Hemin- and temperature-dependent proteome alteration of Porphyromonas gingivalis
Ontology highlight
ABSTRACT:
INSTRUMENT(S):
ORGANISM(S): Bacteria Porphyromonas Gingivalis Atcc 33277
DISEASE(S): Periodontitis
SUBMITTER: 
Tianfan Cheng
LAB HEAD: Lijian Jin
PROVIDER: PXD057081 | Pride | 2026-02-21
REPOSITORIES: Pride
Dataset's files
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| Jin_18May2017_37C_3_1.raw | Raw | |||
| Jin_18May2017_37C_3_2.raw | Raw | |||
| Jin_18May2017_37C_3_3.raw | Raw | |||
| Jin_18May2017_41CHigh_6_1.raw | Raw | |||
| Jin_18May2017_41CHigh_6_2.raw | Raw |
Items per page: 5 1 - 5 of 22 |
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Project description:This study investigated the alteration of P. gingivalis proteome under the combinative conditions of hemin and temperature, revealing perturbation of proteins.
2026-02-21 | PXD057093 | Pride
Project description:Porphyromonas gingivalis, the keystone pathogen responsible for dysbiosis in the oral microbiome, the development of periodontal diseases, and the contribution to systemic comorbidities, is a heme auxotroph. It encodes only four enzymes in the heme biosynthesis pathway, namely HemD, HemN, HemG, and HemH. HemH protein is a ferrochelatase involved in the final step of heme biosynthesis by inserting iron ions (Fe2+) into protoporphyrin IX. This study aimed to analyze the effect of hemH gene deletion on P. gingivalis gene expression, thereby verifying its importance for P. gingivalis.
2026-03-03 | E-MTAB-16130 | biostudies-arrayexpress
Project description:The oral periodontal pathogen Porphyromonas gingivalis must adapt to ever changing environment to survive and cause disease. So far most of the efforts concerning the regulatory mechanisms employed by the bacterium centered on DNA-binding regulators. Here we focused on a RNA-binding protein that is indispensable for the bacterium to survive with host cells. We have determined the proteome affected by deletion of the protein, designated here PgRBP1. Three strains were used: WT, PgRBP1-deficient strain designated V3139 and a complemented strain V3236. In total, 1,393 proteins were identified. 592 proteins in the comparison of P. gingivalis 3139 vs. WT, 228 proteins in the comparison of P. gingivalis 3236 vs. WT, and 276 proteins in the comparison of P. gingivalis 3139 vs. 3236 showed differential level with statistical significance
2025-06-02 | PXD034144 | Pride
Project description:Porphyromonas gingivalis is considered a keystone pathogen responsible for dysbiosis in the oral microbiome, leading to the development of periodontal disease and contributing to various systemic comorbidities. Although P. gingivalis requires heme for growth and virulence, it is unable to synthesize heme de novo and therefore relies on host hemoproteins as its source. To acquire heme, the bacterium utilizes the Hmu system, which is composed of six proteins (HmuYRSTUV). HmuY functions as a hemophore-like protein that sequesters heme from host hemoproteins; HmuR serves as an outer membrane receptor responsible for heme uptake. The remaining four proteins (HmuS, HmuT, HmuU, and HmuV) are uncharacterized. HmuS has been proposed to act as a reverse ferrochelatase, due to its homology with CobN cobaltochelatases; therefore, it could catalyze the removal of iron from heme. The released iron could then be transported into the cytoplasm via the HmuTUV proteins. However, the specific role of HmuS in P. gingivalis has never been studied or confirmed. Therefore, this study aimed to investigate the effect of hmuS gene deletion on global gene expression in P. gingivalis, thereby assessing its role in iron acquisition and overall bacterial fitness.
2026-04-24 | E-MTAB-16197 | biostudies-arrayexpress
Project description:Periodontitis is the most common human infection affecting tooth-supporting structures. It was shown to play a role in aggravating atherosclerosis. To deepen our understanding of the pathogenesis of this disease, we exposed human macrophages to an oral bacteria Porphyromonas gingivalis (P. gingivalis) either as live bacteria, or its lipopolysaccharide (LPS) or fimbria. Microarray data from treated macrophages or control cells were analyzed to define molecular signatures. We focused our analysis on three important groups of genes. Group PG (genes differentially expressed by live bacteria only); Group LFG (genes differentially expressed in response to exposure to LPS and/or FimA); Group CG (core gene set jointly activated by all 3 stimulants). A total of 842 macrophage genes were differentially expressed in at least one of the three conditions compared to naïve cells. Using pathway analysis, we found that group CG activates the initial phagocytosis process and induces genes relevant to immune response, whereas group PG can de-activate the phagocytosis process associated with phagosome-lysosome fusion. LFG mostly affected RIG-I-like receptor signaling pathway. 12 samples in total. 4 conditions (treatment with live P. gingivalis, P. gingivalis LPS, P. gingivalis fimbriae, or saline) were used, and triplicates were performed for each condition. We considered the following comparisons: PG vs. Control (saline), PG-LPS vs. Control, and PG-fimbriae vs. Control. Fold-change > 2.0 and FDR < 0.25 were used to select significantly expressed genes.
2010-10-23 | E-GEOD-24897 | biostudies-arrayexpress
Project description:Porphyromonas gingivalis is a keystone pathogen responsible for oral microbiome dysbiosis, the development of periodontal disease, and may be involved in the development of systemic comorbidities. As a heme auxotroph, P. gingivalis relies on host hemoproteins as its primary sources of heme and iron. Although heme acquisition in P. gingivalis is relatively well characterized, considerably less is known about its pathways for iron uptake and the regulation of iron and heme homeostasis. P. gingivalis encodes four enzymes associated with the heme biosynthesis pathway, namely HemD, HemN, HemG, and HemH. HemH is a ferrochelatase responsible for the final step of heme biosynthesis, catalyzing the insertion of ferrous iron (Fe²⁺) into protoporphyrin IX. In addition, P. gingivalis expresses the Iht system, which plays a role in iron/heme utilization. One of its components, IhtB, is a heme-binding protein homologous to CbiK cobaltochelatases. Based on this homology, IhtB is hypothesized to function as a reverse ferrochelatase, facilitating the removal of iron from heme and thereby contributing to iron acquisition. This study aimed to investigate the effect of ihtB and hemH gene deletions on P. gingivalis gene expression under heme- and iron-replete conditions, to elucidate the roles of IhtB and HemH chelatases in heme and iron homeostasis.
2026-03-03 | E-MTAB-16135 | biostudies-arrayexpress
Project description:The BAM (b-barrel assembly machinery) complex is an evolutionarily conserved, multiprotein machine that catalyses the folding and membrane insertion of newly synthesised b-barrel outer membrane (OM) proteins in Gram-negative bacteria, mitochondria and chloroplasts. Based on Proteobacteria, bacterial BAM is also structurally conserved, with an essential BamAD core and up to three auxilliary periplasmic lipoproteins of poorly defined function. Here we show, using structural biology, quantitative proteomics and functional assays, that the BAM complex is radically different within the Bacteroidetes, a large and important phylum widely distributed within the environment and animal microbiomes. Cryogenic electron microscopy (cryoEM) structures of the BAM complexes from the human gut symbiont Bacteroides thetaiotaomicron and the human oral pathogen Porphyromonas gingivalis show similar, seven-component complexes of ~325 kDa in size with most of the mass in the extracellular space. In addition to canonical BamA and BamD, the complexes contain an integral OM protein named BamF that is essential and intimately associated with BamA, plus four surface-exposed lipoproteins (SLPs) named BamG-J. Together, BamF-J form a large, extracellular dome that likely serves as an assembly cage for the b-barrel-SLP complexes that are a hallmark of the Bacteroidetes. Our data suggest that BAM functionality in Bacteroidetes is substantially extended from that in Proteobacteria and underscores the importance of studying non-Proteobacteria for a more complete understanding of fundamental biological processes.
2025-08-12 | PXD058905 | Pride
Project description:The BAM (b-barrel assembly machinery) complex is an evolutionarily conserved, multiprotein machine that catalyses the folding and membrane insertion of newly synthesised b-barrel outer membrane (OM) proteins in Gram-negative bacteria, mitochondria and chloroplasts. Based on Proteobacteria, bacterial BAM is also structurally conserved, with an essential BamAD core and up to three auxilliary periplasmic lipoproteins of poorly defined function. Here we show, using structural biology, quantitative proteomics and functional assays, that the BAM complex is radically different within the Bacteroidetes, a large and important phylum widely distributed within the environment and animal microbiomes. Cryogenic electron microscopy (cryoEM) structures of the BAM complexes from the human gut symbiont Bacteroides thetaiotaomicron and the human oral pathogen Porphyromonas gingivalis show similar, seven-component complexes of ~325 kDa in size with most of the mass in the extracellular space. In addition to canonical BamA and BamD, the complexes contain an integral OM protein named BamF that is essential and intimately associated with BamA, plus four surface-exposed lipoproteins (SLPs) named BamG-J. Together, BamF-J form a large, extracellular dome that likely serves as an assembly cage for the b-barrel-SLP complexes that are a hallmark of the Bacteroidetes. Our data suggest that BAM functionality in Bacteroidetes is substantially extended from that in Proteobacteria and underscores the importance of studying non-Proteobacteria for a more complete understanding of fundamental biological processes.
2025-08-12 | PXD058903 | Pride
Project description:Polyphosphate (polyP) is a ubiquitous and abundant compound found in bacteria, fungi, algae, plant, and animals. Among roles of intracellular polyP in bacteria are resistance and survival in the stationary phase of the growth against stress and stringent condition. Therefore, intracellular polyP is considered as a virulence factor of bacteria. In contrast, exogenous polyP has an antimicrobial activity against a variety of microorganisms. To date, much has been numerous studies of antibacterial effect of polyP against gram positive bacteria and fungi while relatively little reports have been published concerning gram negative bacteria. Here we describe bactericidal effect of polyP against gram negative periodontopathic bacterium, Porphyromonas gingivalis, and the transcriptional change by polyP in this bacterium. The bacterial growth was inhibited by polyP (chain length of P3~P75) at concentration of 0.02~0.03%, but not by Pi and PPi at the concentrations. polyP75 was chosen for further experiments, which suppressed the further growth of P. gingivalis as low as 0.03%. polyP75 completely killed the bacterial cells at the concentration of 0.035%. Microarray analysis was employed to identify genes that showed a greater than 1.5-fold difference in the expression by polyP75 at the concentration of 0.03%. It was found that 155 genes were up-regulated and 173 were down-regulated. Down-regulated genes include groups of energy metabolism-related genes, cell envelope-related genes, and genes in relation to biosynthesis of cofactors, prosthetic groups and carriers. Among the down-regulated genes were several involved in DNA replication, cell division protein, and biosynthesis of purines, pyrimidines, nucleosides and nucleotides. In contrast, a large number of ribosomal proteins, transciptional regulators and transposases were up-regulated. Oxidative stress-related genes and iron storage proteins also appeared to be increased in the expression. Real-time PCR confirmed up- and down-regulation of some selected genes. The overall results suggest that polyP has a bactericidal activity against P. gingivalis, interfering with translation, energy metabolism, DNA replication, cell division, and biosynthesis of purines, pyrimidines, nucleoside and nucleotides. polyP may be used as an agent for prevention and treatment of periodontal infections. Polyp-treated vs. untreated intensity ratio data linked below as a supplementary file. Keywords: agent response Twenty μg of each total RNA sample was used in separate hybridization experiments on identical arrays. The whole genome of 1,909 genes of P. gingivalis W83 (GenBank accession no. NC_002950) was submitted to NimbleGen System Inc. (Madison, WI) for microarray design and manufacture using maskless, digital micromirror technology. Five replicates of the genome were included per chip. An average of 19 different 60-base oligonucleotides (60-mer probes) represented each gene in the genome. Sixty-mer probes were selected such that each probe had at least three mismatches compared to all other 60-mers in the target genome. A quality control check (hybridization) was performed for each array, which contained on-chip control oligonucleotides. The arrays were analyzed using an Axon GenePix 4000B microarray scanner with associated software (Molecular Devices Corp., Sunnyvale, CA). Gene expression levels were calculated with NimbleScan Version 2.3 (NimbleGen). Relative signal intensities for each gene were generated using the Robust Multi-Array Average algorithm. The data were processed based on quantile normalization method using the R package. This normalization method aims to make the distribution of intensities for each array in a set of arrays the same. The background-adjusted, normalized, and log transformed intensity values were then analyzed using GeneSpring GX 7.3.1 (Silicon Genetics, Palo Alto, CA).
2008-05-30 | E-GEOD-11471 | biostudies-arrayexpress
Project description:Porphyromonas gingivalis and Treponema denticola are periodontalpathogens that are associated with the severity and progression of periodontal diseases. This study investigates the gene expression of Porphyromonas gingivalis during co-culture with Treponema denticola
2014-03-31 | E-MTAB-2214 | biostudies-arrayexpress