scholarly journals Sequence Analysis of Hypothetical Proteins fromHelicobacter pylori26695 to Identify Potential Virulence Factors

2016 ◽  
Vol 14 (3) ◽  
pp. 125 ◽  
Author(s):  
Ahmad Abu Turab Naqvi ◽  
Farah Anjum ◽  
Faez Iqbal Khan ◽  
Asimul Islam ◽  
Faizan Ahmad ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Virulence Factors ◽  
Hypothetical Proteins

scholarly journals Sequencing of Gliotoxin Genes in Clinical and Environmental Aspergillus fumigatus isolates in Iraq

2018 ◽  
Vol 12 (1) ◽  
pp. 33-39
Author(s):  
Russel S. Abdulhadi ◽  
Nemat J. Abdulbaqi
Keyword(s):  
Molecular Weight ◽  
Sequence Analysis ◽  
Aspergillus Fumigatus ◽  
Virulence Factors ◽  
High Specificity ◽  
Conventional Pcr ◽  
Pcr Product ◽  
Positive Results ◽  
Commercial Kit ◽  
Forward Primer

Gliotoxin is an important virulence factors in Aspergillus fumigatus. The biosynthesis of this mycotoxin is regulated and expressed by the presence of gliP genes. This study aimed to identify Aspergillus fumigatus isolates in clinical and environmental sources with glip genes using conventional PCR and sequence. To achieve this, DNA was isolated from twenty A. fumigatus isolates using commercial kit. The range of the DNA extracted was 65-210 ng/μl with a purity of 1.5-1.9. Species identification of the A. fumigatus isolates was achieved to a high specificity by using tailored primer. The results showed that all isolates had positive results to the primer and all isolates were able to produce gliotoxin. PCR detected the gliotoxin genes, glip in five isolates. The five PCR product samples were sent for sequence analysis and 25 µl (10 pmol) from the forward primer. The results of all the samples  indicated have a  single band of the desired product of gliP gene of A.fumigatus and the samples sent for sequencing related to molecular weight 190 bp.

scholarly journals The relationship between phylogenetic classification, virulence and antibiotic resistance of extraintestinal pathogenic Escherichia coli in İzmir province, Turkey

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5470 ◽  
Author(s):  
Elif Bozcal ◽  
Vahap Eldem ◽  
Sohret Aydemir ◽  
Mikael Skurnik
Keyword(s):  
Escherichia Coli ◽  
Antibiotic Resistance ◽  
Sequence Analysis ◽  
16S Rrna ◽  
Virulence Factors ◽  
Phylogenetic Group ◽  
Multi Locus Sequence Typing ◽  
Partial Sequence ◽  
Phylogenetic Classification ◽  
Tract Infections

Background Extraintestinal pathogenic Escherichia coli (ExPEC) is an important bacterium and responsible for many bloodstream infections, including urinary tract infections and even fatal bacteremia. The aim of this research was to investigate whether ExPEC strains isolated from Turkish blood cultures have a relationship between 16S rRNA based phylogenetic clusters and antibiotic resistance profiles, virulence factors or clonal lineages. Methods Phenotypically identified ExPEC blood culture isolates (n = 104) were included in this study. The 16S rRNA partial sequence analysis was performed for genotypic identification of ExPEC isolates. Antibiotic susceptibility and Extended-Spectrum β-Lactamase testing of isolates were performed. Phylogenetic classification (A, B1, B2 and D), Multi Locus Sequence Typing analysis and virulence-associated genes were investigated. Results Based on 16S rRNA partial sequence analysis, 97 out of 104 (93.26%) ExPEC isolates were confirmed as E. coli. Ampicillin (74.22%) and cefuroxime axetil (65.97%) resistances had the highest frequencies among the ExPEC isolates. In terms of phylogenetic classification of ExPEC, D (38.14%, 37/97) was the most prevalent group after A (29.89%, 29/97), B2 (20.61%, 20/97), and B1 (11.34%, 11/97). The sequence types of the 20 ExPEC isolates belonging to the B2 phylogenetic group were analyzed by Multi Locus Sequence Typing. Ten isolates out of 20 (50.0%) were identified as ST131. The other STs were ST95 (n = 1), ST14 (n = 1), ST10 (n = 1), ST69 (n = 1), ST1722 (n = 2), ST141 (n = 1), ST88 (n = 1), ST80 (n = 1), and ST998 (n = 1). Of the ST131 strains, six (60%, 6/10) represented serogroup O25. The most common virulence factor genes were serum resistance factor gene, traT (55.7%) aerobactin siderophore receptor and yersiniabactin encoding genes iutA (45.3%) and fyuA (50.5%), respectively. In addition, PAI (41.2%), iroN (23.7%), hlyA (15.4%), kpsII (13.4%), ompT (13.4%), papG (12.4%), iss (9.3%), cnf1 (7.2%), ibeA (2.06%), and sfaS (2.06%) genes were present in the ExPEC isolates. Conclusion The 16S rRNA-based phylogenetic relationship tree analysis showed that a large cluster was present among 97 ExPEC isolates along with related reference strains. There were 21 main clusters with 32 closely related subclusters. Based on our findings, different clonal lineages of ExPEC can display different antibiotic susceptibilities and virulence properties. We also concluded that virulence factors were not distributed depending on phylogenetic groups (A, B1, B2, and D). The ExPEC isolates belonging to the same phylogenetic group and sequence type could display different resistance and virulence characteristics.

scholarly journals Sequence analysis of the genes encoding for the major virulence factors ofBacillus anthracisvaccine strain `Carbosap'

2002 ◽  
Vol 93 (1) ◽  
pp. 117-121 ◽  
Author(s):  
R. Adone ◽  
P. Pasquali ◽  
G. La Rosa ◽  
C. Marianelli ◽  
M. Muscillo ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Virulence Factors ◽  
Genes Encoding

In Silico Drug Target Discovery Through Proteome Mining from M. tuberculosis: An Insight into Antivirulent Therapy

2020 ◽  
Vol 23 (3) ◽  
pp. 253-268
Author(s):  
Shreya Bhattacharya ◽  
Puja Ghosh ◽  
Debasmita Banerjee ◽  
Arundhati Banerjee ◽  
Sujay Ray
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Virulence Factors ◽  
Spectrum Analysis ◽  
Drug Target ◽  
Drug Targets ◽  
Physicochemical Characterization ◽  
Specific Drug ◽  
Hypothetical Proteins ◽  
Drug Target Discovery ◽  
Domain Annotation

Aim and Objective: One of the challenges to conventional therapies against Mycobacterium tuberculosis is the development of multi-drug resistant pathogenic strains. This study was undertaken to explore new therapeutic targets for the revolutionary antivirulence therapy utilizing the pathogen’s essential hypothetical proteins, serving as virulence factors, which is the essential first step in novel drug designing. Methods: Functional annotations of essential hypothetical proteins from Mycobacterium tuberculosis (H37Rv strain) were performed through domain annotation, Gene Ontology analysis, physicochemical characterization and prediction of subcellular localization. Virulence factors among the essential hypothetical proteins were predicted, among which pathogen-specific drug target candidates, non-homologous to human and gut microbiota, were identified. This was followed by druggability and spectrum analysis of the identified targets. Results and conclusion: The study successfully assigned functions of 83 essential hypothetical proteins of Mycobacterium tuberculosis, among which 25 were identified as virulence factors. Out of 25, 12 virulence factors were observed as potential pathogen-specific drug target candidates. Nine potential targets had druggable properties and rest three were considered as novel targets. Exploration of these targets will provide new insights into future drug development. Characterization of subcellular localizations revealed that most of the predicted targets were cytoplasmic which could be ideal for intracellular drugs, while two drug targets were membranebound, ideal for vaccines. Spectrum analysis identified one broad-spectrum and 11 narrowspectrum targets. This study would, therefore, instigate designing novel therapeutics for antivirulence therapy, which have the potential to serve as revolutionary treatment instead of conventional antibiotic therapies to overcome the lethality of antibiotic-resistant strains.

scholarly journals Sequence Analysis of the Staphylococcus aureus srrAB Loci Reveals that Truncation of srrA Affects Growth and Virulence Factor Expression

2007 ◽  
Vol 189 (20) ◽  
pp. 7515-7519 ◽  
Author(s):  
Alexa A. Pragman ◽  
Lisa Herron-Olson ◽  
Laura C. Case ◽  
Sara M. Vetter ◽  
Evan E. Henke ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Phylogenetic Analysis ◽  
Sequence Analysis ◽  
Virulence Factors ◽  
Virulence Factor ◽  
Nucleotide Polymorphisms ◽  
Low Oxygen ◽  
Factor Expression ◽  
Oxygen Conditions

ABSTRACT The SrrAB system regulates metabolism and virulence factors in Staphylococcus aureus. We sequenced the srrAB loci of 21 isolates and performed a phylogenetic analysis. Vaginal and bovine isolates clustered together, while skin isolates were genetically diverse. Few nucleotide polymorphisms were observed, and most were synonymous. Two strains (N2 and N19) with N-terminal truncations in SrrA displayed defects in growth and abnormally upregulated virulence factor expression under low-oxygen conditions.

Reannotation of Mycoplasma hyopneumoniae hypothetical proteins revealed novel potential virulence factors

2022 ◽  
Vol 162 ◽  
pp. 105344
Author(s):  
Bryan Augusto da Rosa Tavares ◽  
Jéssica Andrade Paes ◽  
Arnaldo Zaha ◽  
Henrique Bunselmeyer Ferreira
Keyword(s):  
Virulence Factors ◽  
Mycoplasma Hyopneumoniae ◽  
Hypothetical Proteins

Bioinformatics Annotation of the Hypothetical Proteins Found by Omics Techniques Can Help to Disclose Additional Virulence Factors

2009 ◽  
Vol 59 (4) ◽  
pp. 451-456 ◽  
Author(s):  
Sergio Hernández ◽  
Antonio Gómez ◽  
Juan Cedano ◽  
Enrique Querol
Keyword(s):  
Virulence Factors ◽  
Hypothetical Proteins

scholarly journals Crystal Structure of the Human tRNA Guanine Transglycosylase Catalytic Subunit QTRT1

Biomolecules ◽  
2018 ◽  
Vol 8 (3) ◽  
pp. 81 ◽  
Author(s):  
Sven Johannsson ◽  
Piotr Neumann ◽  
Ralf Ficner
Keyword(s):  
Crystal Structure ◽  
Sequence Analysis ◽  
Drug Design ◽  
Virulence Factors ◽  
Catalytic Subunit ◽  
Rna Modifications ◽  
Enzyme Class

RNA modifications have been implicated in diverse and important roles in all kingdoms of life with over 100 of them present on tRNAs. A prominent modification at the wobble base of four tRNAs is the 7-deaza-guanine derivative queuine which substitutes the guanine at position 34. This exchange is catalyzed by members of the enzyme class of tRNA guanine transglycosylases (TGTs). These enzymes incorporate guanine substituents into tRNAAsp, tRNAAsn tRNAHis, and tRNATyr in all kingdoms of life. In contrast to the homodimeric bacterial TGT, the active eukaryotic TGT is a heterodimer in solution, comprised of a catalytic QTRT1 subunit and a noncatalytic QTRT2 subunit. Bacterial TGT enzymes, that incorporate a queuine precursor, have been identified or proposed as virulence factors for infections by pathogens in humans and therefore are valuable targets for drug design. To date no structure of a eukaryotic catalytic subunit is reported, and differences to its bacterial counterpart have to be deducted from sequence analysis and models. Here we report the first crystal structure of a eukaryotic QTRT1 subunit and compare it to known structures of the bacterial TGT and murine QTRT2. Furthermore, we were able to determine the crystal structure of QTRT1 in complex with the queuine substrate.

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