scholarly journals In silico identification of GPI-anchored proteins in Paracoccidioides

2018 ◽  
Author(s):  
L.R. Basso ◽  
R.A. Gonçales ◽  
E.J.R Vasconcelos ◽  
T.F. Reis ◽  
P. C. Ruy ◽  
...  
Keyword(s):  
Cell Wall ◽  
In Silico ◽  
Glycoside Hydrolases ◽  
Cellular Mechanisms ◽  
Dimorphic Fungi ◽  
A Genome ◽  
Paracoccidioides Spp ◽  
Gpi Proteins ◽  
Eukaryotic Organisms ◽  
Prediction Approach

ABSTRACTGlycosylphosphatidylinositol-anchored proteins (GPI-proteins) are widely found in eukaryotic organisms. In fungi, GPI-proteins are thought to be involved in diverse cellular mechanisms such as cell wall biosynthesis and cell wall remodeling, adhesion, antigenicity, and virulence. The conserved structural domains of GPI-protein allow the utilization ofin silicoprediction approach to identify this class of proteins using a genome-wide analysis. We used different previously characterized algorithms to search for genes that encode predicted GPI-proteins in the genome ofP. brasiliensis and P. lutzii, thermal dimorphic fungi that causes paracoccidioidomycosis (PCM). By using these methods, 98 GPI-proteins were found inP. brasiliensiswith orthologs inP. lutzii. A series of 28 GPI-proteins were classified in functional categories (such as glycoside hydrolases, chitin-processing proteins, and proteins involved in the biogenesis of the cell wall). Furthermore, 70 GPI-proteins exhibited homology with hypothetical conserved proteins of unknown function. These data will be an important resource for the future analysis of GPI-proteins inParacoccidioides spp.

Paracoccin overexpression in Paracoccidioides brasiliensis enhances fungal virulence by remodeling chitin properties of the cell wall

2020 ◽  
Author(s):  
Relber Aguiar Gonçales ◽  
Rafael Ricci-Azevedo ◽  
Vanessa C S Vieira ◽  
Fabrício F Fernandes ◽  
Sandra M de O Thomaz ◽  
...  
Keyword(s):  
Cell Wall ◽  
Paracoccidioides Brasiliensis ◽  
Chitinase Activity ◽  
Growth Media ◽  
Lung Pathology ◽  
Dimorphic Fungi ◽  
Fungal Virulence ◽  
Paracoccidioides Spp ◽  
Cell Growth And Viability ◽  
Etiological Agents

Abstract Background The thermo-dimorphic fungi Paracoccidioides spp. are the etiological agents of paracoccidioidomycosis. Although poorly studied, paracoccin (PCN) from P. brasiliensis has been shown to harbor lectinic, enzymatic, and immunomodulatory properties that impact disease development. Methods Mutants of P. brasiliensis overexpressing PCN (ov-PCN) were constructed by Agrobacterium tumefaciens-mediated transformation. Ov-PCN strains were analyzed and inoculated intranasally or intravenously to mice. Fungal burden, lung pathology, and survival were monitored to evaluate virulence. Electron microscopy was used to evaluate the size of chito-oligomer particles released by ov-PCN or wild-type strains to growth media. Results ov-PCN strains revealed no differences in cell growth and viability, although PCN overexpression favored cell separation, chitin processing that results in the release of smaller chito-oligomer particles, and enhanced virulence. Our data show that PCN triggers a critical effect in the cell wall biogenesis through the chitinase activity resulting from overexpression of PCN. As such, PCN overexpression aggravates the disease caused by P. brasiliensis. Conclusions Our data is consistent with a model in which PCN modulates the cell wall architecture via its chitinase activity. These findings highlight the potential for exploiting PCN function in future therapeutic approaches.

In silico identification of glycosylphosphatidylinositol-anchored proteins in Paracoccidioides spp.

2021 ◽  
Author(s):  
Relber A Gonçales ◽  
Ayda LM Salamanca ◽  
Luiz RB Júnior ◽  
Kleber SF e Silva ◽  
Elton JR de Vasconcelos ◽  
...  
Keyword(s):  
Cell Wall ◽  
In Silico ◽  
Paracoccidioides Brasiliensis ◽  
In Silico Analysis ◽  
Diagnostic Tools ◽  
Future Research ◽  
Immunological Tests ◽  
Paracoccidioides Spp ◽  
In Silico Identification ◽  
In Silico Analyses

Aim: To predict glycosylphosphatidylinositol (GPI)-anchored proteins in the genome of Paracoccidioides brasiliensis and Paracoccidioides lutzii. Materials & methods: Five different bioinformatics tools were used for predicting GPI-anchored proteins; we considered as GPI-anchored proteins those detected by at least two in silico analysis methods. We also performed the proteomic analysis of P. brasiliensis cell wall by mass spectrometry. Results: Hundred GPI-anchored proteins were predicted in P. brasiliensis and P. lutzii genomes. A series of 57 proteins were classified in functional categories and 43 conserved proteins were reported with unknown functions. Four proteins identified by in silico analyses were also identified in the cell wall proteome. Conclusion: The data obtained in this study are important resources for future research of GPI-anchored proteins in Paracoccidioides spp. to identify targets for new diagnostic tools, drugs and immunological tests.

scholarly journals Interacting with Hemoglobin: Paracoccidioides spp. Recruits hsp30 on Its Cell Surface for Enhanced Ability to Use This Iron Source

2021 ◽  
Vol 7 (1) ◽  
pp. 21
Author(s):  
Aparecido Ferreira de Souza ◽  
Mariana Vieira Tomazett ◽  
Kleber Santiago Freitas e Silva ◽  
Juliana Santana de Curcio ◽  
Christie Ataides Pereira ◽  
...  
Keyword(s):  
Cell Wall ◽  
Protein Expression ◽  
Paracoccidioides Brasiliensis ◽  
Severe Illness ◽  
Primary Role ◽  
Dimorphic Fungi ◽  
Proteomic Data ◽  
Hemoglobin Binding ◽  
Paracoccidioides Spp ◽  
Essential Nutrient

Paracoccidioides spp. are thermally dimorphic fungi that cause paracoccidioidomycosis and can affect both immunocompetent and immunocompromised individuals. The infection can lead to moderate or severe illness and death. Paracoccidioides spp. undergo micronutrients deprivation within the host, including iron. To overcome such cellular stress, this genus of fungi responds in multiple ways, such as the utilization of hemoglobin. A glycosylphosphatidylinositol (GPI)-anchored fungal receptor, Rbt5, has the primary role of acquiring the essential nutrient iron from hemoglobin. Conversely, it is not clear if additional proteins participate in the process of using hemoglobin by the fungus. Therefore, in order to investigate changes in the proteomic level of P. lutzii cell wall, we deprived the fungus of iron and then treated those cells with hemoglobin. Deprived iron cells were used as control. Next, we performed cell wall fractionation and the obtained proteins were submitted to nanoUPLC-MSE. Protein expression levels of the cell wall F1 fraction of cells exposed to hemoglobin were compared with the protein expression of the cell wall F1 fraction of iron-deprived cells. Our results showed that P. lutzii exposure to hemoglobin increased the level of adhesins expression by the fungus, according to the proteomic data. We confirmed that the exposure of the fungus to hemoglobin increased its ability to adhere to macrophages by flow cytometry. In addition, we found that HSP30 of P. lutzii is a novel hemoglobin-binding protein and a possible heme oxygenase. In order to investigate the importance of HSP30 in the Paracoccidioides genus, we developed a Paracoccidioides brasiliensis knockdown strain of HSP30 via Agrobacterium tumefaciens-mediated transformation and demonstrated that silencing this gene decreases the ability of P. brasiliensis to use hemoglobin as a nutrient source. Additional studies are needed to establish HSP30 as a virulence factor, which can support the development of new therapeutic and/or diagnostic approaches.

scholarly journals Evaluation of a Genome-ScaleIn SilicoMetabolic Model for Geobacter metallireducens by Using Proteomic Data from a Field Biostimulation Experiment

2012 ◽  
Vol 78 (24) ◽  
pp. 8735-8742 ◽  
Author(s):  
Yilin Fang ◽  
Michael J. Wilkins ◽  
Steven B. Yabusaki ◽  
Mary S. Lipton ◽  
Philip E. Long
Keyword(s):  
Proteomic Analysis ◽  
In Silico ◽  
Field Experiments ◽  
Metabolic Model ◽  
Geobacter Metallireducens ◽  
Content Type ◽  
Proteomic Data ◽  
Subsurface Environment ◽  
A Genome ◽  
Genome Scale

ABSTRACTAccurately predicting the interactions between microbial metabolism and the physical subsurface environment is necessary to enhance subsurface energy development, soil and groundwater cleanup, and carbon management. This study was an initial attempt to confirm the metabolic functional roles within anin silicomodel using environmental proteomic data collected during field experiments. Shotgun global proteomics data collected during a subsurface biostimulation experiment were used to validate a genome-scale metabolic model ofGeobacter metallireducens—specifically, the ability of the metabolic model to predict metal reduction, biomass yield, and growth rate under dynamic field conditions. The constraint-basedin silicomodelof G. metallireducensrelates an annotated genome sequence to the physiological functions with 697 reactions controlled by 747 enzyme-coding genes. Proteomic analysis showed that 180 of the 637G. metallireducensproteins detected during the 2008 experiment were associated with specific metabolic reactions in thein silicomodel. When the field-calibrated Fe(III) terminal electron acceptor process reaction in a reactive transport model for the field experiments was replaced with the genome-scale model, the model predicted that the largest metabolic fluxes through thein silicomodel reactions generally correspond to the highest abundances of proteins that catalyze those reactions. Central metabolism predicted by the model agrees well with protein abundance profiles inferred from proteomic analysis. Model discrepancies with the proteomic data, such as the relatively low abundances of proteins associated with amino acid transport and metabolism, revealed pathways or flux constraints in thein silicomodel that could be updated to more accurately predict metabolic processes that occur in the subsurface environment.

scholarly journals A genome-scale metabolic model of Saccharomyces cerevisiae that integrates expression constraints and reaction thermodynamics

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Omid Oftadeh ◽  
Pierre Salvy ◽  
Maria Masid ◽  
Maxime Curvat ◽  
Ljubisa Miskovic ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Expression System ◽  
Biomass Composition ◽  
Industrial Biotechnology ◽  
Overflow Metabolism ◽  
Cellular Expression ◽  
A Genome ◽  
Wide Range ◽  
Eukaryotic Organisms ◽  
Genome Scale

AbstractEukaryotic organisms play an important role in industrial biotechnology, from the production of fuels and commodity chemicals to therapeutic proteins. To optimize these industrial systems, a mathematical approach can be used to integrate the description of multiple biological networks into a single model for cell analysis and engineering. One of the most accurate models of biological systems include Expression and Thermodynamics FLux (ETFL), which efficiently integrates RNA and protein synthesis with traditional genome-scale metabolic models. However, ETFL is so far only applicable for E. coli. To adapt this model for Saccharomyces cerevisiae, we developed yETFL, in which we augmented the original formulation with additional considerations for biomass composition, the compartmentalized cellular expression system, and the energetic costs of biological processes. We demonstrated the ability of yETFL to predict maximum growth rate, essential genes, and the phenotype of overflow metabolism. We envision that the presented formulation can be extended to a wide range of eukaryotic organisms to the benefit of academic and industrial research.

scholarly journals In silico and functional characterization of the promoter of a Eucalyptussecondary cell wall associated cellulose synthase gene (EgCesA1)

2011 ◽  
Vol 5 (S7) ◽  
Author(s):  
Nicky Creux ◽  
Minique De Castro ◽  
Martin Ranik ◽  
Antanas Spokevicius ◽  
Gerd Bossinger ◽  
...  
Keyword(s):  
Cell Wall ◽  
In Silico ◽  
Functional Characterization ◽  
Cellulose Synthase ◽  
Cellulose Synthase Gene

scholarly journals Mecanismos de tolerancia a elementos potencialmente tóxicos en plantas

2017 ◽  
pp. 53 ◽  
Author(s):  
Daniel González-Mendoza ◽  
Omar Zapata-Pérez
Keyword(s):  
Heavy Metals ◽  
Cell Wall ◽  
Plasma Membrane ◽  
Toxic Elements ◽  
Potentially Toxic Elements ◽  
Free Proline ◽  
Potentially Toxic Metals ◽  
Cellular Mechanisms ◽  
Mycorrhizal Associations ◽  
Broad Overview

Plants possess a wide array of potential cellular mechanisms that may be involved in the tolerance to potentially toxic elements. These mechanisms include mycorrhizal associations, heavy metals binding to cell wall, precipitation by extracellular exudates; reduction in uptake or efflux pumping of metals at the plasma membrane, chelation of metals in the cytosol by peptides such as phytochelatins, metallothionein, histidina free, proline free , and the compartmentation of metals in the vacuole by tono-plast- located transporters. This review provides a broad overview of the evidence of the involvement of each mechanism in plants' tolerance to potentially toxic metals.

scholarly journals eMED-DNA: An in silico operating system for clinical medical data storage within the human genome

2019 ◽  
Author(s):  
Md. Jakaria ◽  
Kowshika Sarker ◽  
Mostofa Rafid Uddin ◽  
Md. Mohaiminul Islam ◽  
Trisha Das ◽  
...  
Keyword(s):  
Operating System ◽  
Clinical Practice ◽  
Data Storage ◽  
Real World ◽  
In Silico ◽  
Clinical Medicine ◽  
Genomic Medicine ◽  
Integrative System ◽  
A Genome ◽  
Storage Technologies

AbstractThe propitious developments in molecular biology and next generation sequencing have enabled the possibility for DNA storage technologies. However, the full application and power of our genomic revolution have not been fully utilized in clinical medicine given a lack of transition from research to real world clinical practice. This has identified an increasing need for an operating system which allows for the transition from research to clinical use. We present eMED-DNA, an in silico operating system for archiving and managing all forms of electronic health records (EHRs) within one’s own copy of the sequenced genome to aid in the application and integration of genomic medicine within real world clinical practice. We incorporated an efficient and sophisticated in-DNA file management system for the lossless management of EHRs within a genome. This represents the first in silico integrative system which would bring closer the utopian ideal for integrating genotypic data with phenotypic clinical data for future medical practice.

scholarly journals A family of cell wall transglutaminases is essential for appressorium development and pathogenicity in Phytophthora infestans

2021 ◽  
Author(s):  
Maja Brus-Szkalej ◽  
Christian B. Andersen ◽  
Ramesh R. Vetukuri ◽  
Laura J. Grenville-Briggs Didymus
Keyword(s):  
Cell Wall ◽  
Phytophthora Infestans ◽  
Sequence Similarity ◽  
Turgor Pressure ◽  
Intermediate Phenotype ◽  
Entire Family ◽  
Drug Concentrations ◽  
Lower Drug ◽  
Chemical Inhibition ◽  
Eukaryotic Organisms

Transglutaminases (TGases) are enzymes highly conserved among prokaryotic and eukaryotic organisms, where their role is to catalyse protein cross-linking. One of the putative TGases of Phytophthora infestans has previously been shown to be localised to the cell wall. Based on sequence similarity we were able to identify six more genes annotated as putative TGases and show that these seven genes group together in phylogenetic analysis. All of the seven proteins are predicted to contain transmembrane helices and both a TGase domain and a MANSC domain, the latter of which was previously shown to play a role in protein stability. Chemical inhibition of transglutaminase activity and silencing of the entire family of the putative cell wall TGases are both lethal to P. infestans indicating the importance of these proteins in cell wall formation and stability. The intermediate phenotype obtained with lower drug concentrations and less efficient silencing displays a number of deformations to germ tubes and appressoria. Both chemically treated and silenced lines show lower pathogenicity than the wild type in leaf infection assays. Finally, we show that appressoria of P. infestans possess the ability to build up turgor pressure and that this ability is decreased by chemical inhibition of TGases.

Sign in / Sign up

Export Citation Format

Share Document