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87 results for “Porphyromonas”
Interplay between Porphyromonas gingivalis hemophore-like protein HmuY and Kgp/RgpA gingipains plays a superior role in heme supply - yet unpublished supplementary data regarding Fig. 4C and Fig. 6D.
<p>The upload contains raw data files for the article "Interplay between <em>Porphyromonas gingivalis</em> hemophore-like protein HmuY and Kgp/RgpA gingipains plays a superior role in heme supply" which shows the production of the HmuY protein in various <em>P. gingivalis</em> mutant strains. These data are not present in the supplementary data of publication.</p> <p><strong>Article abstract</strong></p> <p>To acquire heme as a source of iron and protoporphyrin IX, <em>Porphyromonas gingivalis</em> uses gingipains, Hmu, and Hus systems. The aim of this study was to assess the correlation between the production and function of the most important virulence factors of <em>P. gingivalis</em> involved in heme supply, namely, hemophore-like proteins (HmuY and HusA) and gingipains. Respective mutant strains were used, and the expression of genes at the transcript and protein levels, as well as the importance of these genes’ products for virulence potential, was examined. We found that HmuY and Kgp/RgpA gingipains are among the main <em>P. gingivalis</em> virulence factors synergistically engaged in heme supply. Their expression is related mainly when <em>P. gingivalis</em> grows in conditions rich in iron and heme sources, resembling those found in severe periodontitis. We confirmed that HmuY production is strictly dependent on the availability of heme and iron in the external environment, whereas we did not observe such dependence in the production of HusA. Moreover, we found that the HmuY protein can easily sequester heme from the HusA protein. The only correlation in the production of HmuY and HusA hemophore-like proteins could occur in <em>P. gingivalis</em> grown in conditions rich in iron and heme sources, mimicking an environment typical for severe periodontitis. Based on our observations, we suggest that HmuY is the major heme-binding protein produced by <em>P. gingivalis</em>, especially in iron- and heme-depleted conditions, typical for healthy periodontium and the initial stages of infection. The HusA protein could play a supporting role in <em>P. gingivalis</em> heme uptake. </p> <p>The Word document (Data description.docx) contains a description of files.</p>
Data from Matrishin et al. "Phages are important unrecognized players in the ecology of the oral pathogen Porphyromonas gingivalis"
<p>Data files associated with Matrishin et al. "Phages are important unrecognized players in the ecology of the oral pathogen <em>Porphyromonas gingivalis</em>".</p> <p><strong>Please see the table in 00.README.xlsx for key information regarding nomenclature</strong>. We caution that the same locus tag identifiers refer to different genes in the Zenodo files than in NCBI. This difference resulted from use of the same Locus Tag Prefixes for in house gene calls using Bakta for the manuscript analyses as for the PGAP analyses ultimately performed upon submission of the assemblies to GenBank. Unlike the Supplementary Data Files submitted with the manuscript, see below, it was not possible to readily update all the Zenodo-deposited files to their updated final GCA and distinct locus tag identifiers because of the complexity of some of the included filetypes, therefore all files in the Zenodo set were left unchanged from the nomenclature used in the original in house analyses based on Bakta.</p> <table align="left"> <thead> <tr> <th scope="col">Directory</th> <th scope="col">Contents</th> </tr> </thead> <tbody> <tr> <td><strong>00.README</strong></td> <td>Important information regarding nomenclature differences across data types.</td> </tr> <tr> <td><strong>01.bax.bakta</strong></td> <td>Results of Bakta annotation of 88 <em>Pg</em> genomes.</td> </tr> <tr> <td><strong>02.bax.ppanggolin</strong></td> <td>Results of PPanGGOLiN pangenome analysis of 88 <em>Pg</em> genomes.</td> </tr> <tr> <td><strong>03.bax.combo</strong></td> <td>Results of multiple analyses used to inform identification and curation of prophages in <em>Pg</em> genomes, provided as bacterial genome fastas and gff files that can be uploaded together to genome viewer tools (e.g. Geneious) and visualized as tracks. Note, these do not include final prophage calls.</td> </tr> <tr> <td><strong>04.phage.genomes</strong></td> <td><em>Pg</em> phage genomes in fasta format.</td> </tr> <tr> <td><strong>05.phage.prots</strong></td> <td><em>Pg</em> phage proteins in fasta format, clipped proteins at the beginnings and ends of genomes are excluded.</td> </tr> <tr> <td><strong>06.phage.gbs</strong></td> <td><em>Pg</em> phage information in GenBank format, clipped proteins at the beginnings and ends of genomes are excluded.</td> </tr> <tr> <td><strong>07.phage.families.virclust</strong></td> <td>Results of VirClust analysis used to inform resolution family-level units.</td> </tr> <tr> <td><strong>08.phage.families.victor</strong></td> <td>Results of VICTOR analysis used to inform resolution of family-level units.</td> </tr> </tbody> </table> <p> </p>
Analysis of heme and iron influence on Porphyromonas gingivalis A7436 and ATCC 33277 strains genes expression (microarray results)
<p>The aim of this study was to analyze phenotypic differences between <i>P. gingivalis</i> more virulent A7436 and less virulent ATCC 33277 (33277) strains. The analysis comprised the influence of heme and iron on <i>P. gingivalis</i> gene expression. </p><p><i>P. gingivalis</i> A7436 and 33277 strains were cultured in basal medium (3% trypticase soy broth and 0.5% yeast extract), supplemented with 3.6 mM L-cysteine hydrochloride, and 0.5 mg/l menadione, in anaerobic conditions (80% N2, 10% H2 and 10% CO2). To generate heme and iron-limited conditions, the medium was supplemented with 0.16 mM of the iron chelator 2,2-dipyridyl (DIP conditions). To generate heme and iron-rich conditions, the medium was supplemented with 0.0077mM hemin chloride (Hm conditions). Three sample replicates of A7436 and 33277 strains were grown in Hm or DIP conditions for 20 hours. RNA isolation and microarray analysis were performed in IMGM laboratories (Martinsried, Germany), as described by Śmiga et al. (2023).</p><p>The online tool eArray (http://earray.chem.agilent.com/; Agilent Technologies, Santa Clara, CA, USA) was used to design an Agilent Custom <i>Porphyromonas gingivalis</i> A7436 Gene Expression Microarray (8×15K format). Probes were prepared based on <i>P. gingivalis</i> transcriptome information derived from the NCBI reference sequence NZ_CP011995.1. Total RNA isolation, RNA quantity, and quality were determined as described by Curaszkiewicz et al. 2014. For internal labeling control, the total RNA was spiked with <i>in vitro </i>synthesized polyadenylated transcripts (One-Color RNA Spike-In Mix; Agilent Technologies). Subsequently, samples were reverse transcribed into cDNA and then converted into cyanine-3-labeled complementary RNA (cRNA) with Low Input Quick-Amp Labeling Kit One-Color (Agilent Technologies). For microarray hybridization, a Gene Expression Hybridization Kit (Agilent Technologies) was used. Labeled cRNA was hybridized for 17 hours at 65℃ on Agilent Custom GE 8×15K Microarrays, washed according to the manufacturer's protocol, and dried with acetonitrile (Sigma-Aldrich). The fluorescence of samples was detected with Scan Control A.8.4.1 software (Agilent Technologies) on the Agilent DNA Microarray Scanner (Agilent Technologies) and extracted from the images using Feature Extraction 10.7.3.1 software (Agilent Technologies). For data analysis, Feature Extraction 10.7.3.1 (Agilent Technologies), GeneSpring GX 13.1.1 (Agilent Technologies), and Excel 2010 (Microsoft, Redmond, WA, USA) were used. For statistical analysis, Welch's approximate <i>t</i>-test was used. Differences in gene expression are shown as fold change values (FC). The average was calculated from the normalized signal values and they were transformed from the log2 to the linear scale. Increases and decreases in gene expression are shown as positive and negative numbers, respectively. The fold change in gene expression was considered significant for FC ≥ 2 or FC ≤ -2 and <i>P</i>-value ≤ 0.05</p><ul><li>Ciuraszkiewicz J, Śmiga M, Mackiewicz P, Gmiterek A, Bielecki M, Olczak M, Olczak T. 2014. Fur homolog regulates <i>Porphyromonas gingivalis </i>virulence under low-iron/heme conditions through a complex regulatory network. Mol Oral Microbiol 29:333-353. doi: 10.1111/omi.12077.</li><li>Śmiga M, Ślęzak P, Olczak T. 2023. Comparative analysis of <i>Porphyromonas gingivalis</i> A7436 and ATCC 33277 strains reveals differences in the expression of heme acquisition systems. Microbiol Spectr (revised manuscript under revision).</li></ul>
Basic data that show effect of Panax ginseng and Symphytum officinale boost metronidazole on quorum sensing and biofilm disruption in Porphyromonas gingivalis
<p>Basic data that show effect of Panax ginseng and Symphytum officinale boost metronidazole on quorum sensing and biofilm disruption in Porphyromonas gingivalis</p>
Characterizing Gingival and Periodontal Ligament Fibroblasts Reaction to Infection With the Bacteria Porphyromonas Gingivalis
ClinicalTrials.gov study NCT01599091. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Prevalence of Porphyromonas Gingivalis Fimbrial Subunit Genotype in Smokers and Nonsmokers After Periodontal Therapy
ClinicalTrials.gov study NCT02879903. IPD Sharing: YES. Countries: 0. Publications: 4.
Porphyromonas gingivalis affects gene expression in skeletal muscle, soleus muscle
GEO Series GSE146635. Mus musculus. 8 samples. Type: Expression profiling by array.
Antibacterial characterization of polyphosphate against Porphyromonas spp. implicated in companion animal periodontitis
GEO Series GSE93901. Porphyromonas gulae. 4 samples. Type: Expression profiling by high throughput sequencing.
Role of an extracytoplasmic function sigma factor, PGN_0319, in hemin utilization by Porphyromonas gingivalis
GEO Series GSE78048. Porphyromonas gingivalis ATCC 33277; Porphyromonas gingivalis. 4 samples. Type: Expression profiling by array.
Effect of deletion of trkA on gene expression of Porphyromonas gingivalis W83
GEO Series GSE210663. Porphyromonas gingivalis W83. 6 samples. Type: Expression profiling by high throughput sequencing.
CRISPR-Cas protein Cas3 controls virulence in the oral pathogen Porphyromonas gingivalis.
GEO Series GSE154569. Galleria mellonella; Porphyromonas gingivalis. 46 samples. Type: Expression profiling by high throughput sequencing.
Porphyromonas gingivalis alters gene expressions in the liver and brown adipose tissue, and induces gestational obesity and underweight of fetus in pregnant mice [Liver]
GEO Series GSE180189. Mus musculus. 8 samples. Type: Expression profiling by array.
Differential miRNA expression in gingival epithelial cells infected with Porphyromonas gingivalis
GEO Series GSE28635. Homo sapiens. 6 samples. Type: Non-coding RNA profiling by array.
Gene expression of Porphyromonas gingivalis ATCC 33277 when growing in an in vitro multispecies biofilm
GEO Series GSE132157. Porphyromonas gingivalis ATCC 33277; Porphyromonas gingivalis. 6 samples. Type: Expression profiling by array.
Effect of infection with Aggregatibacter actinomycetemcomitans or Porphyromonas gingivalis on primary murine bone marrow-derived dendritic cells
GEO Series GSE41383. Mus musculus. 9 samples. Type: Expression profiling by array.
Strand-specific transcriptome profiles of the oral pathogen Porphyromonas gingivalis using genomic tiling microarray and RNA sequencing
GEO Series GSE30452. Porphyromonas gingivalis W83. 3 samples. Type: Expression profiling by high throughput sequencing.
CRISPR-cas cas7 influences the host-pathogen interaction of Porphyromonas gingivalis
GEO Series GSE300980. Porphyromonas gingivalis. 12 samples. Type: Expression profiling by high throughput sequencing.
Porphyromonas gingivalis leads to dysplasia of normal esophageal epithelial cells via Sonic hedgehog pathway
GEO Series GSE210408. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
Regulation of Olfactomedin 4 by Porphyromonas gingivalis in the community context
GEO Series GSE159868. Homo sapiens. 32 samples. Type: Expression profiling by high throughput sequencing.
Porphyromonas gingivalis transcriptome in presence or absence of pABA
GEO Series GSE78126. Porphyromonas gingivalis. 4 samples. Type: Expression profiling by high throughput sequencing.
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