scholarly journals Comparative Analysis of the Core Proteomes among the Pseudomonas Major Evolutionary Groups Reveals Species-Specific Adaptations for Pseudomonas aeruginosa and Pseudomonas chlororaphis

Diversity ◽  
2020 ◽  
Vol 12 (8) ◽  
pp. 289
Author(s):  
Marios Nikolaidis ◽  
Dimitris Mossialos ◽  
Stephen G. Oliver ◽  
Grigorios D. Amoutzias
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Pseudomonas Syringae ◽  
Pseudomonas Stutzeri ◽  
Phylogenomic Analysis ◽  
Pseudomonas Chlororaphis ◽  
Phylogenetic Groups ◽  
The Core ◽  
Core Proteins ◽  
Core Proteome ◽  
Species Specific

The Pseudomonas genus includes many species living in diverse environments and hosts. It is important to understand which are the major evolutionary groups and what are the genomic/proteomic components they have in common or are unique. Towards this goal, we analyzed 494 complete Pseudomonas proteomes and identified 297 core-orthologues. The subsequent phylogenomic analysis revealed two well-defined species (Pseudomonas aeruginosa and Pseudomonas chlororaphis) and four wider phylogenetic groups (Pseudomonas fluorescens, Pseudomonas stutzeri, Pseudomonas syringae, Pseudomonas putida) with a sufficient number of proteomes. As expected, the genus-level core proteome was highly enriched for proteins involved in metabolism, translation, and transcription. In addition, between 39–70% of the core proteins in each group had a significant presence in each of all the other groups. Group-specific core proteins were also identified, with P. aeruginosa having the highest number of these and P. fluorescens having none. We identified several P. aeruginosa-specific core proteins (such as CntL, CntM, PlcB, Acp1, MucE, SrfA, Tse1, Tsi2, Tse3, and EsrC) that are known to play an important role in its pathogenicity. Finally, a holin family bacteriocin and a mitomycin-like biosynthetic protein were found to be core-specific for P. cholororaphis and we hypothesize that these proteins may confer a competitive advantage against other root-colonizers.

scholarly journals EpitoCore: mining conserved epitope vaccine candidates in the core proteome of multiple bacteria strains

2019 ◽  
Author(s):  
T.S. Fiuza ◽  
J.P.M.S. Lima ◽  
G.A. de Souza
Keyword(s):  
Peptide Vaccine ◽  
Computational Prediction ◽  
Reverse Vaccinology ◽  
Automated Identification ◽  
Single Strain ◽  
Vaccine Candidates ◽  
The Core ◽  
Core Proteins ◽  
Conserved Genes ◽  
Core Proteome

ABSTRACTIn reverse vaccinology approaches, complete proteomes of bacteria are submitted to multiple computational prediction steps in order to filter proteins that are possible vaccine candidates. Most available tools perform such analysis only in a single strain, or a very limited number of strains. But the vast amount of genomic data had shown that most bacteria contain pangenomes, i.e. their genomic information contains core, conserved genes, and random accessory genes specific to each strain. Therefore, it is of the utmost importance to define core proteins, and also core epitopes, in reverse vaccinology methods. EpitoCore is a decision-tree pipeline developed to fulfill that need. It provides surfaceome prediction of proteins from related strains, defines clusters of core proteins within those, calculate the immunogenicity of such clusters, predicts epitopes for a given set of MHC alleles defined by the user, and then reports if epitopes are located extracellularly and if they are conserved among the core homologues. Pipeline performance is illustrated by mining peptide vaccine candidates in Mycobacterium avium hominissuis strains. From a total proteome of approximately 4,800 proteins per strain, EpitoCore mined 103 highly immunogenic core homologues located at cell surface, many of those related to virulence and drug resistance. Conserved epitopes identified among these homologues allows the users to define sets of peptides with potential to immunize the largest coverage of tested HLA alleles using peptide-based vaccines. Therefore, EpitoCore is able to provide automated identification of conserved epitopes in bacterial pangenomic datasets.

scholarly journals Identification of Cross-Protective Potential Antigens against PathogenicBrucellaspp. through Combining Pan-Genome Analysis with Reverse Vaccinology

2018 ◽  
Vol 2018 ◽  
pp. 1-15 ◽  
Author(s):  
Yasmin Hisham ◽  
Yaqoub Ashhab
Keyword(s):  
Brucella Melitensis ◽  
Cell Epitope ◽  
Reverse Vaccinology ◽  
Pathogenic Species ◽  
The Core ◽  
Protective Antigens ◽  
Cumulative Score ◽  
Core Proteins ◽  
Associated Proteins ◽  
Core Proteome

Brucellosis is a zoonotic infectious disease caused by bacteria of the genusBrucella.Brucella melitensis,Brucella abortus, andBrucella suisare the most pathogenic species of this genus causing the majority of human and domestic animal brucellosis. There is a need to develop a safe and potent subunit vaccine to overcome the serious drawbacks of the live attenuatedBrucellavaccines. The aim of this work was to discover antigen candidates conserved among the three pathogenic species. In this study, we employed a reverse vaccinology strategy to compute the core proteome of 90 completed genomes: 55B. melitensis, 17B. abortus, and 18B. suis. The core proteome was analyzed by a metasubcellular localization prediction pipeline to identify surface-associated proteins. The identified proteins were thoroughly analyzed using variousin silicotools to obtain the most potential protective antigens. The number of core proteins obtained from analyzing the 90 proteomes was 1939 proteins. The surface-associated proteins were 177. The number of potential antigens was 87; those with adhesion score ≥ 0.5 were considered antigen with “high potential,” while those with a score of 0.4–0.5 were considered antigens with “intermediate potential.” According to a cumulative score derived from protein antigenicity, density of MHC-I and MHC-II epitopes, MHC allele coverage, and B-cell epitope density scores, a final list of 34 potential antigens was obtained. Remarkably, most of the 34 proteins are associated with bacterial adhesion, invasion, evasion, and adaptation to the hostile intracellular environment of macrophages which is adjusted to depriveBrucellaof required nutrients. Our results provide a manageable list of potential protective antigens for developing a potent vaccine against brucellosis. Moreover, our elaborated analysis can provide further insights into novelBrucellavirulence factors. Our next step is to test some of these antigens using an appropriate antigen delivery system.

Conservation of the multidrug resistance efflux gene oprM in Pseudomonas aeruginosa.

1997 ◽  
Vol 41 (4) ◽  
pp. 853-856 ◽  
Author(s):  
N Bianco ◽  
S Neshat ◽  
K Poole
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Multidrug Resistance ◽  
Pseudomonas Syringae ◽  
Genomic Dna ◽  
Resistance Mechanisms ◽  
Pseudomonas Chlororaphis ◽  
Multidrug Efflux ◽  
Efflux System ◽  
Multidrug Resistance Gene ◽  
Multidrug Efflux System

An intragenic probe derived from the multidrug resistance gene oprM hybridized with genomic DNA from all 20 serotypes of Pseudomonas aeruginosa and from all 34 environmental and clinical isolates tested, indicating that the MexA-MexB-OprM multidrug efflux system is highly conserved in this organism. The oprM probe also hybridized with genomic DNA from Pseudomonas aureofaciens, Pseudomonas chlororaphis, Pseudomonas syringae, Burkholderia pseudomallei, and Pseudomonas putida, suggesting that efflux-mediated multidrug resistance mechanisms may be somewhat broadly distributed.

scholarly journals A Comprehensive Computer Aided Vaccine Design Approach to Propose a Multi-Epitopes Subunit Vaccine against Genus Klebsiella Using Pan-Genomics, Reverse Vaccinology, and Biophysical Techniques

Vaccines ◽  
2021 ◽  
Vol 9 (10) ◽  
pp. 1087
Author(s):  
Khaled S. Allemailem
Keyword(s):  
Molecular Dynamics ◽  
Binding Free Energy ◽  
Water Soluble ◽  
Dynamics Simulation ◽  
Reverse Vaccinology ◽  
World Health ◽  
Potential Core ◽  
The Core ◽  
Core Proteins ◽  
Core Proteome

Klebsiella is a genus of nosocomial bacterial pathogens and is placed in the most critical list of World Health Organization (WHO) for development of novel therapeutics. The pathogens of the genus are associated with high mortality and morbidity. Owing to their strong resistance profile against different classes of antibiotics and nonavailability of a licensed vaccine, urgent efforts are required to develop a novel vaccine candidate that can tackle all pathogenic species of the Klebsiella genus. The present study aims to design a broad-spectrum vaccine against all species of the Klebsiella genus with objectives to identify the core proteome of pathogen species, prioritize potential core vaccine proteins, analyze immunoinformatics of the vaccine proteins, construct a multi-epitopes vaccine, and provide its biophysical analysis. Herein, we investigated all reference species of the genus to reveal their core proteome. The core proteins were then subjected to multiple reverse vaccinology checks that are mandatory for the prioritization of potential vaccine candidates. Two proteins (TonB-dependent siderophore receptor and siderophore enterobactin receptor FepA) were found to fulfill all vaccine parameters. Both these proteins harbor several potent B-cell-derived T-cell epitopes that are antigenic, nonallergic, nontoxic, virulent, water soluble, IFN-γ producer, and efficient binder of DRB*0101 allele. The selected epitopes were modeled into a multi-epitope peptide comprising linkers and Cholera Toxin B adjuvant. For docking with innate immune and MHC receptors and afterward molecular dynamics simulations and binding free energy analysis, the vaccine structure was modeled for tertiary structure and refined for structural errors. To assess the binding affinity and presentation of the designed vaccine construct, binding mode and interactions analysis were performed using molecular docking and molecular dynamics simulation techniques. These biophysical approaches illustrated the vaccine as a good binder to the immune receptors and revealed robust interactions energies. The vaccine sequence was further translated to nucleotide sequence and cloned into an appropriate vector for expressing it at high rate in Escherichia coli K12 strain. In addition, the vaccine was illustrated to generate a good level of primary, secondary, and tertiary immune responses, proving good immunogenicity of the vaccine. Based on the reported results, the vaccine can be a good candidate to be evaluated for effectiveness in wet laboratory validation studies.

scholarly journals Experimental Tests for Measuring Individual Attentional Characteristics in Songbirds

Animals ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 2233
Author(s):  
Loïc Pougnault ◽  
Hugo Cousillas ◽  
Christine Heyraud ◽  
Ludwig Huber ◽  
Martine Hausberger ◽  
...  
Keyword(s):  
Cognitive Processes ◽  
Comparative Research ◽  
Visual Stimuli ◽  
Experimental Tests ◽  
European Starling ◽  
Auditory Stimuli ◽  
The Core ◽  
Cognitive Studies ◽  
Individual Variations ◽  
Species Specific

Attention is defined as the ability to process selectively one aspect of the environment over others and is at the core of all cognitive processes such as learning, memorization, and categorization. Thus, evaluating and comparing attentional characteristics between individuals and according to situations is an important aspect of cognitive studies. Recent studies showed the interest of analyzing spontaneous attention in standardized situations, but data are still scarce, especially for songbirds. The present study adapted three tests of attention (towards visual non-social, visual social, and auditory stimuli) as tools for future comparative research in the European starling (Sturnus vulgaris), a species that is well known to present individual variations in social learning or engagement. Our results reveal that attentional characteristics (glances versus gazes) vary according to the stimulus broadcasted: more gazes towards unusual visual stimuli and species-specific auditory stimuli and more glances towards species-specific visual stimuli and hetero-specific auditory stimuli. This study revealing individual variations shows that these tests constitute a very useful and easy-to-use tool for evaluating spontaneous individual attentional characteristics and their modulation by a variety of factors. Our results also indicate that attentional skills are not a uniform concept and depend upon the modality and the stimulus type.

scholarly journals The Global Arginine Regulator ArgR Controls Expression of argF in Pseudomonas syringae pv. phaseolicola but Is Not Required for the Synthesis of Phaseolotoxin or for the Regulated Expression of argK

2004 ◽  
Vol 186 (11) ◽  
pp. 3653-3655 ◽  
Author(s):  
José Luis Hernández-Flores ◽  
Karina López-López ◽  
Rogelio Garcidueñas-Piña ◽  
Alba E. Jofre-Garfias ◽  
Ariel Alvarez-Morales
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Pseudomonas Syringae ◽  
Ornithine Carbamoyltransferase ◽  
Regulated Expression

ABSTRACT In Pseudomonas syringae pv. phaseolicola the enzyme ornithine carbamoyltransferase (OCTase), encoded by argF, is negatively regulated by argR, similar to what has been reported for Pseudomonas aeruginosa. However, production of the phaseolotoxin-resistant OCTase encoded by argK, synthesis of phaseolotoxin, and infectivity for bean pods occur independently of the ArgR protein.

scholarly journals Antigenic diversity and seroprevalences of Torque teno viruses in children and adults by ORF2-based immunoassays

2013 ◽  
Vol 94 (2) ◽  
pp. 409-417 ◽  
Author(s):  
Tingting Chen ◽  
Elina Väisänen ◽  
Petri S. Mattila ◽  
Klaus Hedman ◽  
Maria Söderlund-Venermo
Keyword(s):  
Serum Samples ◽  
Phylogenetic Groups ◽  
Single Strain ◽  
New Approach ◽  
Antiviral Antibody ◽  
Specific Igg ◽  
Species Specific ◽  
Multiple Strains ◽  
Antigenic Relationships

Torque teno viruses (TTVs) circulate widely among humans, causing persistent viraemia in healthy individuals. Numerous TTV isolates with high genetic variability have been identified and segregated into 29 species of five major phylogenetic groups. To date, the diversity of TTV sequences, challenges in protein expression and the subsequent lack of serological assays have hampered TTV seroprevalence studies. Moreover, the antigenic relationships of different TTVs and their specific seroprevalences in humans remain unknown. For five TTV strains – belonging to different species of four genogroups – we developed, using recombinant glutathione S-transferase (GST)-fused TTV ORF2 proteins, glutathione–GST capture enzyme immunoassays (EIAs) detecting antibodies towards conformational epitopes. We then analysed serum samples from 178 healthy adults and 108 children; IgG reactivities were observed either towards a single strain or towards multiple strains, which pointed to antigenic distinction of TTV species. The overall seroprevalence for the five TTVs peaked at 43 % (18 of 42) in children 2–4 years of age, subsequently declined, and again reached 42 % (74 of 178) among adults. TTV6 species-specific IgG predominated in children, whereas that for TTV13 predominated in adults. During a 3 year follow-up of the same children, both species-specific seroconversions and seroreversions occurred. This is the first EIA-based study of different TTVs, providing a new approach for seroepidemiology and diagnosis of TTV infections. Our data suggest that different TTVs in humans may differ in antiviral antibody profiles, infection patterns and epidemiology.

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