Ancestral genomes are inferred in both clades using two types of methods: first, Count , a gene tree unaware method that models gene duplications, gains and losses to explain the observed numbers of genes present in a genome; second, ALE, a more recent gene tree-aware method that reconciles gene trees with a species tree using a model of gene duplication, loss and transfer. We compare their merits and their ability to quantify the role of transfers, and assess the impact of taxonomic sampling on their inferences. We present what we believe is compelling evidence that gene transfer plays a significant role in the evolution of fungi.

scholarly journals Host–Receptor Post-Translational Modifications Refine Staphylococcal Leukocidin Cytotoxicity

Toxins ◽  
2020 ◽  
Vol 12 (2) ◽  
pp. 106 ◽  
Author(s):  
Angelino T. Tromp ◽  
Michiel Van Gent ◽  
Joris P. Jansen ◽  
Lisette M. Scheepmaker ◽  
Anneroos Velthuizen ◽  
...  
Keyword(s):  
Ectopic Expression ◽  
Dependent Manner ◽  
Post Translational Modification ◽  
Toxin Resistance ◽  
Additional Layer ◽  
A Genome ◽  
Genes Encoding ◽  
Library Screen ◽  
Structural Architecture ◽  
The Impact

Staphylococcal bi-component pore-forming toxins, also known as leukocidins, target and lyse human phagocytes in a receptor-dependent manner. S-components of the leukocidins Panton-Valentine leukocidin (PVL), γ-haemolysin AB (HlgAB) and CB (HlgCB), and leukocidin ED (LukED) specifically employ receptors that belong to the class of G-protein coupled receptors (GPCRs). Although these receptors share a common structural architecture, little is known about the conserved characteristics of the interaction between leukocidins and GPCRs. In this study, we investigated host cellular pathways contributing to susceptibility towards S. aureus leukocidin cytotoxicity. We performed a genome-wide CRISPR/Cas9 library screen for toxin-resistance in U937 cells sensitized to leukocidins by ectopic expression of different GPCRs. Our screen identifies post-translational modification (PTM) pathways involved in the sulfation and sialylation of the leukocidin-receptors. Subsequent validation experiments show differences in the impact of PTM moieties on leukocidin toxicity, highlighting an additional layer of refinement and divergence in the staphylococcal host-pathogen interface. Leukocidin receptors may serve as targets for anti-staphylococcal interventions and understanding toxin-receptor interactions will facilitate the development of innovative therapeutics. Variations in the genes encoding PTM pathways could provide insight into observed differences in susceptibility of humans to infections with S. aureus.

Mechanically-Tunable Quantum Interference in Ferrocene-Based Single-Molecule Junctions

2020 ◽  
Author(s):  
María Camarasa-Gómez ◽  
Daniel Hernangómez-Pérez ◽  
Michael S. Inkpen ◽  
Giacomo Lovat ◽  
E-Dean Fung ◽  
...  
Keyword(s):  
Single Molecule ◽  
Quantum Interference ◽  
Degrees Of Freedom ◽  
Building Blocks ◽  
Ferrocene Derivative ◽  
Single Molecule Junctions ◽  
Molecule Junction ◽  
Single Molecule Junction ◽  
The Impact ◽  
D Orbitals

Ferrocenes are ubiquitous organometallic building blocks that comprise a Fe atom sandwiched between two cyclopentadienyl (Cp) rings that rotate freely at room temperature. Of widespread interest in fundamental studies and real-world applications, they have also attracted<br>some interest as functional elements of molecular-scale devices. Here we investigate the impact of<br>the configurational degrees of freedom of a ferrocene derivative on its single-molecule junction<br>conductance. Measurements indicate that the conductance of the ferrocene derivative, which is<br>suppressed by two orders of magnitude as compared to a fully conjugated analog, can be modulated<br>by altering the junction configuration. Ab initio transport calculations show that the low conductance is a consequence of destructive quantum interference effects that arise from the hybridization of metal-based d-orbitals and the ligand-based π-system. By rotating the Cp rings, the hybridization, and thus the quantum interference, can be mechanically controlled, resulting in a conductance modulation that is seen experimentally.<br>

Effects of Transport Medium Composition on in vitro Drug Permeation across Excised Pig Intestinal Tissue

2020 ◽  
Vol 10 ◽  
Author(s):  
Bianca Peterson ◽  
Henrico Heystek ◽  
Josias H. Hamman ◽  
Johan D. Steyn
Keyword(s):  
Medium Composition ◽  
Screening Tests ◽  
Intestinal Tissue ◽  
Predictive Values ◽  
Transport Medium ◽  
Intestinal Fluids ◽  
Lower Permeability ◽  
The Impact ◽  
Simulated Intestinal Fluids

Background:: Knowledge of the permeation characteristics of new chemical entities across biological membranes is essential to drug research and development. Transport medium composition may affect the absorption of compounds during in vitro drug transport testing. To preserve the predictive values of screening tests, the possible influence of transport media on the solubility of model drugs, and on the activities of tight junctions and efflux transporter proteins (e.g. P-glycoprotein) must be known. Objective:: The aim of this study was to compare the impact of different transport media on the bi-directional transport of standard compounds, selected from the four classes of the Biopharmaceutical Classification System (BCS), across excised pig intestinal tissue. Methods:: The Sweetana-Grass diffusion apparatus was used for the transport studies. Krebs-Ringer bicarbonate (KRB) buffer and simulated intestinal fluids in the fed (FeSSIF) and fasted (FaSSIF) states were used as the three transport media, while the chosen compounds were abacavir (BCS class 1), dapsone (BCS class 2), lamivudine (BCS class 3) and furosemide (BCS class 4). Results:: Abacavir exhibited lower permeability in both the simulated intestinal fluids than in the KRB buffer. Dapsone showed similar permeability in all media. Lamivudine exhibited lower permeability in FaSSIF than in the other two media. Furosemide exhibited improved transport with pronounced efflux in FaSSIF. Conclusion:: Different permeation behaviors were observed for the selected drugs in the respective media, which may have resulted from their different physico-chemical properties, as well as from the effects that dissimilar transport media components had on excised pig intestinal tissue.

scholarly journals The halo model as a versatile tool to predict intrinsic alignments

2020 ◽  
Author(s):  
Maria Cristina Fortuna ◽  
Henk Hoekstra ◽  
Benjamin Joachimi ◽  
Harry Johnston ◽  
Nora Elisa Chisari ◽  
...  
Keyword(s):  
Degrees Of Freedom ◽  
Power Spectra ◽  
Stage Iv ◽  
Stage Iii ◽  
Radial Dependence ◽  
Additional Parameter ◽  
Small Scales ◽  
Cosmic Shear ◽  
Galaxy Populations ◽  
The Impact

Abstract Intrinsic alignments (IAs) of galaxies are an important contaminant for cosmic shear studies, but the modelling is complicated by the dependence of the signal on the source galaxy sample. In this paper, we use the halo model formalism to capture this diversity and examine its implications for Stage-III and Stage-IV cosmic shear surveys. We account for the different IA signatures at large and small scales, as well for the different contributions from central/satellite and red/blue galaxies, and we use realistic mocks to account for the characteristics of the galaxy populations as a function of redshift. We inform our model using the most recent observational findings: we include a luminosity dependence at both large and small scales and a radial dependence of the signal within the halo. We predict the impact of the total IA signal on the lensing angular power spectra, including the current uncertainties from the IA best-fits to illustrate the range of possible impact on the lensing signal: the lack of constraints for fainter galaxies is the main source of uncertainty for our predictions of the IA signal. We investigate how well effective models with limited degrees of freedom can account for the complexity of the IA signal. Although these lead to negligible biases for Stage-III surveys, we find that, for Stage-IV surveys, it is essential to at least include an additional parameter to capture the redshift dependence.

scholarly journals Pathogenic Determinants of the Mycobacterium kansasii Complex: An Unsuspected Role for Distributive Conjugal Transfer

2021 ◽  
Vol 9 (2) ◽  
pp. 348
Author(s):  
Florian Tagini ◽  
Trestan Pillonel ◽  
Claire Bertelli ◽  
Katia Jaton ◽  
Gilbert Greub
Keyword(s):  
Genomic Analysis ◽  
Comparative Genomic ◽  
Mycobacterium Kansasii ◽  
Type Vii Secretion ◽  
A Genome ◽  
Genes Encoding ◽  
Associated Proteins ◽  
Immunosuppressed Patients ◽  
Type Vii Secretion System ◽  
Clinical Records

The Mycobacterium kansasii species comprises six subtypes that were recently classified into six closely related species; Mycobacterium kansasii (formerly M. kansasii subtype 1), Mycobacterium persicum (subtype 2), Mycobacterium pseudokansasii (subtype 3), Mycobacterium ostraviense (subtype 4), Mycobacterium innocens (subtype 5) and Mycobacterium attenuatum (subtype 6). Together with Mycobacterium gastri, they form the M. kansasii complex. M. kansasii is the most frequent and most pathogenic species of the complex. M. persicum is classically associated with diseases in immunosuppressed patients, and the other species are mostly colonizers, and are only very rarely reported in ill patients. Comparative genomics was used to assess the genetic determinants leading to the pathogenicity of members of the M. kansasii complex. The genomes of 51 isolates collected from patients with and without disease were sequenced and compared with 24 publicly available genomes. The pathogenicity of each isolate was determined based on the clinical records or public metadata. A comparative genomic analysis showed that all M. persicum, M. ostraviense, M innocens and M. gastri isolates lacked the ESX-1-associated EspACD locus that is thought to play a crucial role in the pathogenicity of M. tuberculosis and other non-tuberculous mycobacteria. Furthermore, M. kansasii was the only species exhibiting a 25-Kb-large genomic island encoding for 17 type-VII secretion system-associated proteins. Finally, a genome-wide association analysis revealed that two consecutive genes encoding a hemerythrin-like protein and a nitroreductase-like protein were significantly associated with pathogenicity. These two genes may be involved in the resistance to reactive oxygen and nitrogen species, a required mechanism for the intracellular survival of bacteria. Three non-pathogenic M. kansasii lacked these genes likely due to two distinct distributive conjugal transfers (DCTs) between M. attenuatum and M. kansasii, and one DCT between M. persicum and M. kansasii. To our knowledge, this is the first study linking DCT to reduced pathogenicity.

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