scholarly journals In silico analysis of phag-like protein in Ralstonia Euthropa H16, potentially involved in polyhydroxyalkanoates synthesis

2019 ◽  
Vol 15 (29) ◽  
pp. 55-64
Author(s):  
Melissa Uribe Acosta ◽  
Andrés Felipe Villa Restrepo
Keyword(s):  
Gene Deletion ◽  
De Novo ◽  
Ralstonia Eutropha ◽  
Carbon Sources ◽  
Model Organism ◽  
In Silico Analysis ◽  
De Novo Synthesis ◽  
Storage Material ◽  
Fas Pathway ◽  
Silico Analysis

Polyhydroxyalkanoates (PHA) are synthesised by bacteria as carbon storage material. The protein PhaG directs carbon from non-related carbon sources such as glycerol, metabolised through fatty acid de novo synthesis (FAS) pathway, with PHA synthesis. The gene that codifies for this protein has not yet been found in the genome of Ralstonia eutropha H16, a model organism. By bioinformatic comparison to already known PhaG proteins, a PhaG-like protein was found codified by gene H16_A0147 and presence of the gene was preliminary confirmed by PCR. This is the first study that shows the presence and characteristics of a PhaG-like protein in R. eutropha H16 and represents the first step for the identification of a connection between FAS and PHA pathways in this model bacterium. Further gene deletion and enzymatic activity studies are necessary to confirm this potential relationship, which could improve industrial PHA production and utilisation of agro-industrial residues such as glycerol.

scholarly journals 2,2’4,4’-Tetrabromodiphenyl Ether (PBDE-47) Modulates the Intracellular miRNA Profile, sEV Biogenesis and Their miRNA Cargo Exacerbating the LPS-Induced Pro-Inflammatory Response in THP-1 Macrophages

2021 ◽  
Vol 12 ◽  
Author(s):  
Valeria Longo ◽  
Alessandra Longo ◽  
Giorgia Adamo ◽  
Antonino Fiannaca ◽  
Sabrina Picciotto ◽  
...  
Keyword(s):  
Immune Response ◽  
Inflammatory Response ◽  
Innate Immune Response ◽  
De Novo ◽  
In Silico Analysis ◽  
Innate Immune ◽  
Macrophage Cell ◽  
Intracellular Expression ◽  
Different Levels ◽  
Silico Analysis

The 2,2’4,4’-tetrabromodiphenyl ether (PBDE-47) is one of the most prominent PBDE congeners detected in the environment and in animal and human tissues. Animal model experiments suggested the occurrence of PBDE-induced immunotoxicity leading to different outcomes and recently we demonstrated that this substance can impair macrophage and basophil activities. In this manuscript, we decided to further examine the effects induced by PBDE-47 treatment on innate immune response by looking at the intracellular expression profile of miRNAs as well as the biogenesis, cargo content and activity of human M(LPS) macrophage cell-derived small extracellular vesicles (sEVs). Microarray and in silico analysis demonstrated that PBDE-47 can induce some epigenetic effects in M(LPS) THP-1 cells modulating the expression of a set of intracellular miRNAs involved in biological pathways regulating the expression of estrogen-mediated signaling and immune responses with particular reference to M1/M2 differentiation. In addition to the cell-intrinsic modulation of intracellular miRNAs, we demonstrated that PBDE-47 could also interfere with the biogenesis of sEVs increasing their number and selecting a de novo population of sEVs. Moreover, PBDE-47 induced the overload of specific immune related miRNAs in PBDE-47 derived sEVs. Finally, culture experiments with naïve M(LPS) macrophages demonstrated that purified PBDE-47 derived sEVs can modulate macrophage immune response exacerbating the LPS-induced pro-inflammatory response inducing the overexpression of the IL-6 and the MMP9 genes. Data from this study demonstrated that PBDE-47 can perturb the innate immune response at different levels modulating the intracellular expression of miRNAs but also interfering with the biogenesis, cargo content and functional activity of M(LPS) macrophage cell-derived sEVs.

scholarly journals Conservation of the Prion Properties of Ure2p through Evolution

2003 ◽  
Vol 14 (8) ◽  
pp. 3449-3458 ◽  
Author(s):  
Agnès Baudin-Baillieu ◽  
Eric Fernandez-Bellot ◽  
Fabienne Reine ◽  
Eric Coissac ◽  
Christophe Cullin
Keyword(s):  
Functional Analysis ◽  
Candida Albicans ◽  
Gene Deletion ◽  
Yeast Species ◽  
Kluyveromyces Lactis ◽  
In Silico Analysis ◽  
Functional Domain ◽  
Extreme Situation ◽  
Homologous Genes ◽  
Silico Analysis

The yeast inheritable [URE3] element corresponds to a prion form of the nitrogen catabolism regulator Ure2p. We have isolated several orthologous URE2 genes in different yeast species: Saccharomyces paradoxus, S. uvarum, Kluyveromyces lactis, Candida albicans, and Schizosaccharomyces pombe. We show here by in silico analysis that the GST-like functional domain and the prion domain of the Ure2 proteins have diverged separately, the functional domain being more conserved through the evolution. The more extreme situation is found in the two S. pombe genes, in which the prion domain is absent. The functional analysis demonstrates that all the homologous genes except for the two S. pombe genes are able to complement the URE2 gene deletion in a S. cerevisiae strain. We show that in the two most closely related yeast species to S. cerevisiae, i.e., S. paradoxus and S. uvarum, the prion domains of the proteins have retained the capability to induce [URE3] in a S. cerevisiae strain. However, only the S. uvarum full-length Ure2p is able to behave as a prion. We also show that the prion inactivation mechanisms can be cross-transmitted between the S. cerevisiae and S. uvarum prions.

scholarly journals A Whole Germline BRCA2 Gene Deletion: How to Learn from CNV In Silico Analysis

2018 ◽  
Vol 19 (4) ◽  
pp. 961 ◽  
Author(s):  
Giovanni Scaglione ◽  
Paola Concolino ◽  
Maria De Bonis ◽  
Elisa De Paolis ◽  
Angelo Minucci ◽  
...  
Keyword(s):  
In Silico ◽  
Gene Deletion ◽  
Brca2 Gene ◽  
In Silico Analysis ◽  
Silico Analysis

scholarly journals Functional Prediction of Biological Profile During Eutrophication in Marine Environment

2022 ◽  
Vol 16 ◽  
pp. 117793222110639
Author(s):  
Yousra Sbaoui ◽  
Badreddine Nouadi ◽  
Abdelkarim Ezaouine ◽  
Mohamed Rida Salam ◽  
Mariame Elmessal ◽  
...  
Keyword(s):  
Marine Environment ◽  
Surface Waters ◽  
Algal Blooms ◽  
Model Organism ◽  
In Silico Analysis ◽  
Potential Candidate ◽  
Biological Profile ◽  
Driving Mechanisms ◽  
K 12 ◽  
Silico Analysis

In the marine environment, coastal nutrient pollution and algal blooms are increasing in many coral reefs and surface waters around the world, leading to higher concentrations of dissolved organic carbon (DOC), nitrogen (N), phosphate (P), and sulfur (S) compounds. The adaptation of the marine microbiota to this stress involves evolutionary processes through mutations that can provide selective phenotypes. The aim of this in silico analysis is to elucidate the potential candidate hub proteins, biological processes, and key metabolic pathways involved in the pathogenicity of bacterioplankton during excess of nutrients. The analysis was carried out on the model organism Escherichia coli K-12, by adopting an analysis pipeline consisting of a set of packages from the Cystoscape platform. The results obtained show that the metabolism of carbon and sugars generally are the 2 driving mechanisms for the expression of virulence factors.

DDRE-22. DISRUPTING REDOX BALANCE VIA THE TETRAHYDROBIOPTERIN PATHWAY IN GLIOBLASTOMA

2021 ◽  
Vol 23 (Supplement_6) ◽  
pp. vi79-vi79
Author(s):  
Kaysaw Tuy ◽  
Sajina GC ◽  
Wei Chen ◽  
David Harrison ◽  
John Aleman ◽  
...  
Keyword(s):  
Preliminary Data ◽  
De Novo ◽  
In Silico Analysis ◽  
Redox Balance ◽  
De Novo Synthesis ◽  
Tumor Initiating Cells ◽  
Recurrent Gliomas ◽  
Mitochondrial Ros ◽  
Therapeutic Opportunity ◽  
Approved Drugs

Abstract Aberrant redox statuses are observed in glioblastoma (GBM), and we previously identified GTP cyclohydrolase I (GCH1) to be a redox regulator upregulated in brain tumor initiating cells (BTICs). GCH1 is a rate-limiting enzyme in the de novo synthesis of tetrahydrobiopterin (BH4), a cofactor that produces catecholamine precursors and nitric oxide (NO) and, once used, becomes 7,8-dihydrobiopterin (BH2). Regeneration of BH2 into BH4 by dihydrofolate reductase (DHFR) helps to maintain proper BH4/BH2 ratios for redox balance. Although the BH4 pathway has traditionally been studied in the vasculature system for its regulation of NO, our previous work and that of others suggests the GCH1/BH4 pathway plays a critical redox role including in neoplastic cells. In silico analysis of primary and recurrent gliomas indicate high expression of BH4 related enzymes that correlated with worse patient survival in both primary and recurrent gliomas. The observed elevation of the BH4 pathway not only emphasizes its importance, but a therapeutic opportunity for improving survival in glioma patients. By repurposing FDA approved drugs known to cross the blood brain barrier and previously suggested as anti-glioma therapies, combining inhibitors for the de novo synthesis (sulfasalazine) and regeneration (pyrimethamine) of BH4 could prove to be an effective strategy for targeting the GCH1/BH4 through redox disruption. Preliminary data BTICs isolated from patient derived xenografts (PDXs) indicated reduced viability when treated with sulfasalazine (SASP) and pyrimethamine (PYR). Furthermore, we observed lower/depleted levels of BH4 relative to BH2 when BTICs were treated with SASP and PYR. Lastly, there is an increase in mitochondrial ROS upon SASP and PYR treatment, suggesting dysregulated redox states. Importantly, temozolomide resistant GBM cells remained sensitive to SASP and PYR. Taken together, our preliminary data suggests the plausibility of targeting the GCH1/BH4 pathway with SASP and PYR to disrupt redox balance in glioma through the depletion of BH4.

scholarly journals In-Depth In Silico Search for Cuttlefish (Sepia officinalis) Antimicrobial Peptides Following Bacterial Challenge of Haemocytes

Marine Drugs ◽  
2020 ◽  
Vol 18 (9) ◽  
pp. 439
Author(s):  
Louis Benoist ◽  
Baptiste Houyvet ◽  
Joël Henry ◽  
Erwan Corre ◽  
Bruno Zanuttini ◽  
...  
Keyword(s):  
Immune Response ◽  
Antimicrobial Peptides ◽  
In Silico ◽  
De Novo ◽  
In Silico Analysis ◽  
Sepia Officinalis ◽  
Vibrio Splendidus ◽  
Pattern Searches ◽  
Sequence Characteristics ◽  
Silico Analysis

Cuttlefish (Sepia officinalis) haemocytes are potential sources of antimicrobial peptides (AMPs). To study the immune response to Vibrio splendidus and identify new AMPs, an original approach was developed based on a differential transcriptomic study and an in-depth in silico analysis using multiple tools. Two de novo transcriptomes were retrieved from cuttlefish haemocytes following challenge by V. splendidus or not. A first analysis of the annotated transcripts revealed the presence of Toll/NF-κB pathway members, including newly identified factors such as So-TLR-h, So-IKK-h and So-Rel/NF-κB-h. Out of the eight Toll/NF-κB pathway members, seven were found up-regulated following V. splendidus challenge. Besides, immune factors involved in the immune response were also identified and up-regulated. However, no AMP was identified based on annotation or conserved pattern searches. We therefore performed an in-depth in silico analysis of unannotated transcripts based on differential expression and sequence characteristics, using several tools available like PepTraq, a homemade software program. Finally, five AMP candidates were synthesized. Among them, NF19, AV19 and GK28 displayed antibacterial activity against Gram-negative bacteria. Each peptide had a different spectrum of activity, notably against Vibrio species. GK28—the most active peptide—was not haemolytic, whereas NF19 and AV19 were haemolytic at concentrations between 50 and 100 µM, 5 to 10 times higher than their minimum inhibitory concentration.

scholarly journals Untargeted metabolomics analysis of Ralstonia eutropha during plant oil cultivations reveals the presence of a fucose salvage pathway

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Björn Gutschmann ◽  
Martina C. E. Bock ◽  
Stefan Jahns ◽  
Peter Neubauer ◽  
Christopher J. Brigham ◽  
...  
Keyword(s):  
De Novo ◽  
Ralstonia Eutropha ◽  
Wild Type ◽  
Salvage Pathway ◽  
De Novo Synthesis ◽  
Plant Oil ◽  
Microbial Physiology ◽  
Medium Chain Length ◽  
Metabolic States ◽  
Metabolomic Study

AbstractProcess engineering of biotechnological productions can benefit greatly from comprehensive analysis of microbial physiology and metabolism. Ralstonia eutropha (syn. Cupriavidus necator) is one of the best studied organisms for the synthesis of biodegradable polyhydroxyalkanoate (PHA). A comprehensive metabolomic study during bioreactor cultivations with the wild-type (H16) and an engineered (Re2058/pCB113) R. eutropha strain for short- and or medium-chain-length PHA synthesis has been carried out. PHA production from plant oil was triggered through nitrogen limitation. Sample quenching allowed to conserve the metabolic states of the cells for subsequent untargeted metabolomic analysis, which consisted of GC–MS and LC–MS analysis. Multivariate data analysis resulted in identification of significant changes in concentrations of oxidative stress-related metabolites and a subsequent accumulation of antioxidative compounds. Moreover, metabolites involved in the de novo synthesis of GDP-l-fucose as well as the fucose salvage pathway were identified. The related formation of fucose-containing exopolysaccharides potentially supports the emulsion-based growth of R. eutropha on plant oils.

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